text:
{siegle2011,
  title = {Markovian Embedding of Fractional Superdiffusion},
  volume = {93},
  number = {2},
  journal = {EPL (Europhysics Letters)},
  author = {Siegle, P. and Goychuk, I. and H\"anggi, P.},
  year = {2011},
  pages = {20002},
  file = {/home/bbeltr1/Documents/paper-collection/HänggiP/Siegle et al_2011_Markovian embedding of fractional superdiffusion.pdf}
}

@article{amitai2017,
  title = {Polymer Physics of Nuclear Organization and Function},
  journal = {Physics Reports},
  author = {Amitai, Assaf and Holcman, David},
  year = {2017},
  file = {/home/bbeltr1/Documents/paper-collection/HolcmanD/Amitai_Holcman_2017_Polymer physics of nuclear organization and function.pdf}
}

@article{marshall2016,
  title = {Modeling Meiotic Chromosome Pairing: Nuclear Envelope Attachment, Telomere-Led Active Random Motion, and Anomalous Diffusion},
  volume = {13},
  issn = {1478-3975},
  shorttitle = {Modeling Meiotic Chromosome Pairing},
  abstract = {The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.},
  language = {en},
  number = {2},
  journal = {Phys. Biol.},
  doi = {10.1088/1478-3975/13/2/026003},
  author = {Marshall, Wallace F. and Fung, Jennifer C.},
  year = {2016},
  pages = {026003},
  file = {/home/bbeltr1/Documents/paper-collection/FungJ/Marshall_Fung_2016_Modeling meiotic chromosome pairing.pdf}
}

@article{mine-hattab2013,
  title = {{{DNA}} in Motion during Double-Strand Break Repair},
  volume = {23},
  issn = {0962-8924},
  abstract = {DNA organization and dynamics profoundly affect many biological processes
such as gene regulation and DNA repair. In this review, we present the latest
studies on DNA mobility in the context of DNA damage. Recent studies demonstrate
that DNA mobility is dramatically increased in the presence of double-strand
breaks (DSBs) in the yeast Saccharomyces cerevisiae. As a
consequence, chromosomes explore a larger nuclear volume, facilitating
homologous pairing but also increasing the rate of ectopic recombination.
Increased DNA dynamics is dependent on several homologous recombination (HR)
proteins and we are just beginning to understand how chromosome dynamics is
regulated after DNA damage.},
  number = {11},
  journal = {Trends Cell Biol},
  doi = {10.1016/j.tcb.2013.05.006},
  author = {{Min\'e-Hattab}, Judith and Rothstein, Rodney},
  month = nov,
  year = {2013},
  file = {/home/bbeltr1/Documents/paper-collection/RothsteinR/Miné-Hattab_Rothstein_2013_DNA in motion during double-strand break repair.pdf},
  pmid = {23867212},
  pmcid = {PMC3820367}
}

@article{nachman2007,
  title = {Dissecting {{Timing Variability}} in {{Yeast Meiosis}}},
  volume = {131},
  issn = {0092-8674, 1097-4172},
  language = {English},
  number = {3},
  journal = {Cell},
  doi = {10.1016/j.cell.2007.09.044},
  author = {Nachman, Iftach and Regev, Aviv and Ramanathan, Sharad},
  month = nov,
  year = {2007},
  keywords = {DEVBIO,SYSBIO},
  pages = {544-556},
  file = {/home/bbeltr1/Documents/paper-collection/RamanathanS/Nachman et al_2007_Dissecting Timing Variability in Yeast Meiosis.pdf;/home/bbeltr1/Documents/zotero/storage/ND5DRCHG/S0092-8674(07)01285-8.html},
  pmid = {17981121}
}

@article{novak2008,
  title = {Cohesin {{Smc1$\beta$}} Determines Meiotic Chromatin Axis Loop Organization},
  volume = {180},
  issn = {0021-9525, 1540-8140},
  language = {en},
  number = {1},
  journal = {The Journal of Cell Biology},
  doi = {10.1083/jcb.200706136},
  author = {Novak, Ivana and Wang, Hong and Revenkova, Ekaterina and Jessberger, Rolf and Scherthan, Harry and H\"o\"og, Christer},
  month = jan,
  year = {2008},
  pages = {83-90},
  file = {/home/bbeltr1/Documents/paper-collection/HöögC/Novak et al_2008_Cohesin Smc1β determines meiotic chromatin axis loop organization.pdf}
}

@article{ishiguro2014,
  title = {Meiosis-Specific Cohesin Mediates Homolog Recognition in Mouse Spermatocytes},
  volume = {28},
  issn = {0890-9369},
  language = {en},
  number = {6},
  journal = {Genes \& Development},
  doi = {10.1101/gad.237313.113},
  author = {Ishiguro, K.-i. and Kim, J. and Shibuya, H. and {Hernandez-Hernandez}, A. and Suzuki, A. and Fukagawa, T. and Shioi, G. and Kiyonari, H. and Li, X. C. and Schimenti, J. and Hoog, C. and Watanabe, Y.},
  month = mar,
  year = {2014},
  pages = {594-607},
  file = {/home/bbeltr1/Documents/paper-collection/WatanabeY/Ishiguro et al_2014_Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes.pdf}
}

@article{oh2011,
  title = {Development of {{Time}}-{{Integrated Multipoint Moment Analysis}} for {{Spatially Resolved Fluctuation Spectroscopy}} with {{High Time Resolution}}},
  volume = {101},
  issn = {0006-3495},
  abstract = {Spatial gradients in the behaviors of soluble proteins are thought to underlie many phenomena in cell and developmental biology, but the nature and even the existence of these gradients are often unclear because few techniques can adequately characterize them. Methods with sufficient temporal resolution to study the dynamics of diffusing molecules can only sample relatively small regions, whereas methods that are capable of imaging larger areas cannot probe fast timescales. To overcome these limitations, we developed and implemented time-integrated multipoint moment analysis (TIMMA), a form of fluorescence fluctuation spectroscopy that is capable of probing timescales down to 20 {$\mu$}s at hundreds of different locations simultaneously in a sample. We show that TIMMA can be used to measure the diffusion of small-molecule dyes and fluorescent colloids, and that it can create spatial maps of the behavior of soluble fluorescent proteins throughout mammalian tissue culture cells. We also demonstrate that TIMMA can characterize internal gradients in the diffusion of freely moving proteins in single cells.},
  number = {6},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2011.08.013},
  author = {Oh, Doogie and Zidovska, Alexandra and Xu, Yangqing and Needleman, Daniel J.},
  month = sep,
  year = {2011},
  pages = {1546-1554},
  file = {/home/bbeltr1/Documents/paper-collection/NeedlemanD/Oh et al_2011_Development of Time-Integrated Multipoint Moment Analysis for Spatially.pdf;/home/bbeltr1/Documents/zotero/storage/MI6NMIXS/S0006349511009581.html}
}

@article{zidovska2013,
  title = {Micron-Scale Coherence in Interphase Chromatin Dynamics},
  volume = {110},
  issn = {0027-8424, 1091-6490},
  abstract = {Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4\textendash{}5 {$\mathrm{\mu}$}m) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces.},
  language = {en},
  number = {39},
  journal = {PNAS},
  doi = {10.1073/pnas.1220313110},
  author = {Zidovska, Alexandra and Weitz, David A. and Mitchison, Timothy J.},
  month = sep,
  year = {2013},
  keywords = {active materials,self-organization,soft matter},
  pages = {15555-15560},
  file = {/home/bbeltr1/Documents/paper-collection/MitchisonT/Zidovska et al_2013_Micron-scale coherence in interphase chromatin dynamics.pdf;/home/bbeltr1/Documents/zotero/storage/DQD28S98/15555.html},
  pmid = {24019504}
}

@article{bruinsma2014,
  title = {Chromatin {{Hydrodynamics}}},
  volume = {106},
  issn = {0006-3495},
  abstract = {Following recent observations of large scale correlated motion of chromatin inside the nuclei of live differentiated cells, we present a hydrodynamic theory\textemdash{}the two-fluid model\textemdash{}in which the content of a nucleus is described as a chromatin solution with the nucleoplasm playing the role of the solvent and the chromatin fiber that of a solute. This system is subject to both passive thermal fluctuations and active scalar and vector events that are associated with free energy consumption, such as ATP hydrolysis. Scalar events drive the longitudinal viscoelastic modes (where the chromatin fiber moves relative to the solvent) while vector events generate the transverse modes (where the chromatin fiber moves together with the solvent). Using linear response methods, we derive explicit expressions for the response functions that connect the chromatin density and velocity correlation functions to the corresponding correlation functions of the active sources and the complex viscoelastic moduli of the chromatin solution. We then derive general expressions for the flow spectral density of the chromatin velocity field. We use the theory to analyze experimental results recently obtained by one of the present authors and her co-workers. We find that the time dependence of the experimental data for both native and ATP-depleted chromatin can be well-fitted using a simple model\textemdash{}the Maxwell fluid\textemdash{}for the complex modulus, although there is some discrepancy in terms of the wavevector dependence. Thermal fluctuations of ATP-depleted cells are predominantly longitudinal. ATP-active cells exhibit intense transverse long wavelength velocity fluctuations driven by force dipoles. Fluctuations with wavenumbers larger than a few inverse microns are dominated by concentration fluctuations with the same spectrum as thermal fluctuations but with increased intensity.},
  number = {9},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2014.03.038},
  author = {Bruinsma, Robijn and Grosberg, Alexander Y. and Rabin, Yitzhak and Zidovska, Alexandra},
  month = may,
  year = {2014},
  pages = {1871-1881},
  file = {/home/bbeltr1/Documents/paper-collection/ZidovskaA/Bruinsma et al_2014_Chromatin Hydrodynamics.pdf;/home/bbeltr1/Documents/zotero/storage/YBADH699/S0006349514003403.html}
}

@article{chu2017,
  title = {On the Origin of Shape Fluctuations of the Cell Nucleus},
  volume = {114},
  issn = {0027-8424, 1091-6490},
  abstract = {The nuclear envelope (NE) presents a physical boundary between the cytoplasm and the nucleoplasm, sandwiched in between two highly active systems inside the cell: cytoskeleton and chromatin. NE defines the shape and size of the cell nucleus, which increases during the cell cycle, accommodating for chromosome decondensation followed by genome duplication. In this work, we study nuclear shape fluctuations at short time scales of seconds in human cells. Using spinning disk confocal microscopy, we observe fast fluctuations of the NE, visualized by fluorescently labeled lamin A, and of the chromatin globule surface (CGS) underneath the NE, visualized by fluorescently labeled histone H2B. Our findings reveal that fluctuation amplitudes of both CGS and NE monotonously decrease during the cell cycle, serving as a reliable cell cycle stage indicator. Remarkably, we find that, while CGS and NE typically fluctuate in phase, they do exhibit localized regions of out-of-phase motion, which lead to separation of NE and CGS. To explore the mechanism behind these shape fluctuations, we use biochemical perturbations. We find the shape fluctuations of CGS and NE to be both thermally and actively driven, the latter caused by forces from chromatin and cytoskeleton. Such undulations might affect gene regulation as well as contribute to the anomalously high rates of nuclear transport by, e.g., stirring of molecules next to NE, or increasing flux of molecules through the nuclear pores.},
  language = {en},
  number = {39},
  journal = {PNAS},
  doi = {10.1073/pnas.1702226114},
  author = {Chu, Fang-Yi and Haley, Shannon C. and Zidovska, Alexandra},
  month = sep,
  year = {2017},
  keywords = {active materials,chromatin,nuclear envelope,nuclear lamina},
  pages = {10338-10343},
  file = {/home/bbeltr1/Documents/paper-collection/ZidovskaA/Chu et al_2017_On the origin of shape fluctuations of the cell nucleus.pdf;/home/bbeltr1/Documents/zotero/storage/TV6EBVQT/10338.html},
  pmid = {28900009}
}

