text:
1/Documents/paper-collection/VoituriezR/Guérin et al_2013_Reactive conformations and non-Markovian cyclization kinetics of a Rouse polymer.pdf}
}

@article{mchale2010a,
  archivePrefix = {arXiv},
  eprinttype = {arxiv},
  eprint = {0908.1177},
  title = {Intramolecular Fluorescence Correlation Spectroscopy in a Feedback Tracking Microscope},
  volume = {99},
  issn = {00063495},
  abstract = {We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system, and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. We show that tracking provides enhanced sensitivity to translational diffusion, molecular size, heterogeneity and long time-scale decays in comparison to traditional fluorescence correlation spectroscopy. We demonstrate our approach by using a three-dimensional tracking microscope to study genomic \$\textbackslash{}lambda\$-phage DNA molecules with various fluorescence label configurations.},
  language = {en},
  number = {1},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2010.03.045},
  author = {McHale, Kevin and Mabuchi, Hideo},
  month = jul,
  year = {2010},
  keywords = {Physics - Biological Physics,Physics - Optics},
  pages = {313-322},
  file = {/home/bbeltr1/Documents/paper-collection/MabuchiH/McHale_Mabuchi_2010_Intramolecular fluorescence correlation spectroscopy in a feedback tracking.pdf}
}

@techreport{spakowitzb,
  title = {Revealing the {{Physical Principles Underlying Epigenetic Regulation Using Theory}}, {{Simulation}}, and {{Experiment}}},
  language = {en},
  author = {Spakowitz, Andrew J},
  pages = {15},
  file = {/home/bbeltr1/Documents/paper-collection/SpakowitzA/Spakowitz_Revealing the Physical Principles Underlying Epigenetic Regulation Using.pdf}
}

@article{wilemski1974a,
  title = {Diffusion-controlled Intrachain Reactions of Polymers. {{I Theory}}},
  volume = {60},
  issn = {0021-9606, 1089-7690},
  language = {en},
  number = {3},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.1681162},
  author = {Wilemski, Gerald and Fixman, Marshall},
  month = feb,
  year = {1974},
  pages = {866-877},
  file = {/home/bbeltr1/Documents/paper-collection/FixmanM/Wilemski_Fixman_1974_Diffusion‐controlled intrachain reactions of polymers2.pdf}
}

@article{lucas2014,
  title = {{{3D Trajectories Adopted}} by {{Coding}} and {{Regulatory DNA Elements}}: {{First}}-{{Passage Times}} for {{Genomic Interactions}}},
  volume = {158},
  issn = {00928674},
  shorttitle = {{{3D Trajectories Adopted}} by {{Coding}} and {{Regulatory DNA Elements}}},
  language = {en},
  number = {2},
  journal = {Cell},
  doi = {10.1016/j.cell.2014.05.036},
  author = {Lucas, Joseph S. and Zhang, Yaojun and Dudko, Olga K. and Murre, Cornelis},
  month = jul,
  year = {2014},
  pages = {339-352},
  file = {/home/bbeltr1/Documents/paper-collection/MurreC/Lucas et al_2014_3D Trajectories Adopted by Coding and Regulatory DNA Elements.pdf}
}

@article{pope2014,
  title = {Topologically Associating Domains Are Stable Units of Replication-Timing Regulation},
  volume = {515},
  copyright = {2014 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program1. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400\textendash{}800 kilobases (`replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements2,3,4,5,6,7. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs)4,5,8,9. Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.},
  language = {en},
  number = {7527},
  journal = {Nature},
  doi = {10.1038/nature13986},
  author = {Pope, Benjamin D. and Ryba, Tyrone and Dileep, Vishnu and Yue, Feng and Wu, Weisheng and Denas, Olgert and Vera, Daniel L. and Wang, Yanli and Hansen, R. Scott and Canfield, Theresa K. and Thurman, Robert E. and Cheng, Yong and G\"ulsoy, G\"unhan and Dennis, Jonathan H. and Snyder, Michael P. and Stamatoyannopoulos, John A. and Taylor, James and Hardison, Ross C. and Kahveci, Tamer and Ren, Bing and Gilbert, David M.},
  month = nov,
  year = {2014},
  pages = {402-405},
  file = {/home/bbeltr1/Documents/paper-collection/GilbertD/Pope et al_2014_Topologically associating domains are stable units of replication-timing.pdf}
}

@article{harmston2017,
  title = {Topologically Associating Domains Are Ancient Features That Coincide with {{Metazoan}} Clusters of Extreme Noncoding Conservation},
  volume = {8},
  copyright = {2017 The Author(s)},
  issn = {2041-1723},
  abstract = {Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture.},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-017-00524-5},
  author = {Harmston, Nathan and {Ing-Simmons}, Elizabeth and Tan, Ge and Perry, Malcolm and Merkenschlager, Matthias and Lenhard, Boris},
  month = sep,
  year = {2017},
  pages = {441},
  file = {/home/bbeltr1/Documents/paper-collection/LenhardB/Harmston et al_2017_Topologically associating domains are ancient features that coincide with.pdf;/home/bbeltr1/Documents/zotero/storage/I9P9ZGLV/s41467-017-00524-5.html}
}

@article{zhang2011a,
  title = {A {{Packing Mechanism}} for {{Nucleosome Organization Reconstituted Across}} a {{Eukaryotic Genome}}},
  volume = {332},
  copyright = {Copyright \textcopyright{} 2011, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Near the 5{${'}$} end of most eukaryotic genes, nucleosomes form highly regular arrays that begin at canonical distances from the transcriptional start site. Determinants of this and other aspects of genomic nucleosome organization have been ascribed to statistical positioning, intrinsically DNA-encoded positioning, or some aspect of transcription initiation. Here, we provide evidence for a different explanation. Biochemical reconstitution of proper nucleosome positioning, spacing, and occupancy levels was achieved across the 5{${'}$} ends of most yeast genes by adenosine triphosphate\textendash{}dependent trans-acting factors. These transcription-independent activities override DNA-intrinsic positioning and maintain uniform spacing at the 5{${'}$} ends of genes even at low nucleosome densities. Thus, an active, nonstatistical nucleosome packing mechanism creates chromatin organizing centers at the 5{${'}$} ends of genes where important regulatory elements reside.
Genome-wide nucleosome positioning is a self-organizing system amenable to in vitro reconstitution.
Genome-wide nucleosome positioning is a self-organizing system amenable to in vitro reconstitution.},
  language = {en},
  number = {6032},
  journal = {Science},
  doi = {10.1126/science.1200508},
  author = {Zhang, Zhenhai and Wippo, Christian J. and Wal, Megha and Ward, Elissa and Korber, Philipp and Pugh, B. Franklin},
  month = may,
  year = {2011},
  pages = {977-980},
  file = {/home/bbeltr1/Documents/paper-collection/PughB/Zhang et al_2011_A Packing Mechanism for Nucleosome Organization Reconstituted Across a.pdf;/home/bbeltr1/Documents/zotero/storage/E855AA7N/977.html},
  pmid = {21596991}
}

@article{collings2017,
  title = {Links between {{DNA}} Methylation and Nucleosome Occupancy in the Human Genome},
  volume = {10},
  issn = {1756-8935},
  abstract = {DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome.},
  journal = {Epigenetics \& Chromatin},
  doi = {10.1186/s13072-017-0125-5},
  author = {Collings, Clayton K. and Anderson, John N.},
  month = apr,
  year = {2017},
  keywords = {Epigenetics,Nucleosome,CpG,DNA methylation,MNase-seq,NOMe-seq},
  pages = {18},
  file = {/home/bbeltr1/Documents/paper-collection/AndersonJ/Collings_Anderson_2017_Links between DNA methylation and nucleosome occupancy in the human genome.pdf;/home/bbeltr1/Documents/zotero/storage/3IT5M475/s13072-017-0125-5.html}
}

@article{kornberg1981,
  title = {The Location of Nucleosomes in Chromatin: Specific or Statistical?},
  volume = {292},
  copyright = {1981 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {The Location of Nucleosomes in Chromatin},
  abstract = {The location of nucleosomes in chromatin: specific or statistical?},
  language = {en},
  number = {5824},
  journal = {Nature},
  doi = {10.1038/292579a0},
  author = {Kornberg, Roger},
  month = aug,
  year = {1981},
  pages = {579-580},
  file = {/home/bbeltr1/Documents/paper-collection/KornbergR/Kornberg_1981_The location of nucleosomes in chromatin.pdf;/home/bbeltr1/Documents/zotero/storage/EXSJ2FCU/292579a0.html}
}

@article{chen2014a,
  title = {Improved Nucleosome-Positioning Algorithm {{iNPS}} for Accurate Nucleosome Positioning from Sequencing Data},
  volume = {5},
  copyright = {2014 Nature Publishing Group},
  issn = {2041-1723},
  abstract = {Accurate determination of genome-wide nucleosome positioning can provide important insights into global gene regulation. Here, we describe the development of an improved nucleosome-positioning algorithm\textemdash{}iNPS\textemdash{}which achieves significantly better performance than the widely used NPS package. By determining nucleosome boundaries more precisely and merging or separating shoulder peaks based on local MNase-seq signals, iNPS can unambiguously detect 60\% more nucleosomes. The detected nucleosomes display better nucleosome `widths' and neighbouring centre\textendash{}centre distance distributions, giving rise to sharper patterns and better phasing of average nucleosome profiles and higher consistency between independent data subsets. In addition to its unique advantage in classifying nucleosomes by shape to reveal their different biological properties, iNPS also achieves higher significance and lower false positive rates than previously published methods. The application of iNPS to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process.},
  language = {en},
  journal = {Nature Communications},
  doi = {10.1038/ncomms5909},
  author = {Chen, Weizhong and Liu, Yi and Zhu, Shanshan and Green, Christopher D. and Wei, Gang and Han, Jing-Dong Jackie},
  month = sep,
  year = {2014},
  pages = {4909},
  file = {/home/bbeltr1/Documents/paper-collection/HanJ/Chen et al_2014_Improved nucleosome-positioning algorithm iNPS for accurate nucleosome.pdf;/home/bbeltr1/Documents/zotero/storage/HS56RVZR/ncomms5909.html}
}

@article{larson2018,
  title = {The {{Role}} of {{Phase Separation}} in {{Heterochromatin Formation}}, {{Function}}, and {{Regulation}}},
  volume = {57},
  issn = {0006-2960, 1520-4995},
  abstract = {In eukaryotic cells, structures called heterochromatin play critical roles in nuclear processes ranging from gene repression to chromosome segregation. Biochemical and in vivo studies over the past several decades have implied that the diverse functions of heterochromatin rely on the ability of these structures to spread across large regions of the genome, to compact the underlying DNA, and to recruit different types of activities. Recent observations have suggested that heterochromatin may possess liquid droplet-like properties. Here, we discuss how these observations provide a new perspective on the mechanisms for the assembly, regulation, and functions of heterochromatin.},
  language = {en},
  number = {17},
  journal = {Biochemistry},
  doi = {10.1021/acs.biochem.8b00401},
  author = {Larson, Adam G. and Narlikar, Geeta J.},
  month = may,
  year = {2018},
  pages = {2540-2548},
  file = {/home/bbeltr1/Documents/paper-collection/NarlikarG/Larson_Narlikar_2018_The Role of Phase Separation in Heterochromatin Formation, Function, and.pdf}
}