@article{koslover2017,
  title = {Cytoplasmic {{Flow}} and {{Mixing Due}} to {{Deformation}} of {{Motile Cells}}},
  volume = {113},
  issn = {0006-3495},
  abstract = {The cytoplasm of a living cell is a dynamic environment through which intracellular components must move and mix. In motile, rapidly deforming cells such as human neutrophils, bulk cytoplasmic flow couples cell deformation to the transport and dispersion of cytoplasmic particles. Using particle-tracking measurements in live neutrophil-like cells, we demonstrate that fluid flow associated with the cell deformation contributes to the motion of small acidic organelles, dominating over diffusion on timescales above a few seconds. We then use a general physical model of particle dispersion in a deforming fluid domain to show that transport of organelle-sized particles between the cell periphery and the bulk can be enhanced by dynamic deformation comparable to that observed in neutrophils. Our results implicate an important mechanism contributing to organelle transport in these motile cells: cytoplasmic flow driven by cell shape deformation.},
  number = {9},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2017.09.009},
  author = {Koslover, Elena F. and Chan, Caleb K. and Theriot, Julie A.},
  month = nov,
  year = {2017},
  pages = {2077-2087},
  file = {/home/bbeltr1/Documents/paper-collection/TheriotJ/Koslover et al_2017_Cytoplasmic Flow and Mixing Due to Deformation of Motile Cells.pdf;/home/bbeltr1/Documents/zotero/storage/SB8U8KLS/S0006349517310202.html}
}

@article{koslover2016,
  title = {Disentangling {{Random Motion}} and {{Flow}} in a {{Complex Medium}}},
  volume = {110},
  issn = {0006-3495},
  abstract = {We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined.},
  number = {3},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2015.11.008},
  author = {Koslover, Elena F. and Chan, Caleb K. and Theriot, Julie A.},
  month = feb,
  year = {2016},
  pages = {700-709},
  file = {/home/bbeltr1/Documents/paper-collection/TheriotJ/Koslover et al_2016_Disentangling Random Motion and Flow in a Complex Medium.pdf;/home/bbeltr1/Documents/zotero/storage/LVMVDDPS/S0006349515011650.html}
}

@article{jinks-robertson1997,
  title = {Meiotic {{Crossing}} over between {{Nonhomologous Chromosomes Affects Chromosome Segregation}} in {{Yeast}}},
  volume = {146},
  issn = {0016-6731},
  abstract = {Meiotic recombination between artificial repeats positioned on nonhomologous chromosomes occurs efficiently in the yeast Saccharomyces cerevisiae. Both gene conversion and crossover events have been observed, with crossovers yielding reciprocal translocations. In the current study, 5.5-kb ura3 repeats positioned on chromosomes V and XV were used to examine the effect of ectopic recombination on meiotic chromosome segregation. Ura(+) random spores were selected and gene conversion vs. crossover events were distinguished by Southern blot analysis. Approximately 15\% of the crossover events between chromosomes V and XV were associated with missegregation of one of these chromosomes. The missegregation was manifest as hyperploid spores containing either both translocations plus a normal chromosome, or both normal chromosomes plus one of the translocations. In those cases where it could be analyzed, missegregation occurred at the first meiotic division. These data are discussed in terms of a model in which ectopic crossovers compete efficiently with normal allelic crossovers in directing meiotic chromosome segregation.},
  number = {1},
  journal = {Genetics},
  author = {{Jinks-Robertson}, S. and Sayeed, S. and Murphy, T.},
  month = may,
  year = {1997},
  pages = {69-78},
  file = {/home/bbeltr1/Documents/paper-collection/MurphyT/Jinks-Robertson et al_1997_Meiotic Crossing over between Nonhomologous Chromosomes Affects Chromosome.pdf},
  pmid = {9136001},
  pmcid = {PMC1207961}
}

@misc{bardhan2012,
  type = {Research Article},
  title = {Meiotic {{Chromosome Interactions}}: {{Nonhomologous Centromere}} ({{Un}}){{Coupling}} and {{Homologous Synapsis}}},
  shorttitle = {Meiotic {{Chromosome Interactions}}},
  abstract = {The fundamental function of meiosis, segregation of the maternal and paternal chromosomes, is facilitated by reciprocal recombination and intimate juxtaposition (synapsis) between the homologous chromosomes in meiotic prophase. Homolog synapsis, mediated by the synaptonemal complex (SC), is preceded by a stage of pairing between the centromeres of nonhomologous chromosomes. This pairing, named nonhomologous centromere coupling (NCC), depends upon the meiotic cohesin Rec8 and the SC protein Zip1. Nonhomologously coupled centromeres (NCCs), if remain tethered, must interfere with complete homolog synapsis (SC formation). Recent experiments demonstrate the existence of a mechanism that regulates NCC. Importantly, this is part of a regulatory network which couples dissolution of the NCCs with SC formation between the homologous chromosomes, thereby ensuring appropriate meiotic chromosome interactions. This paper reviews this network and presents speculations relating to the initiation of SC formation at centromere.},
  language = {en},
  journal = {International Scholarly Research Notices},
  howpublished = {https://www.hindawi.com/journals/isrn/2012/890475/},
  author = {Bardhan, Amit},
  year = {2012},
  file = {/home/bbeltr1/Documents/paper-collection/BardhanA/Bardhan_2012_Meiotic Chromosome Interactions.pdf;/home/bbeltr1/Documents/zotero/storage/SFQ6M6V2/890475.html},
  doi = {10.5402/2012/890475}
}

@article{daines2014,
  title = {Recombination-{{Independent Mechanisms}} and {{Pairing}} of {{Homologous Chromosomes}} during {{Meiosis}} in {{Plants}}},
  volume = {7},
  issn = {1674-2052},
  abstract = {Meiosis is the specialized eukaryotic cell division that permits the halving of ploidy necessary for gametogenesis in sexually reproducing organisms. This involves a single round of DNA replication followed by two successive divisions. To ensure balanced segregation, homologous chromosome pairs must migrate to opposite poles at the first meiotic division and this means that they must recognize and pair with each other beforehand. Although understanding of the mechanisms by which meiotic chromosomes find and pair with their homologs has greatly advanced, it remains far from being fully understood. With some notable exceptions such as male Drosophila, the recognition and physical linkage of homologs at the first meiotic division involves homologous recombination. However, in addition to this, it is clear that many organisms, including plants, have also evolved a series of recombination-independent mechanisms to facilitate homolog recognition and pairing. These implicate chromosome structure and dynamics, telomeres, centromeres, and, most recently, small RNAs. With a particular focus on plants, we present here an overview of understanding of these early, recombination-independent events that act in the pairing of homologous chromosomes during the first meiotic division.
SUMMARY
Meiosis is the specialized cell division which carries out the necessary halving of the chromosome complement in eukaryotic gametogenesis. The ordered segregation of meiotic chromosomes is ensured by recombination in most eukaryotes, but other mechanisms also act. With a particular focus on plants, we present here an overview of understanding of these early, recombination-independent events that act in the pairing of homologous chromosomes during the first meiotic division.},
  number = {3},
  journal = {Molecular Plant},
  doi = {10.1093/mp/sst172},
  author = {Da Ines, Olivier and Gallego, Maria E. and White, Charles I.},
  month = mar,
  year = {2014},
  keywords = {chromatin,centromeres,homolog pairing,meiosis,telomeres},
  pages = {492-501},
  file = {/home/bbeltr1/Documents/paper-collection/WhiteC/Da Ines et al_2014_Recombination-Independent Mechanisms and Pairing of Homologous Chromosomes.pdf;/home/bbeltr1/Documents/zotero/storage/YRSJT4N6/S1674205214602501.html}
}

@article{avsaroglu2014,
  title = {Effect of {{Chromosome Tethering}} on {{Nuclear Organization}} in {{Yeast}}},
  volume = {9},
  issn = {1932-6203},
  abstract = {Interphase chromosomes in Saccharomyces cerevisiae are tethered to the nuclear envelope at their telomeres and to the spindle pole body (SPB) at their centromeres. Using a polymer model of yeast chromosomes that includes these interactions, we show theoretically that telomere attachment to the nuclear envelope is a major determinant of gene positioning within the nucleus only for genes within 10 kb of the telomeres. We test this prediction by measuring the distance between the SPB and the silent mating locus (HML) on chromosome III in wild\textendash{}type and mutant yeast strains that contain altered chromosome-tethering interactions. In wild-type yeast cells we find that disruption of the telomere tether does not dramatically change the position of HML with respect to the SPB, in agreement with theoretical predictions. Alternatively, using a mutant strain with a synthetic tether that localizes an HML-proximal site to the nuclear envelope, we find a significant change in the SPB-HML distance, again as predicted by theory. Our study quantifies the importance of tethering at telomeres on the organization of interphase chromosomes in yeast, which has been shown to play a significant role in determining chromosome function such as gene expression and recombination.},
  language = {en},
  number = {7},
  journal = {PLOS ONE},
  doi = {10.1371/journal.pone.0102474},
  author = {Av{\c s}aro{\u g}lu, Bar\i{\c s} and Bronk, Gabriel and {Gordon-Messer}, Susannah and Ham, Jungoh and Bressan, Debra A. and Haber, James E. and Kondev, Jane},
  month = jul,
  year = {2014},
  keywords = {Polymers,Chromosome structure and function,Genetic loci,Probability distribution,Random walk,Saccharomyces cerevisiae,Telomeres,Yeast and fungal models},
  pages = {e102474},
  file = {/home/bbeltr1/Documents/paper-collection/KondevJ/Avşaroğlu et al_2014_Effect of Chromosome Tethering on Nuclear Organization in Yeast.pdf;/home/bbeltr1/Documents/zotero/storage/WLTMTIMK/article.html}
}

@article{rydberg1998,
  title = {Chromatin Conformation in Living Cells: Support for a Zig-Zag Model of the 30 Nm Chromatin {{fiber11Edited}} by {{T}}. {{Richmond}}},
  volume = {284},
  issn = {0022-2836},
  shorttitle = {Chromatin Conformation in Living Cells},
  abstract = {A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell.},
  number = {1},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.1998.2150},
  author = {Rydberg, Bj\"orn and Holley, William R and Mian, I. Saira and Chatterjee, Aloke},
  month = nov,
  year = {1998},
  keywords = {3D,CHO,chromatin fiber,CIP,DNA breaks,ionizing radiation,nucleosome,PBS,zig-zag model},
  pages = {71-84},
  file = {/home/bbeltr1/Documents/paper-collection/ChatterjeeA/Rydberg et al_1998_Chromatin conformation in living cells.pdf;/home/bbeltr1/Documents/zotero/storage/VDAWLHB3/S0022283698921507.html}
}

@article{risca2015,
  title = {Unraveling the {{3D}} Genome: Genomics Tools for Multi-Scale Exploration},
  volume = {31},
  issn = {0168-9525},
  shorttitle = {Unraveling the {{3D}} Genome},
  abstract = {A decade of rapid method development has begun to yield exciting insights into the three-dimensional architecture of the metazoan genome and the roles it may play in regulating transcription. We review here core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pair to megabase scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.},
  number = {7},
  journal = {Trends Genet},
  doi = {10.1016/j.tig.2015.03.010},
  author = {Risca, Viviana I. and Greenleaf, William J.},
  month = jul,
  year = {2015},
  pages = {357-372},
  file = {/home/bbeltr1/Documents/paper-collection/GreenleafW/Risca_Greenleaf_2015_Unraveling the 3D genome.pdf},
  pmid = {25887733},
  pmcid = {PMC4490074}
}

@article{li2011,
  series = {Chromosomes and Expression Mechanisms},
  title = {Chromatin Higher-Order Structures and Gene Regulation},
  volume = {21},
  issn = {0959-437X},
  abstract = {Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a crucial role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation, and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation.},
  number = {2},
  journal = {Current Opinion in Genetics \& Development},
  doi = {10.1016/j.gde.2011.01.022},
  author = {Li, Guohong and Reinberg, Danny},
  month = apr,
  year = {2011},
  pages = {175-186},
  file = {/home/bbeltr1/Documents/paper-collection/Reinberg/Li_Reinberg_2011_Chromatin higher-order structures and gene regulation.pdf;/home/bbeltr1/Documents/paper-collection/ReinbergD/Li_Reinberg_2011_Chromatin higher-order structures and gene regulation.pdf;/home/bbeltr1/Documents/zotero/storage/5TGMZ6YR/S0959437X11000372.html;/home/bbeltr1/Documents/zotero/storage/JWZKVBUY/S0959437X11000372.html}
}

@article{luger2012,
  title = {New Insights into Nucleosome and Chromatin Structure: An Ordered State or a Disordered Affair?},
  volume = {13},
  copyright = {2012 Nature Publishing Group},
  issn = {1471-0080},
  shorttitle = {New Insights into Nucleosome and Chromatin Structure},
  abstract = {The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair. Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components. This is the result of the incorporation of variant histones and post-translational modifications of histone amino acid side chains. The resulting changes in nucleosome structure, stability and dynamics affect the compaction of nucleosomal arrays into higher-order structures. It is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed. This implies that chromatin structure must also be viewed in the context of specific biological functions.},
  language = {en},
  number = {7},
  journal = {Nature Reviews Molecular Cell Biology},
  doi = {10.1038/nrm3382},
  author = {Luger, Karolin and Dechassa, Mekonnen L. and Tremethick, David J.},
  month = jul,
  year = {2012},
  pages = {436-447},
  file = {/home/bbeltr1/Documents/paper-collection/TremethickD/Luger et al_2012_New insights into nucleosome and chromatin structure.pdf;/home/bbeltr1/Documents/zotero/storage/ISQNR6T5/nrm3382.html}
}

@article{eltsov2008,
  title = {Analysis of Cryo-Electron Microscopy Images Does Not Support the Existence of 30-Nm Chromatin Fibers in Mitotic Chromosomes in Situ},
  volume = {105},
  copyright = {\textcopyright{} 2008 by The National Academy of Sciences of the USA},
  issn = {0027-8424, 1091-6490},
  abstract = {Although the formation of 30-nm chromatin fibers is thought to be the most basic event of chromatin compaction, it remains controversial because high-resolution imaging of chromatin in living eukaryotic cells had not been possible until now. Cryo-electron microscopy of vitreous sections is a relatively new technique, which enables direct high-resolution observation of the cell structures in a close-to-native state. We used cryo-electron microscopy and image processing to further investigate the presence of 30-nm chromatin fibers in human mitotic chromosomes. HeLa S3 cells were vitrified by high-pressure freezing, thin-sectioned, and then imaged under the cryo-electron microscope without any further chemical treatment or staining. For an unambiguous interpretation of the images, the effects of the contrast transfer function were computationally corrected. The mitotic chromosomes of the HeLa S3 cells appeared as compact structures with a homogeneous grainy texture, in which there were no visible 30-nm fibers. Power spectra of the chromosome images also gave no indication of 30-nm chromatin folding. These results, together with our observations of the effects of chromosome swelling, strongly suggest that, within the bulk of compact metaphase chromosomes, the nucleosomal fiber does not undergo 30-nm folding, but exists in a highly disordered and interdigitated state, which is, on the local scale, comparable with a polymer melt.},
  language = {en},
  number = {50},
  journal = {PNAS},
  doi = {10.1073/pnas.0810057105},
  author = {Eltsov, Mikhail and MacLellan, Kirsty M. and Maeshima, Kazuhiro and Frangakis, Achilleas S. and Dubochet, Jacques},
  month = dec,
  year = {2008},
  keywords = {chromatin compaction,chromosome structure,contrast,polymer melt,transfer function,vitreous sections},
  pages = {19732-19737},
  file = {/home/bbeltr1/Documents/paper-collection/DubochetJ/Eltsov et al_2008_Analysis of cryo-electron microscopy images does not support the existence of.pdf;/home/bbeltr1/Documents/zotero/storage/UQ4Z8XV2/19732.html},
  pmid = {19064912}
}

@article{bascom2017,
  title = {Linking {{Chromatin Fibers}} to {{Gene Folding}} by {{Hierarchical Looping}}},
  volume = {112},
  issn = {0006-3495},
  abstract = {While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material. With recent advances in experimental and theoretical techniques, a variety of structures have been observed on the fiber, gene, and chromosome levels of genome organization. Here we view chromatin architecture from nucleosomes and fibers to genes and chromosomes, highlighting the rich structural diversity and fiber fluidity emerging from both experimental and theoretical techniques. In this context, we discuss our recently proposed folding mechanism, which we call ``hierarchical looping'', similar to rope flaking used in mountain climbing, where 10-nm zigzag chromatin fibers are compacted laterally into self-associating loops which then stack and fold in space. We propose that hierarchical looping may act as a bridge between fibers and genes as well as provide a mechanism to relate key features of interphase and metaphase chromosome architecture to genome structural changes. This motif emerged by analysis of ultrastructural internucleosome contact data by electron microscopy-assisted nucleosome interaction capture cross-linking experiments, in combination with mesoscale modeling. We suggest that while the local folding of chromatin can be regulated at the fiber level by adjustment of internal factors such as linker-histone binding affinities, linker DNA lengths, and divalent ion levels, hierarchical looping on the gene level can additionally be controlled by posttranslational modifications and external factors such as polycomb group proteins. From a combination of 3C data and mesoscale modeling, we suggest that hierarchical looping could also play a role in epigenetic gene silencing, as stacked loops may occlude access to transcription start sites. With advances in crystallography, single-molecule in~vitro biochemistry, in~vivo imaging techniques, and genome-wide contact data experiments, various modeling approaches are allowing for previously unavailable structural interpretation of these data at multiple spatial and temporal scales. An unprecedented level of productivity and opportunity is on the horizon for the chromatin structure field.},
  number = {3},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2017.01.003},
  author = {Bascom, Gavin and Schlick, Tamar},
  month = feb,
  year = {2017},
  pages = {434-445},
  file = {/home/bbeltr1/Documents/paper-collection/SchlickT/Bascom_Schlick_2017_Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.pdf;/home/bbeltr1/Documents/zotero/storage/MMGJZ5TQ/S0006349517300346.html}
}

@article{li2015,
  series = {{{3D Genome}} Structure.},
  title = {Structure and Organization of Chromatin Fiber in the Nucleus},
  volume = {589},
  issn = {0014-5793},
  abstract = {Eukaryotic genomes are organized hierarchically into chromatin structures by histones. Despite extensive research for over 30years, not only the fundamental structure of the 30-nm chromatin fiber is being debated, but the actual existence of such fiber remains hotly contested. In this review, we focus on the most recent progress in elucidating the structure of the 30-nm fiber upon in vitro reconstitution, and its possible organization inside the nucleus. In addition, we discuss the roles of linker histone H1 as well as the importance of specific nucleosome-nucleosome interactions in the formation of the 30-nm fiber. Finally, we discuss the involvement of structural variations and epigenetic mechanisms available for the regulation of this chromatin form.},
  number = {20, Part A},
  journal = {FEBS Letters},
  doi = {10.1016/j.febslet.2015.04.023},
  author = {Li, Guohong and Zhu, Ping},
  month = oct,
  year = {2015},
  keywords = {Epigenetics,30-nm chromatin fiber,Histone,Nucleosome,Nucleosome repeat length},
  pages = {2893-2904},
  file = {/home/bbeltr1/Documents/paper-collection/ZhuP/Li_Zhu_2015_Structure and organization of chromatin fiber in the nucleus.pdf;/home/bbeltr1/Documents/zotero/storage/WWFUJKC8/S0014579315002811.html}
}

@article{song2014,
  title = {Cryo-{{EM Study}} of the {{Chromatin Fiber Reveals}} a {{Double Helix Twisted}} by {{Tetranucleosomal Units}}},
  volume = {344},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Double Helix, Doubled
Chromatin consists of genomic DNA packaged onto nucleosomes\textemdash{}double donut-shaped complexes of histone proteins. Roughly 150 base pairs of DNA are wrapped around each nucleosome with variable lengths of linker DNA in-between. Using cryogenic electron microscopy, Song et al. (p. 376; see the Perspective by Travers) determined the 11 angstrom\textendash{}resolution structure of a 12-nucleosome string of DNA. The segment forms a 30-nanometer fiber structure, which is itself double-helical, like the DNA it packages.
The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom\textendash{}resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome repeat lengths. The structures show a histone H1-dependent left-handed twist of the repeating tetranucleosomal structural units, within which the four nucleosomes zigzag back and forth with a straight linker DNA. The asymmetric binding and the location of histone H1 in chromatin play a role in the formation of the 30-nanometer fiber. Our results provide mechanistic insights into how nucleosomes compact into higher-order chromatin fibers.
The structure of a segment of chromatin reveals the importance of the linker histone in determining its conformation. [Also see Perspective by Travers]
The structure of a segment of chromatin reveals the importance of the linker histone in determining its conformation. [Also see Perspective by Travers]},
  language = {en},
  number = {6182},
  journal = {Science},
  doi = {10.1126/science.1251413},
  author = {Song, Feng and Chen, Ping and Sun, Dapeng and Wang, Mingzhu and Dong, Liping and Liang, Dan and Xu, Rui-Ming and Zhu, Ping and Li, Guohong},
  month = apr,
  year = {2014},
  pages = {376-380},
  file = {/home/bbeltr1/Documents/paper-collection/LiG/Song et al_2014_Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by.pdf;/home/bbeltr1/Documents/zotero/storage/RM428MLC/376.html},
  pmid = {24763583}
}

@article{hsieh2015,
  title = {Mapping {{Nucleosome Resolution Chromosome Folding}} in {{Yeast}} by {{Micro}}-{{C}}},
  volume = {162},
  issn = {0092-8674, 1097-4172},
  language = {English},
  number = {1},
  journal = {Cell},
  doi = {10.1016/j.cell.2015.05.048},
  author = {Hsieh, Tsung-Han S. and Weiner, Assaf and Lajoie, Bryan and Dekker, Job and Friedman, Nir and Rando, Oliver J.},
  month = jul,
  year = {2015},
  pages = {108-119},
  file = {/home/bbeltr1/Documents/paper-collection/RandoO/Hsieh et al_2015_Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.pdf;/home/bbeltr1/Documents/zotero/storage/XEY7D4MR/S0092-8674(15)00638-8.html},
  pmid = {26119342}
}