@misc{zotero-4108,
  title = {Gene {{Expression}} | {{Learn Science}} at {{Scitable}}},
  howpublished = {https://www.nature.com/scitable/topicpage/gene-expression-14121669},
  file = {/home/bbeltr1/Documents/zotero/storage/EP8AA6BM/gene-expression-14121669.html}
}

@article{adhikari2011,
  title = {Phase Separation in Mixtures of Flexible and Semiflexible Polymers},
  volume = {43},
  issn = {0032-3896, 1349-0540},
  language = {en},
  number = {9},
  journal = {Polymer Journal},
  doi = {10.1038/pj.2011.29},
  author = {Adhikari, Narayan P and Straube, Ekkehard},
  month = sep,
  year = {2011},
  pages = {751-756},
  file = {/home/bbeltr1/Documents/paper-collection/StraubeE/Adhikari_Straube_2011_Phase separation in mixtures of flexible and semiflexible polymers.pdf}
}

@article{bilokapic2018,
  title = {Cryo-{{EM}} of Nucleosome Core Particle Interactions in Trans},
  volume = {8},
  copyright = {2018 The Author(s)},
  issn = {2045-2322},
  abstract = {Nucleosomes, the basic unit of chromatin, are repetitively spaced along DNA and regulate genome expression and maintenance. The long linear chromatin molecule is extensively condensed to fit DNA inside the nucleus. How distant nucleosomes interact to build tertiary chromatin structure remains elusive. In this study, we used cryo-EM to structurally characterize different states of long range nucleosome core particle (NCP) interactions. Our structures show that NCP pairs can adopt multiple conformations, but, commonly, two NCPs are oriented with the histone octamers facing each other. In this conformation, the dyad of both nucleosome core particles is facing the same direction, however, the NCPs are laterally shifted and tilted. The histone octamer surface and histone tails in trans NCP pairs remain accessible to regulatory proteins. The overall conformational flexibility of the NCP pair suggests that chromatin tertiary structure is dynamic and allows access of various chromatin modifying machineries to nucleosomes.},
  language = {en},
  number = {1},
  journal = {Scientific Reports},
  doi = {10.1038/s41598-018-25429-1},
  author = {Bilokapic, Silvija and Strauss, Mike and Halic, Mario},
  month = may,
  year = {2018},
  pages = {7046},
  file = {/home/bbeltr1/Documents/paper-collection/HalicM/Bilokapic et al_2018_Cryo-EM of nucleosome core particle interactions in trans.pdf;/home/bbeltr1/Documents/zotero/storage/R2F7AHF6/s41598-018-25429-1.html}
}

@article{muller2014,
  title = {Changing {{Chromatin Fiber Conformation}} by {{Nucleosome Repositioning}}},
  volume = {107},
  issn = {00063495},
  abstract = {Chromatin conformation is dynamic and heterogeneous with respect to nucleosome positions, which can be changed by chromatin remodeling complexes in the cell. These molecular machines hydrolyze ATP to translocate or evict nucleosomes, and establish loci with regularly and more irregularly spaced nucleosomes as well as nucleosome-depleted regions. The impact of nucleosome repositioning on the three-dimensional chromatin structure is only poorly understood. Here, we address this issue by using a coarse-grained computer model of arrays of 101 nucleosomes considering several chromatin fiber models with and without linker histones, respectively. We investigated the folding of the chain in dependence of the position of the central nucleosome by changing the length of the adjacent linker DNA in basepair steps. We found in our simulations that these translocations had a strong effect on the shape and properties of chromatin fibers: i), Fiber curvature and flexibility at the center were largely increased and long-range contacts between distant nucleosomes on the chain were promoted. ii), The highest destabilization of the fiber conformation occurred for a nucleosome shifted by two basepairs from regular spacing, whereas effects of linker DNA changes of \textasciitilde{}10 bp in phase with the helical twist of DNA were minimal. iii), A fiber conformation can stabilize a regular spacing of nucleosomes inasmuch as favorable stacking interactions between nucleosomes are facilitated. This can oppose nucleosome translocations and increase the energetic costs for chromatin remodeling. Our computational modeling framework makes it possible to describe the conformational heterogeneity of chromatin in terms of nucleosome positions, and thus advances theoretical models toward a better understanding of how genome compaction and access are regulated within the cell.},
  language = {en},
  number = {9},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2014.09.026},
  author = {M\"uller, Oliver and Kepper, Nick and Sch\"opflin, Robert and Ettig, Ramona and Rippe, Karsten and Wedemann, Gero},
  month = nov,
  year = {2014},
  pages = {2141-2150},
  file = {/home/bbeltr1/Documents/paper-collection/WedemannG/Müller et al_2014_Changing Chromatin Fiber Conformation by Nucleosome Repositioning.pdf}
}

@incollection{rippe2012a,
  address = {Cambridge},
  title = {Chapter 9. {{Monte Carlo Simulations}} of {{Nucleosome Chains}} to {{Identify Factors}} That {{Control DNA Compaction}} and {{Access}}},
  volume = {2},
  isbn = {978-1-84973-462-2},
  booktitle = {{{RSC Biomolecular Sciences}}},
  publisher = {{Royal Society of Chemistry}},
  author = {Rippe, Karsten and Stehr, Rene and Wedemann, Gero},
  year = {2012},
  pages = {198-235},
  file = {/home/bbeltr1/Documents/paper-collection/WedemannG/Rippe et al_2012_Chapter 9.pdf},
  doi = {10.1039/9781849735056-00198}
}

@article{kepper2008,
  title = {Nucleosome {{Geometry}} and {{Internucleosomal Interactions Control}} the {{Chromatin Fiber Conformation}}},
  volume = {95},
  issn = {0006-3495},
  abstract = {Based on model structures with atomic resolution, a coarse-grained model for the nucleosome geometry was implemented. The dependence of the chromatin fiber conformation on the spatial orientation of nucleosomes and the path and length of the linker DNA was systematically explored by Monte Carlo simulations. Two fiber types were analyzed in detail that represent nucleosome chains without and with linker histones, respectively: two-start helices with crossed-linker DNA (CL conformation) and interdigitated one-start helices (ID conformation) with different nucleosome tilt angles. The CL conformation was derived from a tetranucleosome crystal structure that was extended into a fiber. At thermal equilibrium, the fiber shape persisted but relaxed into a structure with a somewhat lower linear mass density of 3.1{$\pm$}0.1 nucleosomes/11nm fiber. Stable ID fibers required local nucleosome tilt angles between 40\textdegree{} and 60\textdegree. For these configurations, much higher mass densities of up to 7.9{$\pm$}0.2 nucleosomes/11nm fiber were obtained. A model is proposed, in which the transition between a CL and ID fiber is mediated by relatively small changes of the local nucleosome geometry. These were found to be in very good agreement with changes induced by linker histone H1 binding as predicted from the high resolution model structures.},
  number = {8},
  journal = {Biophysical Journal},
  doi = {10.1529/biophysj.107.121079},
  author = {Kepper, Nick and Foethke, Dietrich and Stehr, Rene and Wedemann, Gero and Rippe, Karsten},
  month = oct,
  year = {2008},
  pages = {3692-3705},
  file = {/home/bbeltr1/Documents/paper-collection/RippeK/Kepper et al_2008_Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin.pdf;/home/bbeltr1/Documents/zotero/storage/UQZGMQQJ/S0006349508785126.html}
}

@article{eser2017,
  title = {Form and Function of Topologically Associating Genomic Domains in Budding Yeast},
  volume = {114},
  copyright = {\textcopyright{}  . http://www.pnas.org.stanford.idm.oclc.org/site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  abstract = {The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.},
  language = {en},
  number = {15},
  journal = {PNAS},
  doi = {10.1073/pnas.1612256114},
  author = {Eser, Umut and {Chandler-Brown}, Devon and Ay, Ferhat and Straight, Aaron F. and Duan, Zhijun and Noble, William Stafford and Skotheim, Jan M.},
  month = apr,
  year = {2017},
  keywords = {systems biology,DNA replication,cell cycle,genome organization,budding yeast},
  pages = {E3061-E3070},
  file = {/home/bbeltr1/Documents/paper-collection/SkotheimJ/Eser et al_2017_Form and function of topologically associating genomic domains in budding yeast.pdf;/home/bbeltr1/Documents/zotero/storage/NIWWF8NP/E3061.html},
  pmid = {28348222}
}

@article{werken2017,
  title = {Small Chromosomal Regions Position Themselves Autonomously According to Their Chromatin Class},
  volume = {27},
  issn = {1088-9051, 1549-5469},
  abstract = {The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.},
  language = {en},
  number = {6},
  journal = {Genome Res.},
  doi = {10.1101/gr.213751.116},
  author = {van de Werken, Harmen J. G. and Haan, Josien C. and Feodorova, Yana and Bijos, Dominika and Weuts, An and Theunis, Koen and Holwerda, Sjoerd J. B. and Meuleman, Wouter and Pagie, Ludo and Thanisch, Katharina and Kumar, Parveen and Leonhardt, Heinrich and Marynen, Peter and van Steensel, Bas and Voet, Thierry and de Laat, Wouter and Solovei, Irina and Joffe, Boris},
  month = jan,
  year = {2017},
  pages = {922-933},
  file = {/home/bbeltr1/Documents/paper-collection/JoffeB/Werken et al_2017_Small chromosomal regions position themselves autonomously according to their.pdf;/home/bbeltr1/Documents/zotero/storage/CNMLML3S/922.html},
  pmid = {28341771}
}

@article{therizols2014,
  title = {Chromatin Decondensation Is Sufficient to Alter Nuclear Organization in Embryonic Stem Cells},
  volume = {346},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {During differentiation, thousands of genes are repositioned toward or away from the nuclear envelope. These movements correlate with changes in transcription and replication timing. Using synthetic (TALE) transcription factors, we found that transcriptional activation of endogenous genes by a viral trans-activator is sufficient to induce gene repositioning toward the nuclear interior in embryonic stem cells. However, gene relocation was also induced by recruitment of an acidic peptide that decondenses chromatin without affecting transcription, indicating that nuclear reorganization is driven by chromatin remodeling rather than transcription. We identified an epigenetic inheritance of chromatin decondensation that maintained central nuclear positioning through mitosis even after the TALE transcription factor was lost. Our results also demonstrate that transcriptional activation, but not chromatin decondensation, is sufficient to change replication timing.
Unpacking for travel to the nuclear interior
The position of a gene within the cell nucleus is correlated with its activity. Those near the nuclear periphery are generally repressed, whereas those in the center are (or will be) active. It is not clear whether this relocalization is a cause or a consequence of gene regulation. Therizols et al. found that transcriptional activation or simply chromatin decondensation both drove the relocation of genes to the interior of the nucleus. The nuclear position was maintained in daughter cells, suggesting that the cell has an epigenetic memory of the gene's position within the nucleus.
Science, this issue p. 1238
The position of a gene in the cell nucleus is dictated by the compaction state of its chromatin wrapper.
The position of a gene in the cell nucleus is dictated by the compaction state of its chromatin wrapper.},
  language = {en},
  number = {6214},
  journal = {Science},
  doi = {10.1126/science.1259587},
  author = {Therizols, Pierre and Illingworth, Robert S. and Courilleau, Celine and Boyle, Shelagh and Wood, Andrew J. and Bickmore, Wendy A.},
  month = dec,
  year = {2014},
  pages = {1238-1242},
  file = {/home/bbeltr1/Documents/paper-collection/BickmoreW/Therizols et al_2014_Chromatin decondensation is sufficient to alter nuclear organization in.pdf;/home/bbeltr1/Documents/zotero/storage/RABNF58V/1238.html},
  pmid = {25477464}
}