@article{mobius2013,
  title = {Toward a Unified Physical Model of Nucleosome Patterns Flanking Transcription Start Sites},
  volume = {110},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For Saccharomyces cerevisiae, the average in vivo pattern was previously shown to be quantitatively described by a ``nucleosome gas'' model based on the statistical positioning mechanism. However, this simple physical description is challenged by the fact that the pattern differs quantitatively between species and by recent experiments that appear incompatible with statistical positioning, indicating important roles for chromatin remodelers. We undertake a data-driven search for a unified physical model to describe the nucleosome patterns of 12 yeast species and also consider an extension of the model to capture remodeling effects. We are led to a nucleosome gas that takes into account nucleosome breathing, i.e., transient unwrapping of nucleosomal DNA segments. This known biophysical property of nucleosomes rationalizes a ``pressure''-induced dependence of the effective nucleosome size that is suggested by the data. By fitting this model to the data, we find an average energy cost for DNA unwrapping consistent with previous biophysical experiments. Although the available data are not sufficient to reconstruct chromatin remodeling mechanisms, a minimal model extension by one mechanism yields an ``active nucleosome gas'' that can rationalize the behavior of systems with reduced histone\textendash{}DNA ratio and remodeler knockouts. We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation.},
  language = {en},
  number = {14},
  journal = {PNAS},
  doi = {10.1073/pnas.1214048110},
  author = {M\"obius, Wolfram and Osberg, Brendan and Tsankov, Alexander M. and Rando, Oliver J. and Gerland, Ulrich},
  month = apr,
  year = {2013},
  keywords = {chromatin structure,nucleosome maps,quantitative biology},
  pages = {5719-5724},
  file = {/home/bbeltr1/Documents/paper-collection/Gerland/Möbius et al_2013_Toward a unified physical model of nucleosome patterns flanking transcription.pdf;/home/bbeltr1/Documents/paper-collection/GerlandU/Möbius et al_2013_Toward a unified physical model of nucleosome patterns flanking transcription.pdf;/home/bbeltr1/Documents/zotero/storage/A6QHLCY3/5719.html},
  pmid = {23509245}
}

@article{beshnova2014,
  title = {Regulation of the {{Nucleosome Repeat Length In Vivo}} by the {{DNA Sequence}}, {{Protein Concentrations}} and {{Long}}-{{Range Interactions}}},
  volume = {10},
  issn = {1553-7358},
  abstract = {The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.},
  language = {en},
  number = {7},
  journal = {PLOS Computational Biology},
  doi = {10.1371/journal.pcbi.1003698},
  author = {Beshnova, Daria A. and Cherstvy, Andrey G. and Vainshtein, Yevhen and Teif, Vladimir B.},
  month = jul,
  year = {2014},
  keywords = {Chromatin,Histones,Nucleosomes,DNA sequence analysis,DNA-binding proteins,Genetic oscillators,Mammalian genomics,Nucleosome mapping},
  pages = {e1003698},
  file = {/home/bbeltr1/Documents/paper-collection/TeifV/Beshnova et al_2014_Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein.pdf;/home/bbeltr1/Documents/zotero/storage/584L6Z2V/article.html}
}

@article{cutter2015,
  title = {A {{Brief Review}} of {{Nucleosome Structure}}},
  volume = {589},
  issn = {0014-5793},
  abstract = {The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial \textasciitilde{}7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.},
  number = {20 0 0},
  journal = {FEBS Lett},
  doi = {10.1016/j.febslet.2015.05.016},
  author = {Cutter, Amber and Hayes, Jeffrey J.},
  month = oct,
  year = {2015},
  pages = {2914-2922},
  file = {/home/bbeltr1/Documents/paper-collection/HayesJ/Cutter_Hayes_2015_A Brief Review of Nucleosome Structure.pdf},
  pmid = {25980611},
  pmcid = {PMC4598263}
}

@article{forties2011,
  title = {A Quantitative Model of Nucleosome Dynamics},
  volume = {39},
  issn = {0305-1048},
  abstract = {The expression, replication and repair of eukaryotic genomes require the fundamental organizing unit of chromatin, the nucleosome, to be unwrapped and disassembled. We have developed a quantitative model of nucleosome dynamics which provides a fundamental understanding of these DNA processes. We calibrated this model using results from high precision single molecule nucleosome unzipping experiments, and then tested its predictions for experiments in which nucleosomes are disassembled by the DNA mismatch recognition complex hMSH2-hMSH6. We found that this calibrated model quantitatively describes hMSH2-hMSH6 induced disassembly rates of nucleosomes with two separate DNA sequences and four distinct histone modification states. In addition, this model provides mechanistic insight into nucleosome disassembly by hMSH2-hMSH6 and the influence of histone modifications on this disassembly reaction. This model's precise agreement with current experiments suggests that it can be applied more generally to provide important mechanistic understanding of the numerous nucleosome alterations that occur during DNA processing.},
  number = {19},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gkr422},
  author = {Forties, Robert A. and North, Justin A. and Javaid, Sarah and Tabbaa, Omar P. and Fishel, Richard and Poirier, Michael G. and Bundschuh, Ralf},
  month = oct,
  year = {2011},
  pages = {8306-8313},
  file = {/home/bbeltr1/Documents/paper-collection/BundschuhR/Forties et al_2011_A quantitative model of nucleosome dynamics.pdf},
  pmid = {21764779},
  pmcid = {PMC3201853}
}

@article{tesoro2016,
  title = {A One-Dimensional Statistical Mechanics Model for Nucleosome Positioning on Genomic {{DNA}}},
  volume = {13},
  issn = {1478-3975},
  abstract = {The first level of folding of DNA in eukaryotes is provided by the so-called `10 nm chromatin fibre', where DNA wraps around histone proteins ({$\sim$}10 nm in size) to form nucleosomes, which go on to create a zig-zagging bead-on-a-string structure. In this work we present a one-dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high-resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas [1]. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point-like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro .},
  language = {en},
  number = {1},
  journal = {Phys. Biol.},
  doi = {10.1088/1478-3975/13/1/016004},
  author = {Tesoro, S. and Ali, I. and Morozov, A. N. and Sulaiman, N. and Marenduzzo, D.},
  year = {2016},
  keywords = {Condensed Matter - Soft Condensed Matter,Condensed Matter - Statistical Mechanics,Physics - Biological Physics},
  pages = {016004},
  file = {/home/bbeltr1/Documents/paper-collection/Marenduzzo, D./Tesoro et al_2016_A one-dimensional statistical mechanics model for nucleosome positioning on.pdf;/home/bbeltr1/Documents/paper-collection/MarenduzzoD/Tesoro et al_2016_A one-dimensional statistical mechanics model for nucleosome positioning on.pdf;/home/bbeltr1/Documents/zotero/storage/BTEM467Q/1510.html}
}

@article{teif2010,
  title = {Statistical\textendash{}Mechanical Lattice Models for Protein\textendash{{DNA}} Binding in Chromatin},
  volume = {22},
  issn = {0953-8984, 1361-648X},
  abstract = {Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated proteinDNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.},
  language = {en},
  number = {41},
  journal = {Journal of Physics: Condensed Matter},
  doi = {10.1088/0953-8984/22/41/414105},
  author = {Teif, Vladimir B and Rippe, Karsten},
  month = oct,
  year = {2010},
  pages = {414105},
  file = {/home/bbeltr1/Documents/paper-collection/RippeK/Teif_Rippe_2010_Statistical–mechanical lattice models for protein–DNA binding in chromatin.pdf}
}

@article{chereji2011,
  title = {Statistical {{Mechanics}} of {{Nucleosomes Constrained}} by {{Higher}}-{{Order Chromatin Structure}}},
  volume = {144},
  issn = {0022-4715, 1572-9613},
  abstract = {Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures (Felsenfeld and Groudine in Nature 421:448, 2003). Each nucleosome, the fundamental unit of chromatin, has 147 base pairs (bp) of DNA wrapped around a histone octamer (Richmond and Davey in Nature 423:145, 2003). In order to describe how chromatin fiber formation affects nucleosome positioning and energetics, we have developed a thermodynamic model of finite-size particles with effective nearest-neighbor interactions and arbitrary DNA-binding energies. We show that both oneand two-body interactions can be extracted from one-particle density profiles based on highthroughput maps of in vitro or in vivo nucleosome positions. Although a simpler approach that neglects two-body interactions (even if they are in fact present in the system) can be used to predict sequence determinants of nucleosome positions, the full theory is required to disentangle one- and two-body effects. Finally, we construct a minimal model in which nucleosomes are positioned primarily by steric exclusion and two-body interactions rather than intrinsic histone-DNA sequence preferences. The model reproduces nucleosome occupancy patterns observed over transcribed regions in living cells.},
  language = {en},
  number = {2},
  journal = {Journal of Statistical Physics},
  doi = {10.1007/s10955-011-0214-y},
  author = {Chereji, R{\u a}zvan V. and Morozov, Alexandre V.},
  month = jul,
  year = {2011},
  pages = {379-404},
  file = {/home/bbeltr1/Documents/paper-collection/MorozovA/Chereji_Morozov_2011_Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin.pdf}
}

@article{lubliner2009,
  title = {Modeling Interactions between Adjacent Nucleosomes Improves Genome-Wide Predictions of Nucleosome Occupancy},
  volume = {25},
  issn = {1367-4803},
  abstract = {Motivation: Understanding the mechanisms that govern nucleosome positioning over genomes in vivo is essential for unraveling the role of chromatin organization in transcriptional regulation. Until now, models for predicting genome-wide nucleosome occupancy have assumed that the DNA associations of neighboring nucleosomes on the genome are independent. We present a new model that relaxes this independence assumption by modeling interactions between adjacent nucleosomes., Results: We show that modeling interactions between adjacent nucleosomes improves genome-wide nucleosome occupancy predictions in an in vitro system that includes only nucleosomes and purified DNA, where the resulting model has a preference for short spacings (linkers) of less than 20 bp in length between neighboring nucleosomes. Since nucleosome occupancy in vitro depends only on properties intrinsic to nucleosomes, these results suggest that the interactions we find are intrinsic to nucleosomes and do not depend on other factors, such as transcription factors and chromatin remodelers. We also show that modeling these intrinsic interactions significantly improves genome-wide predictions of nucleosome occupancy in vivo., Contact: eran.segal@weizmann.ac.il, Supplementary information: Supplementary data are available at Bioinformatics online.},
  number = {12},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btp216},
  author = {Lubliner, Shai and Segal, Eran},
  month = jun,
  year = {2009},
  pages = {i348-i355},
  file = {/home/bbeltr1/Documents/paper-collection/SegalE/Lubliner_Segal_2009_Modeling interactions between adjacent nucleosomes improves genome-wide.pdf},
  pmid = {19478009},
  pmcid = {PMC2687970}
}

@article{chereji2011a,
  title = {Statistical Mechanics of Nucleosome Ordering by Chromatin-Structure-Induced Two-Body Interactions},
  volume = {83},
  abstract = {One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into regular chromatin fibers if their rotational setting (defined by the DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with both intrinsic histone-DNA interactions and an effective two-body potential. We infer one- and two-body energies directly from high-throughput maps of nucleosome positions. We show that higher-order chromatin structure helps explains in vitro and in vivo nucleosome ordering in transcribed regions, and plays a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome positions.},
  number = {5},
  journal = {Phys. Rev. E},
  doi = {10.1103/PhysRevE.83.050903},
  author = {Chereji, R{\u a}zvan V. and Tolkunov, Denis and Locke, George and Morozov, Alexandre V.},
  month = may,
  year = {2011},
  pages = {050903},
  file = {/home/bbeltr1/Documents/zotero/storage/9IIFUSH6/PhysRevE.83.html}
}

@article{chou2007,
  title = {Peeling and {{Sliding}} in {{Nucleosome Repositioning}}},
  volume = {99},
  issn = {0031-9007, 1079-7114},
  language = {en},
  number = {5},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.99.058105},
  author = {Chou, Tom},
  month = aug,
  year = {2007},
  file = {/home/bbeltr1/Documents/paper-collection/ChouT/Chou_2007_Peeling and Sliding in Nucleosome Repositioning.pdf}
}

@article{teif2010a,
  title = {A {{Lattice Model}} for {{Transcription Factor Access}} to {{Nucleosomal DNA}}},
  volume = {99},
  issn = {0006-3495},
  abstract = {Nucleosomes, the basic repeating unit of chromatin, consist of 147 basepairs of DNA that are wrapped in almost two turns around a histone protein octamer core. Because {$\sim$}3/4 of the human genomic DNA is found within nucleosomes, their position and DNA interaction is an essential determinant for the DNA access of gene-specific transcription factors and other proteins. Here, a DNA lattice model was developed for describing ligand binding in the presence of a nucleosome. The model takes into account intermediate states, in which DNA is partially unwrapped from the histone octamer. This facilitates access of transcription factors to up to 60 DNA basepairs located in the outer turn of nucleosomal DNA, while the inner DNA turn was found to be more resistant to competitive ligand binding. As deduced from quantitative comparisons with recently published experimental data, our model provides a better description than the previously used all-or-none lattice-binding model. Importantly, nucleosome-occupancy maps predicted by the nucleosome-unwrapping model also differed significantly when partial unwrapping of nucleosomal DNA was considered. In addition, large effects on the cooperative binding of transcription factors to multiple binding sites occluded by the nucleosome were apparent. These findings indicate that partial unwrapping of DNA from the histone octamer needs to be taken into account in quantitative models of gene regulation in chromatin.},
  language = {English},
  number = {8},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2010.08.019},
  author = {Teif, Vladimir B. and Ettig, Ramona and Rippe, Karsten},
  month = oct,
  year = {2010},
  pages = {2597-2607},
  file = {/home/bbeltr1/Documents/paper-collection/RippeK/Teif et al_2010_A Lattice Model for Transcription Factor Access to Nucleosomal DNA.pdf;/home/bbeltr1/Documents/zotero/storage/EECLWWHN/S0006-3495(10)00988-4.html},
  pmid = {20959101}
}

@article{chereji2014,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1305.3986},
  title = {Ubiquitous Nucleosome Unwrapping in the Yeast Genome},
  volume = {111},
  issn = {0027-8424, 1091-6490},
  abstract = {Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of DNA-binding factors to their target sites and thus may provide a dominant pathway for effecting rapid and robust access to DNA packaged into chromatin. Indeed, a recent high-resolution map of distances between neighboring nucleosome dyads in \textbackslash{}emph\{S.cerevisiae\} shows that at least 38.7\textbackslash\% of all nucleosomes are partially unwrapped. The extent of unwrapping follows a stereotypical pattern in the vicinity of genes, reminiscent of the canonical pattern of nucleosome occupancy in which nucleosomes are depleted over promoters and well-positioned over coding regions. To explain these observations, we developed a biophysical model which employs a 10-11 base pair periodic nucleosome energy profile. The profile, based on the pattern of histone-DNA contacts in nucleosome crystal structures and the idea of linker length discretization, accounts for both nucleosome unwrapping and higher-order chromatin structure. Our model reproduces the observed genome-wide distribution of inter-dyad distances, and accounts for patterns of nucleosome occupancy and unwrapping around coding regions. At the same time, our approach explains \textbackslash{}emph\{in vitro\} measurements of accessibility of nucleosome-covered binding sites, and of nucleosome-induced cooperativity between DNA-binding factors. We are able to rule out several alternative scenarios of nucleosome unwrapping as inconsistent with the genomic data.},
  number = {14},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1321001111},
  author = {Chereji, R{\u a}zvan V. and Morozov, Alexandre V.},
  month = apr,
  year = {2014},
  keywords = {Quantitative Biology - Biomolecules,Quantitative Biology - Genomics},
  pages = {5236-5241},
  file = {/home/bbeltr1/Documents/zotero/storage/SXQZ9VCR/1305.html}
}

@article{mcghee1974,
  title = {Theoretical Aspects of {{DNA}}-Protein Interactions: {{Co}}-Operative and Non-Co-Operative Binding of Large Ligands to a One-Dimensional Homogeneous Lattice},
  volume = {86},
  issn = {0022-2836},
  shorttitle = {Theoretical Aspects of {{DNA}}-Protein Interactions},
  abstract = {The interaction of proteins binding non-specifically to DNA, as well as the properties of many other interacting ligand-lattice systems important in molecular biology, requires a fundamentally different type of theoretical analysis than that provided by the classical Scatchard independent-binding-site treatment. Exact and relatively simple equations describing the binding of both non-interacting and interacting (co-operative) ligands to a homogeneous one-dimensional lattice are derived in terms of ligand site size, intrinsic binding constant and ligand-ligand co-operativity (equations (10) and (15) in the text). The mathematical approach is based on simple conditional probabilities, and reveals some largely unrecognized characteristics of such lattice binding systems. The results indicate that the binding of any non-interacting ligand covering more than one lattice residue results in non-linear (convex downward) Scatchard plots. The introduction of positive ligand-ligand co-operativity antagonizes this non-linearity, and eventually leads to plots of the opposite curvature. The maxima, limiting slopes, and intercepts of such plots can be used to estimate the required binding parameters. The method can be extended to systems involving heterogeneous ligands, and some types of heterogeneous lattices. Procedures for applying the method to a variety of interacting systems are presented, and a preliminary analysis is carried out for some selected sets of data from the literature.},
  number = {2},
  journal = {Journal of Molecular Biology},
  doi = {10.1016/0022-2836(74)90031-X},
  author = {McGhee, James D. and {von Hippel}, Peter H.},
  month = jun,
  year = {1974},
  pages = {469-489},
  file = {/home/bbeltr1/Documents/paper-collection/von HippelP/McGhee_von Hippel_1974_Theoretical aspects of DNA-protein interactions.pdf;/home/bbeltr1/Documents/zotero/storage/3XLS87JM/002228367490031X.html}
}

@article{kornberg1988,
  title = {Statistical Distributions of Nucleosomes: Nonrandom Locations by a Stochastic Mechanism.},
  volume = {16},
  issn = {0305-1048},
  shorttitle = {Statistical Distributions of Nucleosomes},
  abstract = {Expressions are derived for distributions of nucleosomes in chromatin. Nucleosomes are placed on DNA at the densities found in bulk chromatin, and their locations are allowed to vary at random. No further assumptions are required to simulate the periodic patterns of digestion obtained with various nucleases. The introduction of a boundary constraint, due for example to sequence-specific protein binding, results in an array of regularly spaced nucleosomes at nonrandom locations, similar to the arrays reported for some genes and other chromosomal regions.},
  number = {14A},
  journal = {Nucleic Acids Res},
  author = {Kornberg, R D and Stryer, L},
  month = jul,
  year = {1988},
  pages = {6677-6690},
  file = {/home/bbeltr1/Documents/paper-collection/StryerL/Kornberg_Stryer_1988_Statistical distributions of nucleosomes.pdf},
  pmid = {3399412},
  pmcid = {PMC338322}
}

@article{fung1998,
  title = {Homologous {{Chromosome Pairing}} in {{Drosophila}} Melanogaster {{Proceeds}} through {{Multiple Independent Initiations}}},
  volume = {141},
  copyright = {\textcopyright{} 1998 Rockefeller University Press},
  issn = {0021-9525, 1540-8140},
  abstract = {The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites.},
  language = {en},
  number = {1},
  journal = {The Journal of Cell Biology},
  doi = {10.1083/jcb.141.1.5},
  author = {Fung, Jennifer C. and Marshall, Wallace F. and Dernburg, Abby and Agard, David A. and Sedat, John W.},
  month = apr,
  year = {1998},
  pages = {5-20},
  file = {/home/bbeltr1/Documents/paper-collection/SedatJ/Fung et al_1998_Homologous Chromosome Pairing in Drosophila melanogaster Proceeds through.pdf;/home/bbeltr1/Documents/zotero/storage/SX28JNVA/5.html},
  pmid = {9531544}
}

@article{mobius2010,
  title = {Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites},
  volume = {6},
  issn = {1553-7358},
  abstract = {The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in Saccharomyces cerevisiae is qualitatively consistent with a "barrier nucleosome model," in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to approximately 1,000 bp to each side.},
  language = {eng},
  number = {8},
  journal = {PLoS Comput. Biol.},
  doi = {10.1371/journal.pcbi.1000891},
  author = {M\"obius, Wolfram and Gerland, Ulrich},
  month = aug,
  year = {2010},
  keywords = {Models; Biological,Base Sequence,Saccharomyces cerevisiae,Nucleosomes,Genome; Fungal,Insulator Elements,Models; Statistical,Transcription Factors,Transcription Initiation Site,Transcription; Genetic},
  pmid = {20808881},
  pmcid = {PMC2924246}
}

@article{mavrich2008,
  title = {A Barrier Nucleosome Model for Statistical Positioning of Nucleosomes throughout the Yeast Genome},
  volume = {18},
  issn = {1088-9051, 1549-5469},
  abstract = {Most nucleosomes are well-organized at the 5{${'}$} ends of S. cerevisiae genes where ``-1'' and ``+1'' nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3{${'}$} NFR that is present at {$>$}95\% of all genes. 3{${'}$} NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3{${'}$} NFRs in gene looping.},
  language = {en},
  number = {7},
  journal = {Genome Res.},
  doi = {10.1101/gr.078261.108},
  author = {Mavrich, Travis N. and Ioshikhes, Ilya P. and Venters, Bryan J. and Jiang, Cizhong and Tomsho, Lynn P. and Qi, Ji and Schuster, Stephan C. and Albert, Istvan and Pugh, B. Franklin},
  month = jan,
  year = {2008},
  pages = {1073-1083},
  file = {/home/bbeltr1/Documents/paper-collection/PughB/Mavrich et al_2008_A barrier nucleosome model for statistical positioning of nucleosomes.pdf;/home/bbeltr1/Documents/zotero/storage/34JAQC2P/1073.html},
  pmid = {18550805}
}

@article{chereji2018,
  title = {Major {{Determinants}} of {{Nucleosome Positioning}}},
  issn = {0006-3495},
  abstract = {The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair. Here, we review our current understanding of the major determinants of nucleosome positioning: DNA sequence, nonhistone DNA-binding proteins, chromatin-remodeling enzymes, and transcription. We outline the major challenges for the future: elucidating the precise mechanisms of chromatin opening and promoter activation, identifying the complexes that occupy promoters, and understanding the multiscale problem of chromatin fiber organization.},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2018.03.015},
  author = {Chereji, R{\u a}zvan V. and Clark, David J.},
  month = apr,
  year = {2018},
  file = {/home/bbeltr1/Documents/paper-collection/ClarkD/Chereji_Clark_2018_Major Determinants of Nucleosome Positioning.pdf;/home/bbeltr1/Documents/zotero/storage/4YWYPYZ7/S0006349518303813.html}
}

@article{partensky2009,
  title = {Chromatin {{Remodelers Act Globally}}, {{Sequence Positions Nucleosomes Locally}}},
  volume = {391},
  issn = {0022-2836},
  abstract = {The precise placement of nucleosomes has large regulatory effects on gene expression. Recent work suggests that nucleosome placement is regulated in part by the affinity of the underlying DNA sequence for the histone octamer. Nucleosome locations are also regulated by several different ATP-dependent chromatin remodeling enzymes. This raises the question of whether DNA sequence influences the activity of chromatin remodeling enzymes. DNA sequence could most simply regulate nucleosome remodeling through its effect on nucleosome stability. In such a model, unstable nucleosomes would be remodeled faster than stable nucleosomes. It is also possible that certain DNA elements could regulate remodeling by inhibiting the interaction of nucleosomes with the remodeling enzyme. A third possibility is that DNA sequence could regulate the outcome of remodeling by influencing how reaction intermediates collapse into a particular set of stable nucleosomal positions. Here we dissect the contribution from these potential mechanisms to the activities of yeast RSC and human ACF, which are representative members of two major classes of remodeling complexes. We find that varying the histone\textendash{}DNA affinity over 3 orders of magnitude has negligible effects on the rates of nucleosome remodeling and ATP hydrolysis by these two enzymes. This suggests that the rate-limiting step for nucleosome remodeling may not involve the disruption of histone\textendash{}DNA contacts. We further find that a specific curved DNA element previously hypothesized to inhibit ACF activity does not inhibit substrate binding or remodeling by ACF. The element, however, does influence the distribution of nucleosome positions generated by ACF. Our data support a model in which remodeling enzymes move nucleosomes to new locations by a general sequence-independent mechanism. However, consequent to the rate-limiting remodeling step, the local DNA sequence promotes a collapse of remodeling intermediates into highly resolved positions that are dictated by thermodynamic differences between adjacent positions.},
  number = {1},
  journal = {Journal of Molecular Biology},
  doi = {10.1016/j.jmb.2009.04.085},
  author = {Partensky, Peretz D. and Narlikar, Geeta J.},
  month = aug,
  year = {2009},
  keywords = {chromatin remodeling,histone–DNA affinity,human ACF,nucleosome positioning,RSC},
  pages = {12-25},
  file = {/home/bbeltr1/Documents/paper-collection/NarlikarG/Partensky_Narlikar_2009_Chromatin Remodelers Act Globally, Sequence Positions Nucleosomes Locally.pdf;/home/bbeltr1/Documents/zotero/storage/IGXVZNLB/S002228360900552X.html}
}