@article{chaumeil2006,
  title = {A Novel Role for {{Xist RNA}} in the Formation of a Repressive Nuclear Compartment into Which Genes Are Recruited When Silenced},
  volume = {20},
  issn = {0890-9369, 1549-5477},
  abstract = {During early mammalian female development, one of the two X chromosomes becomes inactivated. Although X-chromosome coating by Xist RNA is essential for the initiation of X inactivation, little is known about how this signal is transformed into transcriptional silencing. Here we show that exclusion of RNA Polymerase II and transcription factors from the Xist RNA-coated X chromosome represents the earliest event following Xist RNA accumulation described so far in differentiating embryonic stem (ES) cells. Paradoxically, exclusion of the transcription machinery occurs before gene silencing is complete. However, examination of the three-dimensional organization of X-linked genes reveals that, when transcribed, they are always located at the periphery of, or outside, the Xist RNA domain, in contact with the transcription machinery. Upon silencing, genes shift to a more internal location, within the Xist RNA compartment devoid of transcription factors. Surprisingly, the appearance of this compartment is not dependent on the A-repeats of the Xist transcript, which are essential for gene silencing. However, the A-repeats are required for the relocation of genes into the Xist RNA silent domain. We propose that Xist RNA has multiple functions: A-repeat-independent creation of a transcriptionally silent nuclear compartment; and A-repeat-dependent induction of gene repression, which is associated with their translocation into this silent domain.},
  language = {en},
  number = {16},
  journal = {Genes Dev.},
  doi = {10.1101/gad.380906},
  author = {Chaumeil, Julie and Baccon, Patricia Le and Wutz, Anton and Heard, Edith},
  month = aug,
  year = {2006},
  keywords = {3D nuclear organization,differentiation,histone modifications,transcriptional silencing,X inactivation,Xist RNA},
  pages = {2223-2237},
  file = {/home/bbeltr1/Documents/paper-collection/HeardE/Chaumeil et al_2006_A novel role for Xist RNA in the formation of a repressive nuclear compartment.pdf;/home/bbeltr1/Documents/zotero/storage/5G2WL5SR/2223.html},
  pmid = {16912274}
}

@article{giorgetti2016,
  title = {Structural Organization of the Inactive {{X}} Chromosome in the Mouse},
  volume = {535},
  journal = {Nature},
  author = {Giorgetti, Luca and Lajoie, Bryan R. and Carter, Ava C. and Attia, Mikael and Zhan, Ye and Xu, Jin and Chen, Chong Jian and Kaplan, Noam and Chang, Howard Y. and Heard, Edith and Dekker, Job},
  month = jul,
  year = {2016},
  pages = {575}
}

@article{rao2014,
  title = {A {{3D Map}} of the {{Human Genome}} at {{Kilobase Resolution Reveals Principles}} of {{Chromatin Looping}}},
  volume = {159},
  issn = {0092-8674},
  abstract = {Summary
We use in~situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify {$\sim$}10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly ({$>$}90\%) in a convergent orientation, with the asymmetric motifs ``facing'' one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
PaperFlick},
  number = {7},
  journal = {Cell},
  doi = {10.1016/j.cell.2014.11.021},
  author = {Rao, Suhas S. P. and Huntley, Miriam H. and Durand, Neva C. and Stamenova, Elena K. and Bochkov, Ivan D. and Robinson, James T. and Sanborn, Adrian L. and Machol, Ido and Omer, Arina D. and Lander, Eric S. and Aiden, Erez Lieberman},
  month = dec,
  year = {2014},
  pages = {1665-1680},
  file = {/home/bbeltr1/Documents/paper-collection/AidenE/Rao et al_2014_A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of.pdf;/home/bbeltr1/Documents/zotero/storage/XYUGA4C8/S0092867414014974.html}
}

@article{lampo2015a,
  title = {Physical {{Modeling}} of {{Chromosome Segregation}} in {{Escherichia}} Coli {{Reveals Impact}} of {{Force}} and {{DNA Relaxation}}},
  volume = {108},
  issn = {00063495},
  abstract = {The physical mechanism by which Escherichia coli segregates copies of its chromosome for partitioning into daughter cells is unknown, partly due to the difficulty in interpreting the complex dynamic behavior during segregation. Analysis of previous chromosome segregation measurements in E. coli demonstrates that the origin of replication exhibits processive motion with a mean displacement that scales as t0.32. In this work, we develop a model for segregation of chromosomal DNA as a Rouse polymer in a viscoelastic medium with a force applied to a single monomer. Our model demonstrates that the observed power-law scaling of the mean displacement and the behavior of the velocity autocorrelation function is captured by accounting for the relaxation of the polymer chain and the viscoelastic environment. We show that the ratio of the mean displacement to the variance of the displacement during segregation events is a critical metric that eliminates the compounding effects of polymer and medium dynamics and provides the segregation force. We calculate the force of oriC segregation in E. coli to be \textasciitilde{}0.49 pN.},
  language = {en},
  number = {1},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2014.10.074},
  author = {Lampo, Thomas J. and Kuwada, Nathan J. and Wiggins, Paul A. and Spakowitz, Andrew J.},
  month = jan,
  year = {2015},
  pages = {146-153},
  file = {/home/bbeltr1/Documents/zotero/storage/V4446M3B/Lampo et al. - 2015 - Physical Modeling of Chromosome Segregation in Esc.pdf}
}

@article{lupianez2015,
  title = {Disruptions of {{Topological Chromatin Domains Cause Pathogenic Rewiring}} of {{Gene}}-{{Enhancer Interactions}}},
  volume = {161},
  issn = {0092-8674},
  abstract = {Mammalian genomes are organized into megabase-scale topologically associated domains (TADs). We demonstrate that disruption of TADs can rewire long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. This rewiring occurred only if the variant disrupted a CTCF-associated boundary domain. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome.},
  number = {5},
  journal = {Cell},
  doi = {10.1016/j.cell.2015.04.004},
  author = {Lupi\'a\~nez, Dar\'io G. and Kraft, Katerina and Heinrich, Verena and Krawitz, Peter and Brancati, Francesco and Klopocki, Eva and Horn, Denise and Kayserili, H\"ulya and Opitz, John M. and Laxova, Renata and {Santos-Simarro}, Fernando and {Gilbert-Dussardier}, Brigitte and Wittler, Lars and Borschiwer, Marina and Haas, Stefan A. and Osterwalder, Marco and Franke, Martin and Timmermann, Bernd and Hecht, Jochen and Spielmann, Malte and Visel, Axel and Mundlos, Stefan},
  month = may,
  year = {2015},
  pages = {1012-1025},
  file = {/home/bbeltr1/Documents/paper-collection/MundlosS/Lupiáñez et al_2015_Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of.pdf},
  pmid = {25959774},
  pmcid = {PMC4791538}
}

@article{rodriguez-carballo2017,
  title = {The {{HoxD}} Cluster Is a Dynamic and Resilient {{TAD}} Boundary Controlling the Segregation of Antagonistic Regulatory Landscapes},
  issn = {0890-9369, 1549-5477},
  abstract = {The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.},
  language = {en},
  journal = {Genes Dev.},
  doi = {10.1101/gad.307769.117},
  author = {{Rodr\'iguez-Carballo}, Eddie and {Lopez-Delisle}, Lucille and Zhan, Ye and Fabre, Pierre J. and Beccari, Leonardo and {El-Idrissi}, Imane and Huynh, Thi Hanh Nguyen and Ozadam, Hakan and Dekker, Job and Duboule, Denis},
  month = dec,
  year = {2017},
  keywords = {CTCF,Hi-C,TAD,genome architecture,Hox,limb},
  file = {/home/bbeltr1/Documents/paper-collection/DubouleD/Rodríguez-Carballo et al_2017_The HoxD cluster is a dynamic and resilient TAD boundary controlling the.pdf;/home/bbeltr1/Documents/zotero/storage/LAZM5HJZ/gad.307769.html},
  pmid = {29273679}
}

@article{fabre2017,
  title = {Large Scale Genomic Reorganization of Topological Domains at the {{HoxD}} Locus},
  volume = {18},
  issn = {1474-760X},
  abstract = {The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts.},
  journal = {Genome Biology},
  doi = {10.1186/s13059-017-1278-z},
  author = {Fabre, Pierre J. and Leleu, Marion and Mormann, Benjamin H. and {Lopez-Delisle}, Lucille and Noordermeer, Daan and Beccari, Leonardo and Duboule, Denis},
  month = aug,
  year = {2017},
  keywords = {Gene regulation,CTCF,TAD,Hox,Chromatin organization,Enhancer,Limb development,Regulatory landscape,Topologically associating domains},
  pages = {149},
  file = {/home/bbeltr1/Documents/paper-collection/DubouleD/Fabre et al_2017_Large scale genomic reorganization of topological domains at the HoxD locus.pdf;/home/bbeltr1/Documents/zotero/storage/CF73IT2R/s13059-017-1278-z.html}
}

@article{williamson2011,
  title = {Enhancers: {{From Developmental Genetics}} to the {{Genetics}} of {{Common Human Disease}}},
  volume = {21},
  issn = {1534-5807},
  shorttitle = {Enhancers},
  abstract = {In mammals, long-range gene regulation became apparent through simple Mendelian disease genetics in human and developmental genetics in the mouse. Can the insights into gene control, provided by the study of these enhancers, help us understand the functional significance of sequence variation associated with common/complex human disease and quantitative traits?},
  number = {1},
  journal = {Developmental Cell},
  doi = {10.1016/j.devcel.2011.06.008},
  author = {Williamson, Iain and Hill, Robert E. and Bickmore, Wendy A.},
  month = jul,
  year = {2011},
  pages = {17-19},
  file = {/home/bbeltr1/Documents/paper-collection/BickmoreW/Williamson et al_2011_Enhancers.pdf;/home/bbeltr1/Documents/zotero/storage/85VGDHWC/S1534580711002425.html}
}

@article{matharu2015,
  title = {Minor {{Loops}} in {{Major Folds}}: {{Enhancer}}\textendash{{Promoter Looping}}, {{Chromatin Restructuring}}, and {{Their Association}} with {{Transcriptional Regulation}} and {{Disease}}},
  volume = {11},
  issn = {1553-7404},
  shorttitle = {Minor {{Loops}} in {{Major Folds}}},
  abstract = {The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer\textendash{}promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as ``TADopathies.''},
  language = {en},
  number = {12},
  journal = {PLOS Genetics},
  doi = {10.1371/journal.pgen.1005640},
  author = {Matharu, Navneet and Ahituv, Nadav},
  month = dec,
  year = {2015},
  keywords = {Gene expression,Chromatin,Genetic loci,Gene regulation,Transcription factors,DNA transcription,DNA fragment ligation,Transcriptional control},
  pages = {e1005640},
  file = {/home/bbeltr1/Documents/paper-collection/AhituvN/Matharu_Ahituv_2015_Minor Loops in Major Folds.pdf;/home/bbeltr1/Documents/zotero/storage/2MU58ZU6/article.html}
}