@article{chereji2018a,
  title = {Precise Genome-Wide Mapping of Single Nucleosomes and Linkers in Vivo},
  volume = {19},
  issn = {1474-760X},
  abstract = {We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A.Z in defining the chromatin landscape. We present a biophysical model that neglects DNA sequence and shows that steric occlusion suffices to explain the salient features of nucleosome positioning.},
  journal = {Genome Biology},
  doi = {10.1186/s13059-018-1398-0},
  author = {Chereji, R{\u a}zvan V. and Ramachandran, Srinivas and Bryson, Terri D. and Henikoff, Steven},
  month = feb,
  year = {2018},
  keywords = {Biophysical modeling,Chemical cleavage mapping,Linker quantization},
  pages = {19},
  file = {/home/bbeltr1/Documents/paper-collection/HenikoffS/Chereji et al_2018_Precise genome-wide mapping of single nucleosomes and linkers in vivo.pdf;/home/bbeltr1/Documents/zotero/storage/AWSIZQ8H/s13059-018-1398-0.html}
}

@article{clapier2009,
  title = {The {{Biology}} of {{Chromatin Remodeling Complexes}}},
  volume = {78},
  abstract = {The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements. However, this constraint also allows nucleosomes and other chromatin components to actively participate in the regulation of transcription, chromosome segregation, DNA replication, and DNA repair. To enable dynamic access to packaged DNA and to tailor nucleosome composition in chromosomal regions, cells have evolved a set of specialized chromatin remodeling complexes (remodelers). Remodelers use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes. Here, we address many aspects of remodeler biology: their targeting, mechanism, regulation, shared and unique properties, and specialization for particular biological processes. We also address roles for remodelers in development, cancer, and human syndromes.},
  number = {1},
  journal = {Annual Review of Biochemistry},
  doi = {10.1146/annurev.biochem.77.062706.153223},
  author = {Clapier, Cedric R. and Cairns, Bradley R.},
  year = {2009},
  pages = {273-304},
  file = {/home/bbeltr1/Documents/paper-collection/CairnsB/Clapier_Cairns_2009_The Biology of Chromatin Remodeling Complexes.pdf},
  pmid = {19355820}
}

@article{pisano2007,
  title = {Telomeric {{Nucleosomes Are Intrinsically Mobile}}},
  volume = {369},
  issn = {0022-2836},
  abstract = {Nucleosomes are no longer considered only static basic units that package eukaryotic DNA but they emerge as dynamic players in all chromosomal processes. Regulatory proteins can gain access to recognition sequences hidden by the histone octamer through the action of ATP-dependent chromatin remodeling complexes that cause nucleosome sliding. In addition, it is known that nucleosomes are able to spontaneously reposition along the DNA due to intrinsic dynamic properties, but it is not clear yet to what extent sequence-dependent dynamic properties contribute to nucleosome repositioning. Here, we study mobility of nucleosomes formed on telomeric sequences as a function of temperature and ionic strength. We find that telomeric nucleosomes are highly intrinsically mobile under physiological conditions, whereas nucleosomes formed on an average DNA sequence mostly remain in the initial position. This indicates that DNA sequence affects not only the thermodynamic stability and the positioning of nucleosomes but also their dynamic properties. Moreover, our findings suggest that the high mobility of telomeric nucleosomes may be relevant to the dynamics of telomeric chromatin.},
  number = {5},
  journal = {Journal of Molecular Biology},
  doi = {10.1016/j.jmb.2007.04.027},
  author = {Pisano, Sabrina and Marchioni, Enrico and Galati, Alessandra and Mechelli, Rosella and Savino, Maria and Cacchione, Stefano},
  month = jun,
  year = {2007},
  keywords = {chromatin,telomeres,nucleosome,nucleosome mobility,telomeric chromatin},
  pages = {1153-1162},
  file = {/home/bbeltr1/Documents/paper-collection/CacchioneS/Pisano et al_2007_Telomeric Nucleosomes Are Intrinsically Mobile.pdf;/home/bbeltr1/Documents/zotero/storage/IH7S83FT/S0022283607004986.html}
}

@article{deindl2013,
  title = {{{ISWI Remodelers Slide Nucleosomes}} with {{Coordinated Multi}}-{{Base}}-{{Pair Entry Steps}} and {{Single}}-{{Base}}-{{Pair Exit Steps}}},
  volume = {152},
  issn = {0092-8674, 1097-4172},
  abstract = {ISWI-family enzymes remodel chromatin by sliding nucleosomes along DNA, but the nucleosome translocation mechanism remains unclear. Here we use~single-molecule FRET to probe nucleosome translocation by ISWI-family remodelers. Distinct ISWI-family members translocate nucleosomes with a similar stepping pattern maintained by the catalytic subunit of the enzyme. Nucleosome remodeling begins with a 7~bp step of DNA translocation followed by 3~bp subsequent steps toward the exit side of nucleosomes. These multi-bp, compound steps are comprised of 1~bp substeps. DNA movement on the entry side of the nucleosome occurs only after 7~bp of exit-side translocation, and each entry-side step draws in a 3~bp equivalent of DNA that allows three additional base pairs to be moved to the exit side. Our results suggest a remodeling mechanism with well-defined coordination at different nucleosomal sites featuring DNA translocation toward the exit side in 1~bp steps preceding multi-bp steps of DNA movement on the entry side.},
  language = {English},
  number = {3},
  journal = {Cell},
  doi = {10.1016/j.cell.2012.12.040},
  author = {Deindl, Sebastian and Hwang, William L. and Hota, Swetansu K. and Blosser, Timothy R. and Prasad, Punit and Bartholomew, Blaine and Zhuang, Xiaowei},
  month = jan,
  year = {2013},
  pages = {442-452},
  file = {/home/bbeltr1/Documents/paper-collection/ZhuangX/Deindl et al_2013_ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps.pdf;/home/bbeltr1/Documents/zotero/storage/UX2DHU5F/S0092-8674(13)00007-X.html},
  pmid = {23374341}
}

@phdthesis{spakowitz2005,
  type = {{{PhD Thesis}}},
  title = {Semiflexible Polymers: Fundamental Theory and Applications in {{DNA}} Packaging},
  shorttitle = {Semiflexible Polymers},
  school = {California Institute of Technology},
  author = {Spakowitz, Andrew James},
  year = {2005},
  file = {/home/bbeltr1/Documents/paper-collection/SpakowitzA/Spakowitz_2005_Semiflexible polymers.pdf}
}

@article{lepage2017,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1708.02194},
  primaryClass = {physics, q-bio},
  title = {Modeling {{Bacterial DNA}}: {{Simulation}} of {{Self}}-Avoiding {{Supercoiled Worm}}-{{Like Chains Including Structural Transitions}} of the {{Helix}}},
  shorttitle = {Modeling {{Bacterial DNA}}},
  abstract = {Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.},
  journal = {arXiv:1708.02194 [physics, q-bio]},
  author = {Lepage, Thibaut and Junier, Ivan},
  month = aug,
  year = {2017},
  keywords = {Physics - Biological Physics,Quantitative Biology - Biomolecules},
  file = {/home/bbeltr1/Documents/paper-collection/JunierI/Lepage_Junier_2017_Modeling Bacterial DNA.pdf;/home/bbeltr1/Documents/zotero/storage/XSW7ENJR/1708.html}
}

@article{lepage2015,
  title = {Thermodynamics of {{Long Supercoiled Molecules}}: {{Insights}} from {{Highly Efficient Monte Carlo Simulations}}},
  volume = {109},
  issn = {00063495},
  shorttitle = {Thermodynamics of {{Long Supercoiled Molecules}}},
  language = {en},
  number = {1},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2015.06.005},
  author = {Lepage, Thibaut and K\'ep\`es, Fran{\c c}ois and Junier, Ivan},
  month = jul,
  year = {2015},
  pages = {135-143},
  file = {/home/bbeltr1/Documents/paper-collection/JunierI/Lepage et al_2015_Thermodynamics of Long Supercoiled Molecules.pdf}
}

@article{arnold2007,
  title = {Unexpected Relaxation Dynamics of a Self-Avoiding Polymer in Cylindrical Confinement},
  volume = {127},
  issn = {0021-9606},
  abstract = {We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation time of the chain, {$\tau\tau{}<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00001.gif"{$><$}mi{$>\tau{}<$}/mi{$><$}/math{$>$}, with the chain length NN{$<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00002.gif"{$><$}mi{$>$}N{$<$}/mi{$><$}/math{$>$} and pore diameter DD{$<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00003.gif"{$><$}mi{$>$}D{$<$}/mi{$><$}/math{$>$}. An earlier scaling analysis based on the de Gennes blob picture led to {$\tau\sim$}N2D1{$\slash$}3{$\tau\sim$}N2D1{$\slash$}3{$<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00004.gif"{$><$}mrow{$><$}mi{$>\tau{}<$}/mi{$><$}mo{$>\sim{}<$}/mo{$><$}msup{$><$}mi{$>$}N{$<$}/mi{$><$}mn{$>$}2{$<$}/mn{$><$}/msup{$><$}msup{$><$}mi{$>$}D{$<$}/mi{$><$}mrow{$><$}mn{$>$}1{$<$}/mn{$><$}mo{$>\slash{}<$}/mo{$><$}mn{$>$}3{$<$}/mn{$><$}/mrow{$><$}/msup{$><$}/mrow{$><$}/math{$>$}. Our numerical effort that combines molecular dynamics and Monte Carlo simulations, however, consistently produces different {$\tau\tau{}<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00005.gif"{$><$}mi{$>\tau{}<$}/mi{$><$}/math{$>$} results for NN{$<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00006.gif"{$><$}mi{$>$}N{$<$}/mi{$><$}/math{$>$} up to 2000. We argue that the previous scaling prediction is only asymptotically valid in the limit N{$\NestedGreaterGreater$}D5{$\slash$}3{$\NestedGreaterGreater$}1N{$\NestedGreaterGreater$}D5{$\slash$}3{$\NestedGreaterGreater$}1{$<$}math baseline="-0.5" display="inline" overflow="scroll" altimg="eq-00007.gif"{$><$}mrow{$><$}mi{$>$}N{$<$}/mi{$><$}mo{$>\NestedGreaterGreater{}<$}/mo{$><$}msup{$><$}mi{$>$}D{$<$}/mi{$><$}mrow{$><$}mn{$>$}5{$<$}/mn{$><$}mo{$>\slash{}<$}/mo{$><$}mn{$>$}3{$<$}/mn{$><$}/mrow{$><$}/msup{$><$}mo{$>\NestedGreaterGreater{}<$}/mo{$><$}mn{$>$}1{$<$}/mn{$><$}/mrow{$><$}/math{$>$}, which is currently inaccessible to computer simulations and, more interestingly, is also difficult to reach in experiments. Our results are thus relevant for the interpretation of recent experiments with DNA in nano- and microchannels.},
  number = {16},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.2799513},
  author = {Arnold, Axel and Bozorgui, Behnaz and Frenkel, Daan and Ha, Bae-Yeun and Jun, Suckjoon},
  month = oct,
  year = {2007},
  pages = {164903},
  file = {/home/bbeltr1/Documents/paper-collection/JunS/Arnold et al_2007_Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical.pdf;/home/bbeltr1/Documents/zotero/storage/AIK8HCMM/1.html}
}