@article{luger2006,
  title = {Dynamic Nucleosomes},
  volume = {14},
  issn = {0967-3849, 1573-6849},
  abstract = {It is now widely recognized that the packaging of genomic DNA together with core histones, linker histones, and other functional proteins into chromatin profoundly influences nuclear processes such as transcription, replication, repair and recombination. How chromatin structure modulates the expression and maintenance of knowledge encoded in eukaryotic genomes, and how these processes take place within the context of a highly complex and compacted genomic chromatin environment remains a major unresolved question in biology. Here we review recent advances in our understanding of how nucleosome and chromatin structure may have to adapt to promote these vital functions.},
  language = {en},
  number = {1},
  journal = {Chromosome Res},
  doi = {10.1007/s10577-005-1026-1},
  author = {Luger, Karolin},
  month = feb,
  year = {2006},
  pages = {5-16},
  file = {/home/bbeltr1/Documents/paper-collection/LugerK/Luger_2006_Dynamic nucleosomes.pdf;/home/bbeltr1/Documents/zotero/storage/THYUDJT7/10.html}
}

@article{polach1995,
  title = {Mechanism of {{Protein Access}} to {{Specific DNA Sequences}} in {{Chromatin}}: {{A Dynamic Equilibrium Model}} for {{Gene Regulation}}},
  volume = {254},
  issn = {0022-2836},
  shorttitle = {Mechanism of {{Protein Access}} to {{Specific DNA Sequences}} in {{Chromatin}}},
  abstract = {We present evidence for a mechanism by which regulatory proteins may gain access to their target DNA sequences in chromatin. In this model, nucleosomes are dynamic structures, transiently exposing stretches of their DNA. Regulatory proteins gain access to DNA target sites in the exposed state, and bind with an apparent dissociation constant equal to their dissociation constant for naked DNA divided by a position-dependent equilibrium constant for site exposure within the nucleosome. A sensitive assay, based on the kinetics of restriction digestion of sites within nucleosomes, reveals this dynamic behaviour and quantifies the equilibrium constants for site exposure. Our results have implications for many aspects of chromatin function. They offer new mechanisms for cooperativity (synergy) in regulatory protein binding and for active invasion of nucleosomes.},
  number = {2},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.1995.0606},
  author = {Polach, K. J. and Widom, J.},
  month = nov,
  year = {1995},
  keywords = {nucleosome,nucleosome positioning,active invasion,binding,cooperativity},
  pages = {130-149},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Polach_Widom_1995_Mechanism of Protein Access to Specific DNA Sequences in Chromatin.pdf;/home/bbeltr1/Documents/zotero/storage/A7DJJI4G/S0022283685706067.html}
}

@book{polach1996,
  title = {A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target},
  abstract = {Department of Biochemistry The mechanism by which gene regulatory proteins gain access to their Molecular Biology, and Cell DNA target sequences in chromatin is not known. We recently showed that Biology and Department of nucleosomes are intrinsically dynamic, transiently exposing their DNA to Chemistry, Northwestern allow sequence-specific protein binding even at buried sites. Here we show University, Evanston, IL that this dynamic behaviour provides a mechanism for cooperativity 60208-3500, USA (synergy) in the binding of two or more proteins to sites on a single nucleosome, even if those proteins do not interact directly with each other in any way. As a consequence of this cooperativity, two proteins binding to the same nucleosome facilitate each other's binding and also control the level of occupancy at each other's sites. This model, with no adjustable parameters, accounts quantitatively for recent reports of cooperative (synergistic) binding to nucleosomes in vitro. We assess the potential importance of this new cooperativity for gene regulation in vivo by comparing its magnitude to free energies of cooperative protein\textendash{}protein direct contacts having known significance for gene regulation. Possible roles for nucleosome dynamics in eukaryotic gene regulation, and key remaining questions, are discussed.},
  author = {Polach, K. J. and Widom, J.},
  year = {1996},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Polach_Widom_1996_A model for the cooperative binding of eukaryotic regulatory proteins to.pdf;/home/bbeltr1/Documents/zotero/storage/Y7SMAMEN/summary.html}
}

@article{anderson2000,
  title = {Sequence and Position-Dependence of the Equilibrium Accessibility of Nucleosomal {{DNA}} Target {{sites11Edited}} by {{T}}. {{Richmond}}},
  volume = {296},
  issn = {0022-2836},
  abstract = {We have previously shown that nucleosomes are conformationally dynamic: DNA sequences that in the time-average are buried inside nucleosomes are nevertheless transiently accessible, even to large proteins (or any other macromolecule). We refer to this dynamic behavior as ``site exposure''. Here we show that: (i) the equilibrium constants describing this dynamic site exposure decrease progressively from either end of the nucleosomal DNA in toward the middle; and (ii) these position-dependent equilibrium constants are strongly dependent on the nucleosomal DNA sequence. The progressive decrease in equilibrium constant with distance inside the nucleosome supports the hypothesis that access to sites internal to a nucleosome is provided by progressive (transient) release of DNA from the octamer surface, starting from one end of the nucleosomal DNA. The dependence on genomic DNA sequence implies that a specific genomic DNA sequence could be a major determinant of target site occupancies achieved by regulatory proteins in vivo, by either governing the time-averaged accessibility for a given nucleosome position, or biasing the time-averaged positioning (of mobile nucleosomes), which in turn is a major determinant of site accessibility.},
  number = {4},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.2000.3531},
  author = {Anderson, J. D and Widom, J},
  month = mar,
  year = {2000},
  keywords = {chromatin,nucleosome,gene regulation,site exposure},
  pages = {979-987},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Anderson_Widom_2000_Sequence and position-dependence of the equilibrium accessibility of.pdf;/home/bbeltr1/Documents/zotero/storage/5EFSBUIH/S0022283600935319.html}
}

@article{li2004,
  title = {Nucleosomes Facilitate Their Own Invasion},
  volume = {11},
  copyright = {2004 Nature Publishing Group},
  issn = {1545-9985},
  abstract = {DNA wrapped in nucleosomes is sterically occluded, creating obstacles for polymerase, regulatory, remodeling, repair and recombination complexes, which require access to the wrapped DNA. How such complexes recognize and gain access to their DNA target sites is not known. Here we report the direct detection of a dynamic equilibrium conformational transition in nucleosomes that greatly increases the distance between the end of the nucleosomal DNA and the histone core. We quantified the equilibrium constant for this transition under physiological conditions. As predicted by these findings, addition of LexA protein to nucleosomes containing the LexA target site drives this conformational equilibrium toward the unwrapped, accessible state, simultaneously allowing stable LexA binding. This inherent property of nucleosomes allows any protein, whether an energy-dependent machine or a passive binder, to gain access even to buried stretches of nucleosomal DNA.},
  language = {en},
  number = {8},
  journal = {Nature Structural \& Molecular Biology},
  doi = {10.1038/nsmb801},
  author = {Li, Gu and Widom, Jonathan},
  month = aug,
  year = {2004},
  pages = {763-769},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Li_Widom_2004_Nucleosomes facilitate their own invasion.pdf;/home/bbeltr1/Documents/zotero/storage/MW3HZ3HA/nsmb801.html}
}

@article{winogradoff2017,
  title = {The {{Molecular Mechanism}} of {{Nucleosome Breathing}}},
  volume = {112},
  issn = {00063495},
  language = {en},
  number = {3},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2016.11.2014},
  author = {Winogradoff, David and Aksimentiev, Aleksei},
  month = feb,
  year = {2017},
  pages = {371a},
  file = {/home/bbeltr1/Documents/paper-collection/AksimentievA/Winogradoff_Aksimentiev_2017_The Molecular Mechanism of Nucleosome Breathing.pdf}
}

@article{lequieu2016,
  title = {Tension-{{Dependent Free Energies}} of {{Nucleosome Unwrapping}}},
  volume = {2},
  issn = {2374-7943},
  abstract = {Nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.},
  number = {9},
  journal = {ACS Cent. Sci.},
  doi = {10.1021/acscentsci.6b00201},
  author = {Lequieu, Joshua and C\'ordoba, Andr\'es and Schwartz, David C. and {de Pablo}, Juan J.},
  month = sep,
  year = {2016},
  pages = {660-666},
  file = {/home/bbeltr1/Documents/paper-collection/de PabloJ/Lequieu et al_2016_Tension-Dependent Free Energies of Nucleosome Unwrapping.pdf;/home/bbeltr1/Documents/zotero/storage/R3PVN9JN/acscentsci.html}
}

@article{sudhanshu2011,
  title = {Tension-Dependent Structural Deformation Alters Single-Molecule Transition Kinetics},
  volume = {108},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {We analyze the response of a single nucleosome to tension, which serves as a prototypical biophysical measurement where tension-dependent deformation alters transition kinetics. We develop a statistical-mechanics model of a nucleosome as a wormlike chain bound to a spool, incorporating fluctuations in the number of bases bound, the spool orientation, and the conformations of the unbound polymer segments. With the resulting free-energy surface, we perform dynamic simulations that permit a direct comparison with experiments. This simple approach demonstrates that the experimentally observed structural states at nonzero tension are a consequence of the tension and that these tension-induced states cease to exist at zero tension. The transitions between states exhibit substantial deformation of the unbound polymer segments. The associated deformation energy increases with tension; thus, the application of tension alters the kinetics due to tension-induced deformation of the transition states. This mechanism would arise in any system where the tether molecule is deformed in the transition state under the influence of tension.},
  language = {en},
  number = {5},
  journal = {PNAS},
  doi = {10.1073/pnas.1010047108},
  author = {Sudhanshu, B. and Mihardja, S. and Koslover, E. F. and Mehraeen, S. and Bustamante, C. and Spakowitz, A. J.},
  month = feb,
  year = {2011},
  keywords = {chromatin,DNA,polymer physics,single-molecule experiments,statistical mechanics},
  pages = {1885-1890},
  file = {/home/bbeltr1/Documents/paper-collection/SpakowitzA/Sudhanshu et al_2011_Tension-dependent structural deformation alters single-molecule transition.pdf;/home/bbeltr1/Documents/zotero/storage/9G2PLZTP/1885.html},
  pmid = {21245354}
}

@article{ngo2015a,
  title = {Nucleosomes Undergo Slow Spontaneous Gaping},
  volume = {43},
  issn = {0305-1048},
  abstract = {Abstract.  In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two cop},
  language = {en},
  number = {8},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gkv276},
  author = {Ngo, Thuy T. M. and Ha, Taekjip},
  month = apr,
  year = {2015},
  pages = {3964-3971},
  file = {/home/bbeltr1/Documents/paper-collection/HaT/Ngo_Ha_2015_Nucleosomes undergo slow spontaneous gaping.pdf;/home/bbeltr1/Documents/zotero/storage/QP4FY5IF/2414554.html}
}

@article{chen2017a,
  title = {Asymmetric Unwrapping of Nucleosomal {{DNA}} Propagates Asymmetric Opening and Dissociation of the Histone Core},
  volume = {114},
  copyright = {\textcopyright{}  . http://www.pnas.org/site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  abstract = {The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during salt-induced disassembly of canonical NCPs. We find that H2A\textendash{}H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.},
  language = {en},
  number = {2},
  journal = {PNAS},
  doi = {10.1073/pnas.1611118114},
  author = {Chen, Yujie and Tokuda, Joshua M. and Topping, Traci and Meisburger, Steve P. and Pabit, Suzette A. and Gloss, Lisa M. and Pollack, Lois},
  month = jan,
  year = {2017},
  keywords = {contrast variation SAXS,FRET,hexasome,nucleosomes,time resolved},
  pages = {334-339},
  file = {/home/bbeltr1/Documents/paper-collection/PollackL/Chen et al_2017_Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and.pdf;/home/bbeltr1/Documents/zotero/storage/3RNJA428/334.html},
  pmid = {28028239}
}

@article{chen2014b,
  title = {Revealing Transient Structures of Nucleosomes as {{DNA}} Unwinds},
  volume = {42},
  issn = {0305-1048},
  abstract = {Abstract.  The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) co},
  language = {en},
  number = {13},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gku562},
  author = {Chen, Yujie and Tokuda, Joshua M. and Topping, Traci and Sutton, Julie L. and Meisburger, Steve P. and Pabit, Suzette A. and Gloss, Lisa M. and Pollack, Lois},
  month = jul,
  year = {2014},
  pages = {8767-8776},
  file = {/home/bbeltr1/Documents/paper-collection/PollackL/Chen et al_2014_Revealing transient structures of nucleosomes as DNA unwinds.pdf;/home/bbeltr1/Documents/zotero/storage/3MCEKA65/1291473.html}
}

@article{vanderlick1986,
  title = {Solution of {{Percus}}'s Equation for the Density of Hard Rods in an External Field},
  volume = {34},
  abstract = {The theory of a one-dimensional fluid of hard rods has received much attention because it often yields exact results which serve as a guide to understanding the properties of more complicated fluids. Of particular interest recently has been the density distribution of nonuniform fluids in external potentials or between solid walls. The purpose of this paper is to report an explicit solution of the nonlinear integral equation derived by Percus for the density distribution of hard rods.},
  number = {6},
  journal = {Phys. Rev. A},
  doi = {10.1103/PhysRevA.34.5130},
  author = {Vanderlick, T. K. and Scriven, L. E. and Davis, H. T.},
  month = dec,
  year = {1986},
  pages = {5130-5131},
  file = {/home/bbeltr1/Documents/paper-collection/DavisH/Vanderlick et al_1986_Solution of Percus's equation for the density of hard rods in an external field.pdf;/home/bbeltr1/Documents/zotero/storage/KP8ZTD72/PhysRevA.34.html}
}

@article{chevereau2009,
  title = {Thermodynamics of {{Intragenic Nucleosome Ordering}}},
  volume = {103},
  issn = {0031-9007, 1079-7114},
  language = {en},
  number = {18},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.103.188103},
  author = {Chevereau, G. and Palmeira, L. and Thermes, C. and Arneodo, A. and Vaillant, C.},
  month = oct,
  year = {2009},
  file = {/home/bbeltr1/Documents/paper-collection/VaillantC/Chevereau et al_2009_Thermodynamics of Intragenic Nucleosome Ordering.pdf}
}

@article{tillo2010,
  title = {High {{Nucleosome Occupancy Is Encoded}} at {{Human Regulatory Sequences}}},
  volume = {5},
  issn = {1932-6203},
  abstract = {Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high intrinsic nucleosome occupancy. In most cases we examined, these elements also have high experimentally measured nucleosome occupancy in vivo. These regions typically have high G+C content, which correlates positively with intrinsic nucleosome occupancy, and are depleted for nucleosome-excluding poly-A sequences. We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells.},
  language = {en},
  number = {2},
  journal = {PLOS ONE},
  doi = {10.1371/journal.pone.0009129},
  author = {Tillo, Desiree and Kaplan, Noam and Moore, Irene K. and {Fondufe-Mittendorf}, Yvonne and Gossett, Andrea J. and Field, Yair and Lieb, Jason D. and Widom, Jonathan and Segal, Eran and Hughes, Timothy R.},
  month = feb,
  year = {2010},
  keywords = {Chromatin,Saccharomyces cerevisiae,Nucleosomes,Nucleosome mapping,Human genomics,DNA methylation,Transcriptional control,T cells},
  pages = {e9129},
  file = {/home/bbeltr1/Documents/paper-collection/HughesT/Tillo et al_2010_High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences.pdf;/home/bbeltr1/Documents/zotero/storage/G4Q98T3S/article.html}
}

@article{fitz2016,
  title = {Nucleosomal Arrangement Affects Single-Molecule Transcription Dynamics},
  volume = {113},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient, {$\chi$}, which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably, {$\chi$} can be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changes {$\chi$} in a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics.},
  language = {en},
  number = {45},
  journal = {PNAS},
  doi = {10.1073/pnas.1602764113},
  author = {Fitz, Veronika and Shin, Jaeoh and Ehrlich, Christoph and Farnung, Lucas and Cramer, Patrick and Zaburdaev, Vasily and Grill, Stephan W.},
  month = nov,
  year = {2016},
  keywords = {transcription,internucleosomal distance,optical tweezers,Pol II,single-molecule},
  pages = {12733-12738},
  file = {/home/bbeltr1/Documents/paper-collection/GrillS/Fitz et al_2016_Nucleosomal arrangement affects single-molecule transcription dynamics.pdf;/home/bbeltr1/Documents/zotero/storage/KKSRKHGT/12733.html},
  pmid = {27791062}
}

@article{white2001,
  title = {Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Changes in Internucleosome Interactions},
  volume = {20},
  issn = {0261-4189},
  abstract = {Chromatin is composed of nucleosomes, the universally repeating protein\textendash{}DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans. Our results show that yeast nucleosomes are likely to be subtly destabilized as compared with nucleosomes from higher eukaryotes, consistent with the idea that much of the yeast genome remains constitutively open during much of its life cycle. Importantly, minor sequence variations lead to dramatic changes in the way in which nucleosomes pack against each other within the crystal lattice. This has important implications for our understanding of the formation of higher order chromatin structure and its modulation by post-translational modifications. Finally, the yeast nucleosome core particle provides a structural context by which to interpret genetic data obtained from yeast. Coordinates have been deposited with the Protein Data Bank under accession number 1ID3.},
  number = {18},
  journal = {EMBO J},
  doi = {10.1093/emboj/20.18.5207},
  author = {White, Cindy L. and Suto, Robert K. and Luger, Karolin},
  month = sep,
  year = {2001},
  pages = {5207-5218},
  file = {/home/bbeltr1/Documents/paper-collection/LugerK/White et al_2001_Structure of the yeast nucleosome core particle reveals fundamental changes in.pdf},
  pmid = {11566884},
  pmcid = {PMC125637}
}

@misc{ucsf2018,
  title = {{{iROCKET Learning Module}}: {{Prologue Histology Resource}}},
  howpublished = {http://missinglink.ucsf.edu/lm/ids\_101\_histo\_resource/cell\_structure.htm},
  author = {UCSF},
  year = {2018},
  file = {/home/bbeltr1/Documents/zotero/storage/XLWA73X7/cell_structure.html}
}

@article{fudenberg2016,
  title = {Formation of {{Chromosomal Domains}} by {{Loop Extrusion}}},
  volume = {15},
  issn = {2211-1247},
  abstract = {Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet mechanisms of TAD formation remain unclear. Here we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and other fine features of Hi-C data. Contrary to typical illustrations, each TAD consists of multiple loops dynamically formed through extrusion, rather than a single static loop. Loop extrusion both explains diverse experimental observations, including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments, and makes specific predictions for depletion of CTCF versus cohesin. Finally, loop extrusion has additional, potentially far-ranging, consequences for processes including enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.,},
  number = {9},
  journal = {Cell Rep},
  doi = {10.1016/j.celrep.2016.04.085},
  author = {Fudenberg, Geoffrey and Imakaev, Maxim and Lu, Carolyn and Goloborodko, Anton and Abdennur, Nezar and Mirny, Leonid A.},
  month = may,
  year = {2016},
  pages = {2038-2049},
  file = {/home/bbeltr1/Documents/paper-collection/MirnyL/Fudenberg et al_2016_Formation of Chromosomal Domains by Loop Extrusion.pdf},
  pmid = {27210764},
  pmcid = {PMC4889513}
}

@article{barrington2017,
  title = {Cohesin Biology Meets the Loop Extrusion Model},
  volume = {25},
  issn = {0967-3849},
  abstract = {Extensive research has revealed that cohesin acts as a topological device, trapping chromosomal DNA within a large tripartite ring. In so doing, cohesin contributes to the formation of compact and organized genomes. How exactly the cohesin subunits interact, how it opens, closes, and translocates on chromatin, and how it actually tethers DNA strands together are still being elucidated. A comprehensive understanding of these questions will shed light on how cohesin performs its many functions, including its recently proposed role as a chromatid loop extruder. Here, we discuss this possibility in light of our understanding of the molecular properties of cohesin complexes.},
  number = {1},
  journal = {Chromosome Res},
  doi = {10.1007/s10577-017-9550-3},
  author = {Barrington, Christopher and Finn, Ronald and Hadjur, Suzana},
  year = {2017},
  keywords = {review,out of date},
  pages = {51-60},
  file = {/home/bbeltr1/Documents/paper-collection/HadjurS/Barrington et al_2017_Cohesin biology meets the loop extrusion model.pdf},
  pmid = {28210885},
  pmcid = {PMC5346154}
}

@article{tompitak2017,
  title = {Genomes of {{Multicellular Organisms Have Evolved}} to {{Attract Nucleosomes}} to {{Promoter Regions}}},
  volume = {112},
  issn = {0006-3495},
  abstract = {Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our~predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.},
  number = {3},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2016.12.041},
  author = {Tompitak, Marco and Vaillant, C\'edric and Schiessel, Helmut},
  month = feb,
  year = {2017},
  pages = {505-511},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Tompitak et al_2017_Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to.pdf;/home/bbeltr1/Documents/zotero/storage/KVVKMLDM/S0006349517300358.html}
}

@article{ogeen2017,
  title = {{{dCas9}}-Based Epigenome Editing Suggests Acquisition of Histone Methylation Is Not Sufficient for Target Gene Repression},
  volume = {45},
  issn = {0305-1048},
  abstract = {Distinct epigenomic profiles of histone marks have been associated with gene expression, but questions regarding the causal relationship remain. Here we investigated the activity of a broad collection of genomically targeted epigenetic regulators that could write epigenetic marks associated with a repressed chromatin state (G9A, SUV39H1, Kr\"uppel-associated box (KRAB), DNMT3A as well as the first targetable versions of Ezh2 and Friend of GATA-1 (FOG1)). dCas9 fusions produced target gene repression over a range of 0- to 10-fold that varied by locus and cell type. dCpf1 fusions were unable to repress gene expression. The most persistent gene repression required the action of several effector domains; however, KRAB-dCas9 did not contribute to persistence in contrast to previous reports. A `direct tethering' strategy attaching the Ezh2 methyltransferase enzyme to dCas9, as well as a `recruitment' strategy attaching the N-terminal 45 residues of FOG1 to dCas9 to recruit the endogenous nucleosome remodeling and deacetylase complex, were both successful in targeted deposition of H3K27me3. Surprisingly, however, repression was not correlated with deposition of either H3K9me3 or H3K27me3. Our results suggest that so-called repressive histone modifications are not sufficient for gene repression. The easily programmable dCas9 toolkit allowed precise control of epigenetic information and dissection of the relationship between the epigenome and gene regulation.},
  number = {17},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gkx578},
  author = {O'Geen, Henriette and Ren, Chonghua and Nicolet, Charles M. and Perez, Andrew A. and Halmai, Julian and Le, Victoria M. and Mackay, Joel P. and Farnham, Peggy J. and Segal, David J.},
  month = sep,
  year = {2017},
  pages = {9901-9916},
  file = {/home/bbeltr1/Documents/paper-collection/SegalD/O’Geen et al_2017_dCas9-based epigenome editing suggests acquisition of histone methylation is.pdf},
  pmid = {28973434},
  pmcid = {PMC5622328}
}

@article{schwarzer2017,
  title = {Two Independent Modes of Chromatin Organization Revealed by Cohesin Removal},
  volume = {551},
  copyright = {2017 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.},
  language = {en},
  number = {7678},
  journal = {Nature},
  doi = {10.1038/nature24281},
  author = {Schwarzer, Wibke and Abdennur, Nezar and Goloborodko, Anton and Pekowska, Aleksandra and Fudenberg, Geoffrey and {Loe-Mie}, Yann and Fonseca, Nuno A. and Huber, Wolfgang and Haering, Christian H. and Mirny, Leonid and Spitz, Francois},
  month = nov,
  year = {2017},
  pages = {51-56},
  file = {/home/bbeltr1/Documents/paper-collection/SpitzF/Schwarzer et al_2017_Two independent modes of chromatin organization revealed by cohesin removal.pdf;/home/bbeltr1/Documents/zotero/storage/YYY673WA/nature24281.html}
}

@article{rao2017,
  title = {Cohesin {{Loss Eliminates All Loop Domains}}},
  volume = {171},
  issn = {00928674},
  abstract = {The human genome folds to create thousands of intervals, called ``contact domains,'' that exhibit enhanced contact frequency within themselves. ``Loop domains'' form because of tethering between two loci\textemdash{}almost always bound by CTCF and cohesin\textemdash{}lying on the same chromosome. ``Compartment domains'' form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although reformation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.},
  language = {en},
  number = {2},
  journal = {Cell},
  doi = {10.1016/j.cell.2017.09.026},
  author = {Rao, Suhas S.P. and Huang, Su-Chen and Glenn St Hilaire, Brian and Engreitz, Jesse M. and Perez, Elizabeth M. and {Kieffer-Kwon}, Kyong-Rim and Sanborn, Adrian L. and Johnstone, Sarah E. and Bascom, Gavin D. and Bochkov, Ivan D. and Huang, Xingfan and Shamim, Muhammad S. and Shin, Jaeweon and Turner, Douglass and Ye, Ziyi and Omer, Arina D. and Robinson, James T. and Schlick, Tamar and Bernstein, Bradley E. and Casellas, Rafael and Lander, Eric S. and Aiden, Erez Lieberman},
  month = oct,
  year = {2017},
  pages = {305-320.e24},
  file = {/home/bbeltr1/Documents/paper-collection/AidenE/Rao et al_2017_Cohesin Loss Eliminates All Loop Domains.pdf}
}

@article{hajjoul2013,
  title = {High-Throughput Chromatin Motion Tracking in Living Yeast Reveals the Flexibility of the Fiber throughout the Genome},
  volume = {23},
  issn = {1088-9051},
  language = {en},
  number = {11},
  journal = {Genome Research},
  doi = {10.1101/gr.157008.113},
  author = {Hajjoul, Houssam and Mathon, Julien and Ranchon, Hubert and Goiffon, Isabelle and Mozziconacci, Julien and Albert, Benjamin and Carrivain, Pascal and Victor, Jean-Marc and Gadal, Olivier and Bystricky, Kerstin and Bancaud, Aur\'elien},
  month = nov,
  year = {2013},
  pages = {1829-1838},
  file = {/home/bbeltr1/Documents/zotero/storage/VL2K4LTV/Hajjoul et al. - 2013 - High-throughput chromatin motion tracking in livin.pdf}
}

@article{verdaasdonk2013,
  title = {Centromere {{Tethering Confines Chromosome Domains}}},
  volume = {52},
  issn = {1097-2765},
  abstract = {Summary
The organization of chromosomes into territories plays an important role in a wide range of cellular processes, including gene expression, transcription, and DNA repair. Current understanding has largely excluded the spatiotemporal dynamic fluctuations of the chromatin polymer. We combine in~vivo chromatin motion analysis with mathematical modeling to elucidate the physical properties that underlie the formation and fluctuations of territories. Chromosome motion varies in predicted ways along the length of the chromosome, dependent on tethering at the centromere. Detachment of a tether upon inactivation of the centromere results in increased spatial mobility. A confined bead-spring chain tethered at both ends provides a mechanism to generate observed variations in local mobility as a function of distance from the tether. These predictions are realized in experimentally determined higher effective spring constants closer to the centromere. The dynamic fluctuations and territorial organization of chromosomes are, in part, dictated by tethering at the centromere.},
  number = {6},
  journal = {Molecular Cell},
  doi = {10.1016/j.molcel.2013.10.021},
  author = {Verdaasdonk, Jolien Suzanne and Vasquez, Paula Andrea and Barry, Raymond Mario and Barry, Timothy and Goodwin, Scott and Forest, M. Gregory and Bloom, Kerry},
  month = dec,
  year = {2013},
  pages = {819-831},
  file = {/home/bbeltr1/Documents/paper-collection/BloomK/Verdaasdonk et al_2013_Centromere Tethering Confines Chromosome Domains.pdf;/home/bbeltr1/Documents/zotero/storage/PIRI6CS2/S1097276513007879.html}
}

@article{wakamori2015,
  title = {Intra- and Inter-Nucleosomal Interactions of the Histone {{H4}} Tail Revealed with a Human Nucleosome Core Particle with Genetically-Incorporated {{H4}} Tetra-Acetylation},
  volume = {5},
  copyright = {2015 Nature Publishing Group},
  issn = {2045-2322},
  abstract = {Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 \AA{} and 2.2 \AA{} resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.},
  language = {en},
  journal = {Scientific Reports},
  doi = {10.1038/srep17204},
  author = {Wakamori, Masatoshi and Fujii, Yoshifumi and Suka, Noriyuki and Shirouzu, Mikako and Sakamoto, Kensaku and Umehara, Takashi and Yokoyama, Shigeyuki},
  month = nov,
  year = {2015},
  pages = {17204},
  file = {/home/bbeltr1/Documents/paper-collection/YokoyamaS/Wakamori et al_2015_Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with.pdf;/home/bbeltr1/Documents/zotero/storage/P7U64RKM/srep17204.html}
}

@incollection{burgess2002,
  series = {Homology {{Effects}}},
  title = {3 - {{Homologous Chromosome Associations}} and {{Nuclear Order}} in {{Meiotic}} and {{Mitotically Dividing Cells}} of {{Budding Yeast}}},
  volume = {46},
  abstract = {This chapter discusses the relationship between nuclear order and the association of homologous DNA sequences in the budding yeast, Saccharomyces cerevisiae. Homologous chromosomes functionally interact with one another to repair DNA double-strand breaks (DSBs) introduced either environmentally (e.g., by {$\gamma$}-irradiation) or deliberately by the cell (e. g., during meiosis). DNA homology recognition in these instances often involves the (RecA) homolog RAD51 and/or the related gene, DMC1. Evidence for interactions between homologous chromosomes occurring independent of DSB formation and (RecA) homolog function has also been described in meiotic, premeiotic, and mitotically dividing cells of yeast. These interactions presumably depend upon DNA homology but the molecular details of such associations are poorly understood. Both DSB-dependent and -independent homolog associations may be facilitated by the nonrandom organization of chromosomes in the nucleus, including centromere and telomere clustering, which are also discussed.},
  booktitle = {Advances in {{Genetics}}},
  publisher = {{Academic Press}},
  author = {Burgess, Sean M.},
  editor = {Dunlap, Jay C. and -ting Wu, C.},
  month = jan,
  year = {2002},
  pages = {49-90},
  file = {/home/bbeltr1/Documents/paper-collection/WuC/Burgess_2002_3 - Homologous Chromosome Associations and Nuclear Order in Meiotic and.pdf;/home/bbeltr1/Documents/zotero/storage/KQXPAKJV/S006526600246004X.html},
  doi = {10.1016/S0065-2660(02)46004-X}
}

@article{koslover2013,
  title = {Systematic {{Coarse}}-{{Graining}} of {{Microscale Polymer Models}} as {{Effective Elastic Chains}}},
  volume = {46},
  issn = {0024-9297},
  abstract = {One of the key goals of macromolecular modeling is to elucidate how macroscale physical properties arise from the microscale behavior of the polymer constituents. For many biological and industrial applications, a direct simulation approach is impractical due to to the wide range of length scales that must be spanned by the model, necessitating physically sound and practically relevant procedures for coarse-graining polymer systems. We present a highly general systematic coarse-graining procedure that maps any detailed polymer model onto effective elastic-chain models at intermediate and large length scales. Our approach defines a continuous flow of coarse-grained models starting from the detailed microscale model, proceeding through an intermediate-scale stretchable, shearable wormlike chain, and finally resolving to a Gaussian chain at the longest lengths. We demonstrate the utility of this procedure by coarse-graining a wormlike chain with periodic rigid kinks, a model relevant for studying DNA\textendash{}protein arrays and genome packing. The methodology described in this work provides a physically sound foundation for coarse-grained simulation of polymer systems, as well as analytical expressions for chain statistics at intermediate and long length scales.},
  number = {5},
  journal = {Macromolecules},
  doi = {10.1021/ma302056v},
  author = {Koslover, Elena F. and Spakowitz, Andrew J.},
  month = mar,
  year = {2013},
  pages = {2003-2014},
  file = {/home/bbeltr1/Documents/zotero/storage/XP5CHYCY/Koslover and Spakowitz - 2013 - Systematic Coarse-Graining of Microscale Polymer M.pdf;/home/bbeltr1/Documents/zotero/storage/VVWZ4U8U/ma302056v.html}
}

@article{eltsov2018,
  title = {Nucleosome Conformational Variability in Solution and in Interphase Nuclei Evidenced by Cryo-Electron Microscopy of Vitreous Sections},
  volume = {46},
  issn = {0305-1048, 1362-4962},
  language = {en},
  number = {17},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gky670},
  author = {Eltsov, Mikhail and Grewe, Diana and Lemercier, Nicolas and Frangakis, Achilleas and Livolant, Fran{\c c}oise and Leforestier, Am\'elie},
  month = sep,
  year = {2018},
  pages = {9189-9200},
  file = {/home/bbeltr1/Documents/zotero/storage/JF3RGQ4C/Eltsov et al. - 2018 - Nucleosome conformational variability in solution .pdf}
}

@article{senavirathne2017,
  title = {Dynamic Unwrapping of Nucleosomes by {{HsRAD51}} That Includes Sliding and Rotational Motion of Histone Octamers},
  volume = {45},
  issn = {0305-1048, 1362-4962},
  language = {en},
  number = {2},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gkw920},
  author = {Senavirathne, Gayan and Mahto, Santosh K. and Hanne, Jeungphill and O'Brian, Daniel and Fishel, Richard},
  month = jan,
  year = {2017},
  pages = {685-698},
  file = {/home/bbeltr1/Documents/zotero/storage/QMC9YNWJ/Senavirathne et al. - 2017 - Dynamic unwrapping of nucleosomes by HsRAD51 that .pdf}
}

@article{kulaeva2007,
  title = {Transcription {{Through Chromatin}} by {{RNA}} Polymerase {{II}}: {{Histone Displacement}} and {{Exchange}}},
  volume = {618},
  issn = {0027-5107},
  shorttitle = {Transcription {{Through Chromatin}} by {{RNA}} Polymerase {{II}}},
  abstract = {The process of transcript elongation by RNA polymerase II (Pol II) involves transcription-dependent exchange and displacement of all core histones and is tightly controlled by numerous protein complexes modifying chromatin structure. These processes can contribute to regulation of transcription initiation and elongation, as well as the chromatin state. Recent data suggest that the histone octamer is displaced from DNA at a high rate of transcription, but can survive less frequent transcription that is accompanied only by partial loss of H2A/H2B histones. Here we propose that critical density of Pol II molecules could be required for displacement of the histone octamer and discuss mechanisms that are most likely involved in the processes of histone exchange.},
  number = {1-2},
  journal = {Mutat Res},
  doi = {10.1016/j.mrfmmm.2006.05.040},
  author = {Kulaeva, Olga I. and Gaykalova, Daria and Studitsky, Vasily M.},
  month = may,
  year = {2007},
  pages = {116-129},
  file = {/home/bbeltr1/Documents/zotero/storage/LKYUPEL3/Kulaeva et al. - 2007 - Transcription Through Chromatin by RNA polymerase .pdf},
  pmid = {17313961},
  pmcid = {PMC1924643}
}

@article{song2014b,
  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/zotero/storage/LBKMLMB7/Song et al. - 2014 - Cryo-EM Study of the Chromatin Fiber Reveals a Dou.pdf;/home/bbeltr1/Documents/zotero/storage/I4GELIUZ/376.html},
  pmid = {24763583}
}

@article{liu2011,
  title = {Statistical Mechanics of Helical Wormlike Chain Model},
  volume = {134},
  issn = {0021-9606, 1089-7690},
  language = {en},
  number = {6},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.3548885},
  author = {Liu, Ya and P\'erez, Toni and Li, Wei and Gunton, J. D. and Green, Amanda},
  month = feb,
  year = {2011},
  pages = {065107},
  file = {/home/bbeltr1/Documents/zotero/storage/LPCTGZ3G/Liu et al. - 2011 - Statistical mechanics of helical wormlike chain mo.pdf}
}

@article{zhou2003,
  title = {Conformational Statistics of Bent Semiflexible Polymers},
  volume = {119},
  issn = {0021-9606, 1089-7690},
  language = {en},
  number = {9},
  journal = {The Journal of Chemical Physics},
  doi = {10.1063/1.1596911},
  author = {Zhou, Yu and Chirikjian, Gregory S.},
  month = sep,
  year = {2003},
  pages = {4962-4970},
  file = {/home/bbeltr1/Documents/zotero/storage/AQSU7HG6/Zhou and Chirikjian - 2003 - Conformational statistics of bent semiflexible pol.pdf}
}

@article{zhou2006,
  title = {Conformational {{Statistics}} of {{Semiflexible Macromolecular Chains}} with {{Internal Joints}}},
  volume = {39},
  issn = {0024-9297, 1520-5835},
  abstract = {Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semiflexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the noncommutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semiflexible chainlike macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semiflexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities.},
  language = {en},
  number = {5},
  journal = {Macromolecules},
  doi = {10.1021/ma0512556},
  author = {Zhou, Yu and Chirikjian, Gregory S.},
  month = mar,
  year = {2006},
  pages = {1950-1960},
  file = {/home/bbeltr1/Documents/zotero/storage/GUWIN6X3/Zhou and Chirikjian - 2006 - Conformational Statistics of Semiflexible Macromol.pdf}
}

@article{kulic2004a,
  title = {{{DNA Spools}} under {{Tension}}},
  volume = {92},
  issn = {0031-9007, 1079-7114},
  language = {en},
  number = {22},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.92.228101},
  author = {Kuli\'c, I. M. and Schiessel, H.},
  month = jun,
  year = {2004},
  file = {/home/bbeltr1/Documents/zotero/storage/MRFAUMSP/Kulić and Schiessel - 2004 - DNA Spools under Tension.pdf}
}

@article{yamakawa1976,
  title = {Statistical Mechanics of Helical Wormlike Chains. {{I}}. {{Differential}} Equations and Moments},
  volume = {64},
  issn = {0021-9606},
  number = {12},
  journal = {J. Chem. Phys.},
  doi = {10.1063/1.432197},
  author = {Yamakawa, Hiromi and Fujii, Motoharu},
  month = jun,
  year = {1976},
  pages = {5222-5228},
  file = {/home/bbeltr1/Documents/zotero/storage/3VA9W2W8/Yamakawa and Fujii - 1976 - Statistical mechanics of helical wormlike chains. .pdf;/home/bbeltr1/Documents/zotero/storage/XSUJI5VU/1.html}
}

@article{stadler2017,
  title = {Regulation of {{DNA Repair Mechanisms}}: {{How}} the {{Chromatin Environment Regulates}} the {{DNA Damage Response}}},
  volume = {18},
  issn = {1422-0067},
  shorttitle = {Regulation of {{DNA Repair Mechanisms}}},
  abstract = {Cellular DNA is constantly challenged by damage-inducing factors derived from exogenous or endogenous sources. In order to maintain genome stability and integrity, cells have evolved a wide variety of DNA repair pathways which counteract different types of DNA lesions, also referred to as the DNA damage response (DDR). However, DNA in eukaryotes is highly organized and compacted into chromatin representing major constraints for all cellular pathways, including DNA repair pathways, which require DNA as their substrate. Therefore, the chromatin configuration surrounding the lesion site undergoes dramatic remodeling to facilitate access of DNA repair factors and subsequent removal of the DNA lesion. In this review, we focus on the question of how the cellular DNA repair pathways overcome the chromatin barrier, how the chromatin environment is rearranged to facilitate efficient DNA repair, which proteins mediate this re-organization process and, consequently, how the altered chromatin landscape is involved in the regulation of DNA damage responses.},
  number = {8},
  journal = {Int J Mol Sci},
  doi = {10.3390/ijms18081715},
  author = {Stadler, Jens and Richly, Holger},
  month = aug,
  year = {2017},
  file = {/home/bbeltr1/Documents/zotero/storage/S2XZJCIC/Stadler and Richly - 2017 - Regulation of DNA Repair Mechanisms How the Chrom.pdf},
  pmid = {28783053},
  pmcid = {PMC5578105}
}

@article{hauer2017,
  title = {Chromatin and Nucleosome Dynamics in {{DNA}} Damage and Repair},
  volume = {31},
  issn = {0890-9369, 1549-5477},
  abstract = {Chromatin is organized into higher-order structures that form subcompartments in interphase nuclei. Different categories of specialized enzymes act on chromatin and regulate its compaction and biophysical characteristics in response to physiological conditions. We present an overview of the function of chromatin structure and its dynamic changes in response to genotoxic stress, focusing on both subnuclear organization and the physical mobility of DNA. We review the requirements and mechanisms that cause chromatin relocation, enhanced mobility, and chromatin unfolding as a consequence of genotoxic lesions. An intriguing link has been established recently between enhanced chromatin dynamics and histone loss.},
  language = {en},
  number = {22},
  journal = {Genes Dev.},
  doi = {10.1101/gad.307702.117},
  author = {Hauer, Michael H. and Gasser, Susan M.},
  month = nov,
  year = {2017},
  keywords = {chromatin structure,DNA damage,histones,nuclear organization,nucleosome remodelers},
  pages = {2204-2221},
  file = {/home/bbeltr1/Documents/zotero/storage/MU3NEG2J/Hauer and Gasser - 2017 - Chromatin and nucleosome dynamics in DNA damage an.pdf;/home/bbeltr1/Documents/zotero/storage/RFFK64VV/2204.html},
  pmid = {29284710}
}

@article{hubner2013,
  title = {Chromatin {{Organization}} and {{Transcriptional Regulation}}},
  volume = {23},
  issn = {0959-437X},
  abstract = {Cell type specific transcriptional regulation must be adhered to in order to maintain cell identity throughout the lifetime of an organism, yet flexible enough to allow for responses to endogenous and exogenous stimuli. This regulation is mediated not only by molecular factors (e.g. cell type specific transcription factors, histone and DNA modifications), but also on the level of chromatin and genome organization. In this review we focus on recent findings that have contributed to our understanding of higher order chromatin structure and genome organization within the nucleus. We highlight new findings on the dynamic positioning of genes relative to each other, as well as to their chromosome territory and the nuclear lamina, and how the position of genes correlates with their transcriptional activity.},
  number = {2},
  journal = {Curr Opin Genet Dev},
  doi = {10.1016/j.gde.2012.11.006},
  author = {H\"ubner, Michael R. and {Eckersley-Maslin}, M\'elanie A. and Spector, David L.},
  month = apr,
  year = {2013},
  pages = {89-95},
  file = {/home/bbeltr1/Documents/zotero/storage/9VRVIYWY/Hübner et al. - 2013 - Chromatin Organization and Transcriptional Regulat.pdf},
  pmid = {23270812},
  pmcid = {PMC3612554}
}

@article{givens2012,
  title = {Chromatin Architectures at Fission Yeast Transcriptional Promoters and Replication Origins},
  volume = {40},
  issn = {0305-1048},
  abstract = {We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, {$\sim$}152\,bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of pre-replication complex (pre-RC) proteins within large NDRs\textemdash{}a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms.},
  number = {15},
  journal = {Nucleic Acids Res},
  doi = {10.1093/nar/gks351},
  author = {Givens, Robert M. and Lai, William K. M. and Rizzo, Jason M. and Bard, Jonathan E. and Mieczkowski, Piotr A. and Leatherwood, Janet and Huberman, Joel A. and Buck, Michael J.},
  month = aug,
  year = {2012},
  pages = {7176-7189},
  file = {/home/bbeltr1/Documents/zotero/storage/SLJIRE52/Givens et al. - 2012 - Chromatin architectures at fission yeast transcrip.pdf},
  pmid = {22573177},
  pmcid = {PMC3424540}
}

@article{szerlong2010,
  title = {Nucleosome Distribution and Linker {{DNA}}: Connecting Nuclear Function to Dynamic Chromatin Structure},
  volume = {89},
  issn = {0829-8211},
  shorttitle = {Nucleosome Distribution and Linker {{DNA}}},
  abstract = {Genetic information in eukaryotes is managed by strategic hierarchical organization of chromatin structure. Primary chromatin structure describes an unfolded nucleosomal array, often referred to as ``beads on a string''. Chromatin is compacted by the nonlinear rearrangement of nucleosomes to form stable secondary chromatin structures. Chromatin conformational transitions between primary and secondary structures are mediated by both nucleosome-stacking interactions and the intervening linker DNA. Chromatin model system studies find that the topography of secondary structures is sensitive to the spacing of nucleosomes within an array. Understanding the relationship between nucleosome spacing and higher order chromatin structure will likely yield important insights into the dynamic nature of secondary chromatin structure as it occurs in vivo. Genome-wide nucleosome mapping studies find the distance between nucleosomes varies, and regions of uniformly spaced nucleosomes are often interrupted by regions of nonun..., Chez les eucaryotes, l'information g\'en\'etique est contr\^ol\'ee par une organisation de la structure de la chromatine hi\'erarchique et strat\'egique. La structure primaire de la chromatine correspond \`a un r\'eseau non repli\'e de nucl\'eosomes qui ressemble \`a un collier de perles. La chromatine est compact\'ee par le r\'earrangement non-lin\'eaire des nucl\'eosomes afin de formerdes structures secondaires stables de chromatine. Les transitions de conformation de la chromatine entre ses structures primaire et secondaire se r\'ealisent par l'interm\'ediaire d'interactions d'empilement des nucl\'eosomes et d'ADN linker intronique. Des \'etudes portant sur des mod\`eles de chromatine ont montr\'e que la topographie des structures secondaires est sensible \`a l'espacement des nucl\'eosomes \`a l'int\'erieur d'un r\'eseau. La compr\'ehension de la relation qui existe entre l'espacement des nucl\'eosomes et la structure chromatinienne d'ordre sup\'erieur donnera vraisemblablement un bon aper{\c c}u de la nature dynamique de la structure secondaire de la chromatine t...},
  number = {1},
  journal = {Biochem. Cell Biol.},
  doi = {10.1139/O10-139},
  author = {Szerlong, Heather J. and Hansen, Jeffrey C.},
  month = nov,
  year = {2010},
  pages = {24-34},
  file = {/home/bbeltr1/Documents/zotero/storage/U3B5JT2N/Szerlong and Hansen - 2010 - Nucleosome distribution and linker DNA connecting.pdf;/home/bbeltr1/Documents/zotero/storage/MDPQEQ5J/O10-139.html}
}

@article{schones2008,
  title = {Dynamic {{Regulation}} of {{Nucleosome Positioning}} in the {{Human Genome}}},
  volume = {132},
  issn = {0092-8674},
  abstract = {Summary
The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding. Furthermore, the first nucleosome downstream of a start site exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome.},
  number = {5},
  journal = {Cell},
  doi = {10.1016/j.cell.2008.02.022},
  author = {Schones, Dustin E. and Cui, Kairong and Cuddapah, Suresh and Roh, Tae-Young and Barski, Artem and Wang, Zhibin and Wei, Gang and Zhao, Keji},
  month = mar,
  year = {2008},
  keywords = {DNA,SIGNALING},
  pages = {887-898},
  file = {/home/bbeltr1/Documents/zotero/storage/FGPQ2IJ2/Schones et al. - 2008 - Dynamic Regulation of Nucleosome Positioning in th.pdf;/home/bbeltr1/Documents/zotero/storage/C8EHDMCW/S0092867408002705.html}
}

@article{wang2008a,
  title = {Preferentially {{Quantized Linker DNA Lengths}} in {{Saccharomyces}} Cerevisiae},
  volume = {4},
  issn = {1553-734X},
  abstract = {The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, {$\sim$}10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ({$\sim$}10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast., Eukaryotic genomic DNA exists as chromatin, with the DNA wrapped locally into a repeating array of protein\textendash{}DNA complexes (``nucleosomes'') separated by short stretches of unwrapped ``linker'' DNA. Nucleosome arrays further compact into {$\sim$}30-nm-wide higher-order chromatin structures. Despite decades of work, there remains no agreement about the structure of the 30 nm fiber, or even if the structure is ordered or random. The helical symmetry of DNA couples the one-dimensional distribution of nucleosomes along the DNA to an intrinsic three-dimensional structure for the chromatin fiber. Random linker length distributions imply random three-dimensional intrinsic fiber structures, whereas different possible nonrandom length distributions imply different ordered structures. Here we use two independent computational methods, with two independent kinds of experimental data, to experimentally define the probability distribution of linker DNA lengths in yeast. Both methods agree that linker DNA lengths in yeast come in a set of preferentially quantized lengths that differ one from another by {$\sim$}10 bp, the DNA helical repeat, with a preferred phase offset of 5 bp. The preferential quantization of lengths implies that the intrinsic three-dimensional structure for the average chromatin fiber is ordered, not random. The 5 bp offset implies a particular geometry for this intrinsic structure.},
  number = {9},
  journal = {PLoS Comput Biol},
  doi = {10.1371/journal.pcbi.1000175},
  author = {Wang, Ji-Ping and {Fondufe-Mittendorf}, Yvonne and Xi, Liqun and Tsai, Guei-Feng and Segal, Eran and Widom, Jonathan},
  month = sep,
  year = {2008},
  file = {/home/bbeltr1/Documents/zotero/storage/P7977ZP4/Wang et al. - 2008 - Preferentially Quantized Linker DNA Lengths in Sac.pdf},
  pmid = {18787693},
  pmcid = {PMC2522279}
}

@article{woodcock1993,
  title = {A Chromatin Folding Model That Incorporates Linker Variability Generates Fibers Resembling the Native Structures},
  volume = {90},
  issn = {0027-8424, 1091-6490},
  abstract = {The "30-nm" chromatin fibers, as observed in eukaryotic nuclei, are considered a discrete level in a hierarchy of DNA folding. At present, there is considerable debate as to how the nucleosomes and linker DNA are organized within chromatin fibers, and a number of models have been proposed, many of which are based on helical symmetry and imply specific contacts between nucleosomes. However, when observed in nuclei or after isolation, chromatin fibers show considerable structural irregularity. In the present study, chromatin folding is considered solely in terms of the known properties of the nucleosome-linker unit, taking into account the relative rotation between consecutive nucleosomes that results from the helical twist of DNA. Model building based on this premise, and with a constant length of linker DNA between consecutive nucleosomes, results in a family of fiber- and ribbon-like structures. When the linker length between nucleosomes is allowed to vary, as occurs in nature, fibers showing the types of irregularity observed in nuclei and in isolated chromatin are created. The potential application of the model in determining the three-dimensional organization of chromatin in which nucleosome positions are known is discussed.},
  language = {en},
  number = {19},
  journal = {PNAS},
  doi = {10.1073/pnas.90.19.9021},
  author = {Woodcock, C. L. and Grigoryev, S. A. and Horowitz, R. A. and Whitaker, N.},
  month = oct,
  year = {1993},
  pages = {9021-9025},
  file = {/home/bbeltr1/Documents/zotero/storage/58C54VR5/Woodcock et al. - 1993 - A chromatin folding model that incorporates linker.pdf;/home/bbeltr1/Documents/zotero/storage/A8VHPQYH/9021.html},
  pmid = {8415647}
}

@article{grigoryev2016,
  title = {Hierarchical Looping of Zigzag Nucleosome Chains in Metaphase Chromosomes},
  volume = {113},
  copyright = {\textcopyright{}  . http://www.pnas.org.stanford.idm.oclc.org/preview\_site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  abstract = {The architecture of higher-order chromatin in eukaryotic cell nuclei is largely unknown. Here, we use electron microscopy-assisted nucleosome interaction capture (EMANIC) cross-linking experiments in combination with mesoscale chromatin modeling of 96-nucleosome arrays to investigate the internal organization of condensed chromatin in interphase cell nuclei and metaphase chromosomes at nucleosomal resolution. The combined data suggest a novel hierarchical looping model for chromatin higher-order folding, similar to rope flaking used in mountain climbing and rappelling. Not only does such packing help to avoid tangling and self-crossing, it also facilitates rope unraveling. Hierarchical looping is characterized by an increased frequency of higher-order internucleosome contacts for metaphase chromosomes compared with chromatin fibers in vitro and interphase chromatin, with preservation of a dominant two-start zigzag organization associated with the 30-nm fiber. Moreover, the strong dependence of looping on linker histone concentration suggests a hierarchical self-association mechanism of relaxed nucleosome zigzag chains rather than longitudinal compaction as seen in 30-nm fibers. Specifically, concentrations lower than one linker histone per nucleosome promote self-associations and formation of these looped networks of zigzag fibers. The combined experimental and modeling evidence for condensed metaphase chromatin as hierarchical loops and bundles of relaxed zigzag nucleosomal chains rather than randomly coiled threads or straight and stiff helical fibers reconciles aspects of other models for higher-order chromatin structure; it constitutes not only an efficient storage form for the genomic material, consistent with other genome-wide chromosome conformation studies that emphasize looping, but also a convenient organization for local DNA unraveling and genome access.},
  language = {en},
  number = {5},
  journal = {PNAS},
  doi = {10.1073/pnas.1518280113},
  author = {Grigoryev, Sergei A. and Bascom, Gavin and Buckwalter, Jenna M. and Schubert, Michael B. and Woodcock, Christopher L. and Schlick, Tamar},
  month = feb,
  year = {2016},
  keywords = {nucleosome,linker histone,electron microscopy,chromatin higher-order structure,mesoscale modeling},
  pages = {1238-1243},
  file = {/home/bbeltr1/Documents/zotero/storage/NAT374B7/Grigoryev et al. - 2016 - Hierarchical looping of zigzag nucleosome chains i.pdf;/home/bbeltr1/Documents/zotero/storage/GKNYZB9D/1238.html},
  pmid = {26787893}
}

@article{lai2018,
  title = {Principles of Nucleosome Organization Revealed by Single-Cell Micrococcal Nuclease Sequencing},
  volume = {562},
  issn = {0028-0836, 1476-4687},
  language = {en},
  number = {7726},
  journal = {Nature},
  doi = {10.1038/s41586-018-0567-3},
  author = {Lai, Binbin and Gao, Weiwu and Cui, Kairong and Xie, Wanli and Tang, Qingsong and Jin, Wenfei and Hu, Gangqing and Ni, Bing and Zhao, Keji},
  month = oct,
  year = {2018},
  pages = {281-285},
  file = {/home/bbeltr1/Documents/zotero/storage/IEJ9XPV4/Lai et al. - 2018 - Principles of nucleosome organization revealed by .pdf}
}

@article{nuebler2018,
  title = {Chromatin Organization by an Interplay of Loop Extrusion and Compartmental Segregation},
  volume = {115},
  copyright = {Copyright \textcopyright{} 2018 the Author(s). Published by PNAS.. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).},
  issn = {0027-8424, 1091-6490},
  abstract = {Mammalian chromatin is spatially organized at many scales showing two prominent features in interphase: (i) alternating regions (1\textendash{}10 Mb) of active and inactive chromatin that spatially segregate into different compartments, and (ii) domains ({$<$}1 Mb), that is, regions that preferentially interact internally [topologically associating domains (TADs)] and are central to gene regulation. There is growing evidence that TADs are formed by active extrusion of chromatin loops by cohesin, whereas compartmentalization is established according to local chromatin states. Here, we use polymer simulations to examine how loop extrusion and compartmental segregation work collectively and potentially interfere in shaping global chromosome organization. A model with differential attraction between euchromatin and heterochromatin leads to phase separation and reproduces compartmentalization as observed in Hi-C. Loop extrusion, essential for TAD formation, in turn, interferes with compartmentalization. Our integrated model faithfully reproduces Hi-C data from puzzling experimental observations where altering loop extrusion also led to changes in compartmentalization. Specifically, depletion of chromatin-associated cohesin reduced TADs and revealed finer compartments, while increased processivity of cohesin strengthened large TADs and reduced compartmentalization; and depletion of the TAD boundary protein CTCF weakened TADs while leaving compartments unaffected. We reveal that these experimental perturbations are special cases of a general polymer phenomenon of active mixing by loop extrusion. Our results suggest that chromatin organization on the megabase scale emerges from competition of nonequilibrium active loop extrusion and