@article{cacciuto2006,
  title = {Self-{{Avoiding Flexible Polymers}} under {{Spherical Confinement}}},
  volume = {6},
  issn = {1530-6984, 1530-6992},
  language = {en},
  number = {5},
  journal = {Nano Letters},
  doi = {10.1021/nl052351n},
  author = {Cacciuto, Angelo and Luijten, Erik},
  month = may,
  year = {2006},
  pages = {901-905},
  file = {/home/bbeltr1/Documents/paper-collection/LuijtenE/Cacciuto_Luijten_2006_Self-Avoiding Flexible Polymers under Spherical Confinement.pdf}
}

@article{flemming1878,
  title = {Zur {{Kenntniss}} Der {{Zelle}} Und Ihrer {{Theilungs}}-{{Erscheinungen}}},
  volume = {3},
  journal = {Schriften des Naturwissenschaftlichen Vereins f\"ur Schleswig-Holstein},
  author = {Flemming, Walther},
  year = {1878},
  pages = {23--27},
  file = {/home/bbeltr1/Documents/paper-collection/FlemmingW/Flemming_1878_Zur Kenntniss der Zelle und ihrer Theilungs-Erscheinungen.pdf}
}

@article{widom1992,
  title = {A Relationship between the Helical Twist of {{DNA}} and the Ordered Positioning of Nucleosomes in All Eukaryotic Cells.},
  volume = {89},
  issn = {0027-8424, 1091-6490},
  abstract = {A large number of measurements of nucleosome repeat lengths are analyzed and are found to exhibit preferential quantization to a set of values related by integral multiples of the helical twist of DNA. This implies that the nucleosomal DNA content is preferentially quantized, which in turn implies that linker DNA lengths are preferentially quantized. This study confirms and extends previous observations in the literature that had suggested, but not firmly established, that linker lengths might be quantized. The quantization of repeat lengths applies even for very long repeat lengths. This suggests a model for the origin of the quantization, in which the quantization arises from the requirements of higher-order chromatin structure.},
  language = {en},
  number = {3},
  journal = {PNAS},
  doi = {10.1073/pnas.89.3.1095},
  author = {Widom, J.},
  month = feb,
  year = {1992},
  pages = {1095-1099},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Widom_1992_A relationship between the helical twist of DNA and the ordered positioning of.pdf;/home/bbeltr1/Documents/zotero/storage/ZTKTPU3R/1095.html},
  pmid = {1736292}
}

@article{locke2010,
  title = {High-Throughput Sequencing Reveals a Simple Model of Nucleosome Energetics},
  volume = {107},
  issn = {0027-8424, 1091-6490},
  abstract = {We use genome-wide nucleosome maps to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a minor role. Furthermore, similar sequence signatures are exhibited by control experiments in which nucleosome-free genomic DNA is either sonicated or digested with micrococcal nuclease, making it possible that current predictions based on high-throughput nucleosome-positioning maps are biased by experimental artifacts.},
  language = {en},
  number = {49},
  journal = {PNAS},
  doi = {10.1073/pnas.1003838107},
  author = {Locke, George and Tolkunov, Denis and Moqtaderi, Zarmik and Struhl, Kevin and Morozov, Alexandre V.},
  month = dec,
  year = {2010},
  keywords = {chromatin structure,nucleosome positioning,biophysical models,histone-DNA interactions},
  pages = {20998-21003},
  file = {/home/bbeltr1/Documents/paper-collection/Morozov, Alexandre V./Locke et al_2010_High-throughput sequencing reveals a simple model of nucleosome energetics.pdf;/home/bbeltr1/Documents/paper-collection/MorozovA/Locke et al_2010_High-throughput sequencing reveals a simple model of nucleosome energetics.pdf;/home/bbeltr1/Documents/zotero/storage/AC2YU3G9/20998.html},
  pmid = {21084631}
}

@article{percus1976,
  title = {Equilibrium State of a Classical Fluid of Hard Rods in an External Field},
  volume = {15},
  issn = {0022-4715, 1572-9613},
  abstract = {The external field required to produce a given density pattern is obtained explicitly for a classical fluid of hard rods. All direct correlation functions are shown to be of finite range in all pairs of variables. The one-sided factors of the pair direct correlation are also found to be of finite range.},
  language = {en},
  number = {6},
  journal = {J Stat Phys},
  doi = {10.1007/BF01020803},
  author = {Percus, J. K.},
  month = dec,
  year = {1976},
  pages = {505-511},
  file = {/home/bbeltr1/Documents/paper-collection/PercusJ/Percus_1976_Equilibrium state of a classical fluid of hard rods in an external field.pdf;/home/bbeltr1/Documents/zotero/storage/ZAYQEXZZ/BF01020803.html}
}

@article{bintu2016,
  title = {Dynamics of Epigenetic Regulation at the Single-Cell Level},
  volume = {351},
  copyright = {Copyright \textcopyright{} 2016, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Quantitative analysis of epigenetic memory
To explore quantitative and dynamic properties of transcriptional regulation by epigenetic modifications, Bintu et al. monitored a transcriptional reporter gene carried on a human artificial chromosome in Chinese hamster ovary cells (see the Perspective by Keung and Khalil). They measured effects of DNA methylation and histone modifications by methylation or deacetylation in single cells using time-lapse microscopy. Silencing was an all-or-none, stochastic event, so graded adjustments to transcription occurred from changes in the proportion of cells that responded. Furthermore, the duration of recruitment of the chromatin regulators determined the fraction of cells that were silenced. Thus, distinct modifiers can produce different characteristics of epigenetic memory.
Science, this issue p. 720; see also p. 661
Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory.
Quantitative, single-cell measurements reveal characteristics of epigenetic control of transcription. [Also see Perspective by Keung and Khalil]
Quantitative, single-cell measurements reveal characteristics of epigenetic control of transcription. [Also see Perspective by Keung and Khalil]},
  language = {en},
  number = {6274},
  journal = {Science},
  doi = {10.1126/science.aab2956},
  author = {Bintu, Lacramioara and Yong, John and Antebi, Yaron E. and McCue, Kayla and Kazuki, Yasuhiro and Uno, Narumi and Oshimura, Mitsuo and Elowitz, Michael B.},
  month = feb,
  year = {2016},
  pages = {720-724},
  file = {/home/bbeltr1/Documents/paper-collection/ElowitzM/Bintu et al_2016_Dynamics of epigenetic regulation at the single-cell level.pdf;/home/bbeltr1/Documents/zotero/storage/GFWE9W4X/720.html},
  pmid = {26912859}
}

@article{boettiger2016,
  title = {Super-Resolution Imaging Reveals Distinct Chromatin Folding for Different Epigenetic States},
  volume = {529},
  copyright = {2016 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories1,2,3,4,5. At the intermediate scale of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms2,3,4,6,7,8, but understanding this organization remains a challenge. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression9,10,11. Here we investigate the 3D organization of chromatin in different epigenetic states using super-resolution imaging. We classified genomic domains in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and observed distinct chromatin organizations for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins play an important role in these unique packaging properties of the repressed chromatin. Taken together, our super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly relevant to genome regulation.},
  language = {en},
  number = {7586},
  journal = {Nature},
  doi = {10.1038/nature16496},
  author = {Boettiger, Alistair N. and Bintu, Bogdan and Moffitt, Jeffrey R. and Wang, Siyuan and Beliveau, Brian J. and Fudenberg, Geoffrey and Imakaev, Maxim and Mirny, Leonid A. and Wu, Chao-ting and Zhuang, Xiaowei},
  month = jan,
  year = {2016},
  keywords = {chromatin,radius-of-gyration,sequential dna-fish},
  pages = {418-422},
  file = {/home/bbeltr1/Documents/paper-collection/Zhuang, Xiaowei/Boettiger et al_2016_Super-resolution imaging reveals distinct chromatin folding for different.pdf;/home/bbeltr1/Documents/paper-collection/ZhuangX/Boettiger et al_2016_Super-resolution imaging reveals distinct chromatin folding for different.pdf;/home/bbeltr1/Documents/zotero/storage/GUJ8FIEW/nature16496.html}
}

@article{risca2017,
  title = {Variable Chromatin Structure Revealed by {\emph{in Situ}} Spatially Correlated {{DNA}} Cleavage Mapping},
  volume = {541},
  copyright = {2016 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Chromatin structure at the length scale encompassing local nucleosome\textendash{}nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA1,2,3. However, this secondary structure of chromatin remains poorly understood compared with the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions4. Here we report the first genome-wide map of chromatin conformation in human cells at the 1\textendash{}3 nucleosome (50\textendash{}500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq) to identify DNA\textendash{}DNA contacts that are spatially proximal. Unbiased analysis of RICC-seq signal reveals regional enrichment of DNA fragments characteristic of alternating rather than adjacent nucleosome interactions in tri-nucleosome units, particularly in H3K9me3-marked heterochromatin. We infer differences in the likelihood of nucleosome\textendash{}nucleosome contacts among open chromatin, H3K27me3-marked, and H3K9me3-marked repressed chromatin regions. After calibrating RICC-seq signal to three-dimensional distances, we show that compact two-start helical fibre structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked chromatin, while non-compact structures and solenoid structures are consistent with open chromatin. Our data support a model of chromatin architecture in intact interphase nuclei consistent with variable longitudinal compaction of two-start helical fibres.},
  language = {en},
  number = {7636},
  journal = {Nature},
  doi = {10.1038/nature20781},
  author = {Risca, Viviana I. and Denny, Sarah K. and Straight, Aaron F. and Greenleaf, William J.},
  month = jan,
  year = {2017},
  pages = {237-241},
  file = {/home/bbeltr1/Documents/paper-collection/GreenleafW/Risca et al_2017_Variable chromatin structure revealed by iin situ-i spatially correlated.pdf;/home/bbeltr1/Documents/zotero/storage/W36WLDPD/nature20781.html}
}

@article{struhl2013,
  title = {Determinants of Nucleosome Positioning},
  volume = {20},
  copyright = {2013 Nature Publishing Group},
  issn = {1545-9985},
  abstract = {Nucleosome positioning is critical for gene expression and most DNA-related processes. Here we review the dominant patterns of nucleosome positioning that have been observed and summarize the current understanding of their underlying determinants. The genome-wide pattern of nucleosome positioning is determined by the combination of DNA sequence, ATP-dependent nucleosome remodeling enzymes and transcription factors that include activators, components of the preinitiation complex and elongating RNA polymerase II. These determinants influence each other such that the resulting nucleosome positioning patterns are likely to differ among genes and among cells in a population, with consequent effects on gene expression.},
  language = {en},
  number = {3},
  journal = {Nature Structural \& Molecular Biology},
  doi = {10.1038/nsmb.2506},
  author = {Struhl, Kevin and Segal, Eran},
  month = mar,
  year = {2013},
  pages = {267-273},
  file = {/home/bbeltr1/Documents/paper-collection/SegalE/Struhl_Segal_2013_Determinants of nucleosome positioning.pdf;/home/bbeltr1/Documents/zotero/storage/BFP5NZJZ/nsmb.html}
}

@article{teif2016,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {1508.06916},
  title = {Nucleosome Positioning: Resources and Tools Online},
  volume = {17},
  issn = {1467-5463, 1477-4054},
  shorttitle = {Nucleosome Positioning},
  abstract = {Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.},
  number = {5},
  journal = {Briefings in Bioinformatics},
  doi = {10.1093/bib/bbv086},
  author = {Teif, Vladimir B.},
  month = sep,
  year = {2016},
  keywords = {Physics - Biological Physics,Quantitative Biology - Biomolecules,Quantitative Biology - Genomics,Statistics - Machine Learning,QUALSTAR,REVIEWSTAR},
  pages = {745-757},
  file = {/home/bbeltr1/Documents/paper-collection/TeifV/Teif_2016_Nucleosome positioning.pdf;/home/bbeltr1/Documents/zotero/storage/RZXQ9GJV/1508.html}
}

@article{schopflin2013,
  title = {Modeling Nucleosome Position Distributions from Experimental Nucleosome Positioning Maps},
  volume = {29},
  issn = {1367-4803},
  abstract = {Abstract.  Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occup},
  language = {en},
  number = {19},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btt404},
  author = {Sch\"opflin, Robert and Teif, Vladimir B. and M\"uller, Oliver and Weinberg, Christin and Rippe, Karsten and Wedemann, Gero},
  month = oct,
  year = {2013},
  pages = {2380-2386},
  file = {/home/bbeltr1/Documents/paper-collection/WedemannG/Schöpflin et al_2013_Modeling nucleosome position distributions from experimental nucleosome.pdf;/home/bbeltr1/Documents/zotero/storage/XH5XCMCM/186820.html}
}

@article{tims2011,
  title = {Dynamics of {{Nucleosome Invasion}} by {{DNA Binding Proteins}}},
  volume = {411},
  issn = {0022-2836},
  abstract = {Nucleosomes sterically occlude their wrapped DNA from interacting with many large protein complexes. How proteins gain access to nucleosomal DNA target sites in vivo is not known. Outer stretches of nucleosomal DNA spontaneously unwrap and rewrap with high frequency, providing rapid and efficient access to regulatory DNA target sites located there; however, rates for access to the nucleosome interior have not been measured. Here we show that for a selected high-affinity nucleosome positioning sequence, the spontaneous DNA unwrapping rate decreases dramatically with distance inside the nucleosome. The rewrapping rate also decreases, but only slightly. Our results explain the previously known strong position dependence on the equilibrium accessibility of nucleosomal DNA, which is characteristic of both selected and natural sequences. Our results point to slow nucleosome conformational fluctuations as a potential source of cell\textendash{}cell variability in gene activation dynamics, and they reveal the dominant kinetic path by which multiple DNA binding proteins cooperatively invade a nucleosome.},
  number = {2},
  journal = {Journal of Molecular Biology},
  doi = {10.1016/j.jmb.2011.05.044},
  author = {Tims, Hannah S. and Gurunathan, Kaushik and Levitus, Marcia and Widom, Jonathan},
  month = aug,
  year = {2011},
  keywords = {chromatin,gene regulation,fluorescence correlation spectroscopy,fluorescence resonance energy transfer,transcription factor},
  pages = {430-448},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Tims et al_2011_Dynamics of Nucleosome Invasion by DNA Binding Proteins.pdf;/home/bbeltr1/Documents/zotero/storage/YTID57IF/S0022283611006073.html}
}

@article{rufiange2007,
  title = {Genome-{{Wide Replication}}-{{Independent Histone H3 Exchange Occurs Predominantly}} at {{Promoters}} and {{Implicates H3 K56 Acetylation}} and {{Asf1}}},
  volume = {27},
  issn = {1097-2765},
  abstract = {Summary
In yeast, histone H3/H4 exchange independent of replication is poorly understood. Here, we analyzed the deposition of histone H3 molecules, synthesized during G1, using a high-density microarray histone exchange assay. While we found that H3 exchange in coding regions requires high levels of transcription, promoters exchange H3 molecules in the absence of transcription. In inactive promoters, H3 is deposited predominantly in well-positioned nucleosomes surrounding nucleosome-free regions, indicating that some nucleosomes in promoters are dynamic. This could facilitate induction of repressed genes. Importantly, we show that histone H3 K56 acetylation, a replication-associated mark, is also present in replication-independent newly assembled nucleosomes and correlates perfectly with the deposition of new H3. Finally, we found that transcription-dependent incorporation of H3 at promoters is highly dependent on Asf1. Taken together, our data underline the dynamic nature of replication-independent nucleosome assembly/disassembly, specify a link to transcription, and implicate Asf1 and H3 K56 acetylation.},
  number = {3},
  journal = {Molecular Cell},
  doi = {10.1016/j.molcel.2007.07.011},
  author = {Rufiange, Anne and Jacques, Pierre-\'Etienne and Bhat, Wajid and Robert, Fran{\c c}ois and Nourani, Amine},
  month = aug,
  year = {2007},
  keywords = {DNA},
  pages = {393-405},
  file = {/home/bbeltr1/Documents/paper-collection/NouraniA/Rufiange et al_2007_Genome-Wide Replication-Independent Histone H3 Exchange Occurs Predominantly at.pdf;/home/bbeltr1/Documents/zotero/storage/U4RVWY6R/S1097276507004844.html}
}

@article{dion2007,
  title = {Dynamics of {{Replication}}-{{Independent Histone Turnover}} in {{Budding Yeast}}},
  volume = {315},
  copyright = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Chromatin plays roles in processes governed by different time scales. To assay the dynamic behavior of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested Saccharomyces cerevisiae at single-nucleosome resolution over 4\% of the genome, and at lower ({$\sim$}265 base pair) resolution over the entire genome. We find that nucleosomes at promoters are replaced more rapidly than at coding regions and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states.
Regions of chromatin that are epigenetically silenced and highly regulated are coated with histones that rapidly bind and release the DNA.
Regions of chromatin that are epigenetically silenced and highly regulated are coated with histones that rapidly bind and release the DNA.},
  language = {en},
  number = {5817},
  journal = {Science},
  doi = {10.1126/science.1134053},
  author = {Dion, Michael F. and Kaplan, Tommy and Kim, Minkyu and Buratowski, Stephen and Friedman, Nir and Rando, Oliver J.},
  month = mar,
  year = {2007},
  pages = {1405-1408},
  file = {/home/bbeltr1/Documents/paper-collection/RandoO/Dion et al_2007_Dynamics of Replication-Independent Histone Turnover in Budding Yeast.pdf;/home/bbeltr1/Documents/zotero/storage/ZCJ499LG/1405.html},
  pmid = {17347438}
}

@article{kulic2003,
  title = {Chromatin {{Dynamics}}: {{Nucleosomes}} Go {{Mobile}} through {{Twist Defects}}},
  volume = {91},
  issn = {0031-9007, 1079-7114},
  shorttitle = {Chromatin {{Dynamics}}},
  language = {en},
  number = {14},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.91.148103},
  author = {Kuli\'c, I. M. and Schiessel, H.},
  month = oct,
  year = {2003},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Kulić_Schiessel_2003_Chromatin Dynamics.pdf}
}

@article{zuiddam2017,
  title = {Physics behind the Mechanical Nucleosome Positioning Code},
  volume = {96},
  issn = {2470-0045, 2470-0053},
  language = {en},
  number = {5},
  journal = {Physical Review E},
  doi = {10.1103/PhysRevE.96.052412},
  author = {Zuiddam, Martijn and Everaers, Ralf and Schiessel, Helmut},
  month = nov,
  year = {2017},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Zuiddam et al_2017_Physics behind the mechanical nucleosome positioning code.pdf}
}

@article{rosanio2015,
  title = {In Vitro Selection of {{DNAs}} with an Increased Propensity to Form Small Circles},
  volume = {103},
  copyright = {\textcopyright{} 2015 Wiley Periodicals, Inc.},
  issn = {1097-0282},
  abstract = {A protocol was devised to select for DNA molecules that efficiently form circles from a library of 126 base pair DNAs containing 90 randomized base pairs. After six rounds of selection, individual molecules from the library showed 20- to 100-fold greater j-factors compared with the starting library, validating the selection protocol. High-throughput sequencing revealed a sinusoidal pattern of enrichment and de-enrichment of A/T dinucleotides in the random region with a 10.4 base pair period associated with the helicity of DNA. A similar, but more moderate pattern of C/G dinucleotides was offset by precisely half a helical turn. While C/G dinucleotide enrichments were evenly distributed, A/T dinucleotide enrichments displayed a preference to cluster in individual DNA molecules. The most highly enriched 10 base pair sequences in the random region contained adjacent blocks of A/T and C/G trinucleotides present in some, but not all, rapidly cyclizing molecules. The phased dinucleotide enrichments closely match those present in accurately mapped yeast nucleosomes, confirming the importance of DNA bending in nucleosome formation. However, at certain sites the nucleosomal DNAs show dinucleotide enrichments that differ substantially from the cyclization data. These discrepancies can often be correlated with sequence specific contacts that form between histones and DNA. \textcopyright{} 2015 Wiley Periodicals, Inc. Biopolymers 103: 303\textendash{}320, 2015.},
  language = {en},
  number = {6},
  journal = {Biopolymers},
  doi = {10.1002/bip.22608},
  author = {Rosanio, Gabriel and Widom, Jonathan and Uhlenbeck, Olke C.},
  year = {2015},
  keywords = {bending,cyclization,flexibility,SELEX,sequence-dependent},
  pages = {303-320},
  file = {/home/bbeltr1/Documents/paper-collection/UhlenbeckO/Rosanio et al_2015_In vitro selection of DNAs with an increased propensity to form small circles.pdf;/home/bbeltr1/Documents/zotero/storage/V5I8B32U/bip.html}
}

@article{wondergem2017,
  title = {Performing {{SELEX}} Experiments in Silico},
  volume = {147},
  issn = {0021-9606},
  abstract = {Due to the sequence-dependent nature of the elasticity of DNA, many protein-DNA complexes and other systems in which DNA molecules must be deformed have preferences for the type of DNA sequence they interact with. SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments and similar sequence selection experiments have been used extensively to examine the (indirect readout) sequence preferences of, e.g., nucleosomes (protein spools around which DNA is wound for compactification) and DNA rings. We show how recently developed computational and theoretical tools can be used to emulate such experiments in silico. Opening up this possibility comes with several benefits. First, it allows us a better understanding of our models and systems, specifically about the roles played by the simulation temperature and the selection pressure on the sequences. Second, it allows us to compare the predictions made by the model of choice with experimental results. We find agreement on important features between predictions of the rigid base-pair model and experimental results for DNA rings and interesting differences that point out open questions in the field. Finally, our simulations allow application of the SELEX methodology to systems that are experimentally difficult to realize because they come with high energetic costs and are therefore unlikely to form spontaneously, such as very short or overwound DNA rings.},
  number = {17},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.5001394},
  author = {Wondergem, J. a. J. and Schiessel, H. and Tompitak, M.},
  month = nov,
  year = {2017},
  pages = {174101},
  file = {/home/bbeltr1/Documents/paper-collection/TompitakM/Wondergem et al_2017_Performing SELEX experiments in silico.pdf;/home/bbeltr1/Documents/zotero/storage/IV4GHHIG/1.html}
}

@misc{cai2012,
  address = {Stanford University},
  title = {Mechanical {{Engineering 346A}}},
  author = {Cai, Wei},
  year = {2012},
  file = {/home/bbeltr1/Documents/paper-collection/CaiW/Cai_2012_Mechanical Engineering 346A.pdf}
}

@article{valle2005,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {cond-mat/0503577},
  title = {Scaling Exponents and

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib