text:
Probability Distributions of {{DNA}} End-to-End Distance},
  volume = {95},
  issn = {0031-9007, 1079-7114},
  abstract = {Correlation length exponent \$\textbackslash{}nu\$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length \$s\$ by means of atomic force microscopy (AFM). Linear DNA, up to 48'502 base pairs (bp), was irreversibly deposited from a solution onto silanized mica and imaged in air. Under the adsorption conditions used, the DNA is trapped onto the surface without any two-dimensional equilibration. The measured exponent is \$\textbackslash{}nu = 0.589 \textbackslash{}pm 0.006\$, in agreement with the theoretical 3D value of \$\textbackslash{}nu = 0.5880 \textbackslash{}pm 0.0010\$. The persistence length \$\textbackslash{}ell\_p\$ of DNA was estimated to be 44\$\textbackslash{}pm\$3 nm, in agreement with the literature values. The distribution of the end-to-end distances for a given contour length \$s\$ and the exponents characterizing the distribution were determined for different \$s\$. For \$s\$ smaller or comparable to \$\textbackslash{}ell\_p\$, a delta function like distribution was observed, while for larger \$s\$, a probability distribution of the type \$x\^\{d-1\}x\^g e\^\{-bx\^\textbackslash{}delta\}\$ was observed with \$g=0.33\textbackslash{}pm0.22\$ and \$\textbackslash{}delta=2.58\textbackslash{}pm0.76\$. These values are compared to the theoretical exponents for Self-Avoiding Walk (SAW): namely \$g=\textbackslash{}frac\{\textbackslash{}gamma-1\}\{\textbackslash{}nu\}\$ and \$\textbackslash{}delta=(1-\textbackslash{}nu)\^\{-1\}\$. So for \$d=2\$, \$g\textbackslash{}approx0.44\$ and \$\textbackslash{}delta=4\$, while for \$d=3\$, \$g\textbackslash{}approx0.33\$ and \$\textbackslash{}delta\textbackslash{}approx2.5\$. The derived entropic exponent \$\textbackslash{}gamma\$ is \$\textbackslash{}gamma=1.194\textbackslash{}pm0.129\$. The present data indicate that the DNA behaves on large length scales like a 3 dimensional SAW.},
  number = {15},
  journal = {Physical Review Letters},
  doi = {10.1103/PhysRevLett.95.158105},
  author = {Valle, Francesco and Favre, Melanie and Rios, Paolo De Los and Rosa, Angelo and Dietler, Giovanni},
  month = oct,
  year = {2005},
  keywords = {Condensed Matter - Soft Condensed Matter,Condensed Matter - Statistical Mechanics},
  file = {/home/bbeltr1/Documents/paper-collection/DietlerG/Valle et al_2005_Scaling exponents and probability distributions of DNA end-to-end distance.pdf;/home/bbeltr1/Documents/zotero/storage/6TQMEE2I/0503577.html}
}

@misc{kleinert,
  title = {Pthic15.Pdf},
  author = {Kleinert, H.},
  file = {/home/bbeltr1/Documents/paper-collection/KleinertH/Kleinert_pthic15.pdf}
}

@misc{finch2004,
  title = {Ornstein-Uhlenbeck.Pdf},
  author = {Finch, Steven},
  month = may,
  year = {2004},
  file = {/home/bbeltr1/Documents/paper-collection/FinchS/Finch_2004_ornstein-uhlenbeck.pdf}
}

@article{nuebler2017,
  title = {Chromatin {{Organization}} by an {{Interplay}} of {{Loop Extrusion}} and {{Compartmental Segregation}}},
  copyright = {\textcopyright{} 2017, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), CC BY-NC 4.0, as described at http://creativecommons.org/licenses/by-nc/4.0/},
  abstract = {Mammalian chromatin is organized on length scales ranging from individual nucleosomes to chromosomal territories. At intermediate scales two dominant features emerge in interphase: (i) alternating regions ({$<$}5Mb) of active and inactive chromatin that spatially segregate into different compartments, and (ii) domains ({$<$}1Mb), i.e. regions that preferentially interact internally, which are also termed 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 compartments are established by a phase separation process according to local chromatin states. Here we use polymer simulations to examine how the two processes, loop extrusion and compartmental segregation, work collectively and potentially interfere in shaping global chromosome organization. Our integrated model faithfully reproduces Hi-C data from previously puzzling experimental observations, where targeting of the TAD-forming machinery led to changes in compartmentalization. Specifically, depletion of chromatin-associated cohesin reduced TADs and revealed hidden, finer compartments, while increased processivity of cohesin led to stronger 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. This also predicts that interference with chromatin epigenetic states or nuclear volume would affect compartments but not TADs. Our results suggest that chromatin organization on the megabase scale emerges from competition of non-equilibrium active loop extrusion and epigenetically defined compartment structure.},
  language = {en},
  journal = {bioRxiv},
  doi = {10.1101/196261},
  author = {Nuebler, Johannes and Fudenberg, Geoffrey and Imakaev, Maxim and Abdennur, Nezar and Mirny, Leonid},
  month = oct,
  year = {2017},
  pages = {196261},
  file = {/home/bbeltr1/Documents/paper-collection/Mirny, Leonid/Nuebler et al_2017_Chromatin Organization by an Interplay of Loop Extrusion and Compartmental.pdf;/home/bbeltr1/Documents/paper-collection/MirnyL/Nuebler et al_2017_Chromatin Organization by an Interplay of Loop Extrusion and Compartmental.pdf;/home/bbeltr1/Documents/zotero/storage/5LXULJC8/196261.html;/home/bbeltr1/Documents/zotero/storage/YAGMS64X/196261.html}
}

@article{henikoff2011,
  title = {Epigenome Characterization at Single Base-Pair Resolution},
  volume = {108},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {We have combined standard micrococcal nuclease (MNase) digestion of nuclei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including the eviction of nucleosomes. To characterize DNA-binding features of transcription factors, we plotted the length of each fragment versus its position in the genome, which defined the minimal protected region of each factor. This process led to the precise mapping of protected and exposed regions at and around binding sites, and also determination of the degree to which they are flanked by phased nucleosomes and subnucleosome-sized particles. Our protocol and mapping method provide a general strategy for epigenome characterization, including nucleosome phasing and dynamics, ATP-dependent nucleosome remodelers, and transcription factors, from a single-sequenced sample.},
  language = {en},
  number = {45},
  journal = {PNAS},
  doi = {10.1073/pnas.1110731108},
  author = {Henikoff, Jorja G. and Belsky, Jason A. and Krassovsky, Kristina and MacAlpine, David M. and Henikoff, Steven},
  month = nov,
  year = {2011},
  keywords = {Saccharomyces cerevisiae,transcription factor binding sites,V-plot},
  pages = {18318-18323},
  file = {/home/bbeltr1/Documents/paper-collection/HenikoffS/Henikoff et al_2011_Epigenome characterization at single base-pair resolution.pdf;/home/bbeltr1/Documents/zotero/storage/4VZ8MEL5/18318.html},
  pmid = {22025700}
}

@article{ozonov2013,
  title = {Nucleosome {{Free Regions}} in {{Yeast Promoters Result}} from {{Competitive Binding}} of {{Transcription Factors That Interact}} with {{Chromatin Modifiers}}},
  volume = {9},
  issn = {1553-7358},
  abstract = {Because DNA packaging in nucleosomes modulates its accessibility to transcription factors (TFs), unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation. Although there is evidence that intrinsic sequence specificity contributes to nucleosome positioning, the extent to which other factors contribute to nucleosome positioning is currently highly debated. Here we obtained both in vivo and in vitro reference maps of positions that are either consistently covered or free of nucleosomes across multiple experimental data-sets in Saccharomyces cerevisiae. We then systematically quantified the contribution of TF binding to nucleosome positiong using a rigorous statistical mechanics model in which TFs compete with nucleosomes for binding DNA. Our results reconcile previous seemingly conflicting results on the determinants of nucleosome positioning and provide a quantitative explanation for the difference between in vivo and in vitro positioning. On a genome-wide scale, nucleosome positioning is dominated by the phasing of nucleosome arrays over gene bodies, and their positioning is mainly determined by the intrinsic sequence preferences of nucleosomes. In contrast, larger nucleosome free regions in promoters, which likely have a much more significant impact on gene expression, are determined mainly by TF binding. Interestingly, of the 158 yeast TFs included in our modeling, we find that only 10\textendash{}20 significantly contribute to inducing nucleosome-free regions, and these TFs are highly enriched for having direct interations with chromatin remodelers. Together our results imply that nucleosome free regions in yeast promoters results from the binding of a specific class of TFs that recruit chromatin remodelers.},
  language = {en},
  number = {8},
  journal = {PLOS Computational Biology},
  doi = {10.1371/journal.pcbi.1003181},
  author = {Ozonov, Evgeniy A. and van Nimwegen, Erik},
  month = aug,
  year = {2013},
  keywords = {Chromatin,Histones,Saccharomyces cerevisiae,Nucleosomes,DNA sequence analysis,Nucleosome mapping,Genomic signal processing,Sequence analysis},
  pages = {e1003181},
  file = {/home/bbeltr1/Documents/paper-collection/NimwegenE/Ozonov_Nimwegen_2013_Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of.pdf;/home/bbeltr1/Documents/zotero/storage/E7EZP5G7/article.html}
}

@article{yadon2010,
  title = {Chromatin {{Remodeling}} around {{Nucleosome}}-{{Free Regions Leads}} to {{Repression}} of {{Noncoding RNA Transcription}}},
  volume = {30},
  issn = {0270-7306, 1098-5549},
  abstract = {Nucleosome-free regions (NFRs) at the 5{${'}$} and 3{${'}$} ends of genes are general sites of transcription initiation for mRNA and noncoding RNA (ncRNA). The presence of NFRs within transcriptional regulatory regions and the conserved location of transcription start sites at NFRs strongly suggest that the regulation of NFRs profoundly affects transcription initiation. To date, multiple factors are known to facilitate transcription initiation by positively regulating the formation and/or size of NFRs in vivo. However, mechanisms to repress transcription by negatively regulating the size of NFRs have not been identified. We identified four distinct classes of NFRs located at the 5{${'}$} and 3{${'}$} ends of genes, within open reading frames (ORFs), and far from ORFs. The ATP-dependent chromatin-remodeling enzyme Isw2 was found enriched at all classes of NFRs. Analysis of RNA levels also demonstrated Isw2 is required to repress ncRNA transcription from many of these NFRs. Thus, by the systematic annotation of NFRs across the yeast genome and analysis of ncRNA transcription, we established, for the first time, a mechanism by which NFR size is negatively regulated to repress ncRNA transcription from NFRs. Finally, we provide evidence suggesting that one biological consequence of repression of ncRNA, by Isw2 or by the exosome, is prevention of transcriptional interference of mRNA.},
  language = {en},
  number = {21},
  journal = {Mol. Cell. Biol.},
  doi = {10.1128/MCB.00602-10},
  author = {Yadon, Adam N. and de Mark, Daniel Van and Basom, Ryan and Delrow, Jeffrey and Whitehouse, Iestyn and Tsukiyama, Toshio},
  month = jan,
  year = {2010},
  pages = {5110-5122},
  file = {/home/bbeltr1/Documents/paper-collection/TsukiyamaT/Yadon et al_2010_Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of.pdf;/home/bbeltr1/Documents/zotero/storage/EJ3DZSSG/5110.html},
  pmid = {20805356}
}

@article{koslover2010,
  title = {Local {{Geometry}} and {{Elasticity}} in {{Compact Chromatin Structure}}},
  volume = {99},
  issn = {0006-3495},
  abstract = {The hierarchical packaging of DNA into chromatin within a eukaryotic nucleus plays a pivotal role in both the accessibility of genomic information and the dynamics of replication. Our work addresses the role of nanoscale physical and geometric properties in determining the structure of chromatin at the mesoscale level. We study the packaging of DNA in chromatin fibers by optimization of regular helical morphologies, considering the elasticity of the linker DNA as well as steric packing of the nucleosomes and linkers. Our model predicts a broad range of preferred helix structures for a fixed linker length of DNA; changing the linker length alters the predicted ensemble. Specifically, we find that the twist registry of the nucleosomes, as set by the internucleosome repeat length, determines the preferred angle between the nucleosomes and the fiber axis. For~moderate to long linker lengths, we find a number of energetically comparable configurations with different nucleosome-nucleosome interaction patterns, indicating a potential role for kinetic trapping in chromatin fiber formation. Our results highlight the key role played by DNA elasticity and local geometry in regulating the hierarchical packaging of the genome.},
  number = {12},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2010.10.024},
  author = {Koslover, Elena F. and Fuller, Colin J. and Straight, Aaron F. and Spakowitz, Andrew J.},
  month = dec,
  year = {2010},
  pages = {3941-3950},
  file = {/home/bbeltr1/Documents/paper-collection/Spakowitz, Andrew J./Koslover et al_2010_Local Geometry and Elasticity in Compact Chromatin Structure.pdf;/home/bbeltr1/Documents/paper-collection/SpakowitzA/Koslover et al_2010_Local Geometry and Elasticity in Compact Chromatin Structure.pdf;/home/bbeltr1/Documents/zotero/storage/T9FI8NLJ/S0006349510013123.html}
}

@article{segal2006,
  title = {A Genomic Code for Nucleosome Positioning},
  volume = {442},
  copyright = {2006 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome\textendash{}DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain {$\sim$}50\% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.},
  language = {en},
  number = {7104},
  journal = {Nature},
  doi = {10.1038/nature04979},
  author = {Segal, Eran and {Fondufe-Mittendorf}, Yvonne and Chen, Lingyi and Th\aa{}str\"om, AnnChristine and Field, Yair and Moore, Irene K. and Wang, Ji-Ping Z. and Widom, Jonathan},
  month = aug,
  year = {2006},
  pages = {772-778},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Segal et al_2006_A genomic code for nucleosome positioning.pdf;/home/bbeltr1/Documents/zotero/storage/IDSAXMZR/nature04979.html}
}

@article{yuan2012,
  title = {Dense {{Chromatin Activates Polycomb Repressive Complex}} 2 to {{Regulate H3 Lysine}} 27 {{Methylation}}},
  volume = {337},
  copyright = {Copyright \textcopyright{} 2012, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Polycomb repressive complex 2 (PRC2)\textendash{}mediated histone H3 lysine 27 (H3K27) methylation is vital for Polycomb gene silencing, a classic epigenetic phenomenon that maintains transcriptional silencing throughout cell divisions. We report that PRC2 activity is regulated by the density of its substrate nucleosome arrays. Neighboring nucleosomes activate the PRC2 complex with a fragment of their H3 histones (Ala31 to Arg42). We also identified mutations on PRC2 subunit Su(z)12, which impair its binding and response to the activating peptide and its ability in establishing H3K27 trimethylation levels in vivo. In mouse embryonic stem cells, local chromatin compaction occurs before the formation of trimethylated H3K27 upon transcription cessation of the retinoic acid\textendash{}regulated gene CYP26a1. We propose that PRC2 can sense the chromatin environment to exert its role in the maintenance of transcriptional states.
The density and compaction state of chromatin directly regulates the activity of a transcription repressor protein complex.
The density and compaction state of chromatin directly regulates the activity of a transcription repressor protein complex.},
  language = {en},
  number = {6097},
  journal = {Science},
  doi = {10.1126/science.1225237},
  author = {Yuan, Wen and Wu, Tong and Fu, Hang and Dai, Chao and Wu, Hui and Liu, Nan and Li, Xiang and Xu, Mo and Zhang, Zhuqiang and Niu, Tianhui and Han, Zhifu and Chai, Jijie and Zhou, Xianghong Jasmine and Gao, Shaorong and Zhu, Bing},
  month = aug,
  year = {2012},
  pages = {971-975},
  file = {/home/bbeltr1/Documents/paper-collection/ZhuB/Yuan et al_2012_Dense Chromatin Activates Polycomb Repressive Complex 2 to Regulate H3 Lysine.pdf;/home/bbeltr1/Documents/zotero/storage/MER268Q8/971.html},
  pmid = {22923582}
}

@article{ou2017,
  title = {{{ChromEMT}}: {{Visualizing 3D}} Chromatin Structure and Compaction in Interphase and Mitotic Cells},
  volume = {357},
  copyright = {Copyright \textcopyright{} 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org.stanford.idm.oclc.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
  issn = {0036-8075, 1095-9203},
  shorttitle = {{{ChromEMT}}},
  abstract = {A close-up view inside the nucleus
The nuclei of human cells contain 2 meters of genomic DNA. How does it all fit? Compaction starts with the DNA wrapping around histone octamers to form nucleosomes, but it is unclear how these further compress into mitotic chromosomes. Ou et al. describe a DNA-labeling method that allows them to visualize chromatin organization in human cells (see the Perspective by Larson and Misteli). They show that chromatin forms flexible chains with diameters between 5 and 24 nm. In mitotic chromosomes, chains bend back on themselves to pack at high density, whereas during interphase, the chromatin chains are more extended.
Science, this issue p. eaag0025; see also p. 354
Structured Abstract
INTRODUCTIONIn human cells, 2 m of DNA are compacted in the nucleus through assembly with histones and other proteins into chromatin structures, megabase three-dimensional (3D) domains, and chromosomes that determine the activity and inheritance of our genomes. The long-standing textbook model is that primary 11-nm DNA\textendash{}core nucleosome polymers assemble into 30-nm fibers that further fold into 120-nm chromonema, 300- to 700-nm chromatids, and, ultimately, mitotic chromosomes. Further extrapolating from this model, silent heterochromatin is generally depicted as 30- and 120-nm fibers. The hierarchical folding model is based on the in vitro structures formed by purified DNA and nucleosomes and on chromatin fibers observed in permeabilized cells from which other components had been extracted. Unfortunately, there has been no method that enables DNA and chromatin ultrastructure to be visualized and reconstructed unambiguously through large 3D volumes of intact cells. Thus, a remaining question is, what are the local and global 3D chromatin structures in the nucleus that determine the compaction and function of the human genome in interphase cells and mitotic chromosomes?
RATIONALETo visualize and reconstruct chromatin ultrastructure and 3D organization across multiple scales in the nucleus, we developed ChromEMT, which combines electron microscopy tomography (EMT) with a labeling method (ChromEM) that selectivity enhances the contrast of DNA. This technique exploits a fluorescent dye that binds to DNA, and upon excitation, catalyzes the deposition of diaminobenzidine polymers on the surface, enabling chromatin to be visualized with OsO4 in EM. Advances in multitilt EMT allow us to reveal the chromatin ultrastructure and 3D packing of DNA in both human interphase cells and mitotic chromosomes.
RESULTSChromEMT enables the ultrastructure of individual chromatin chains, heterochromatin domains, and mitotic chromosomes to be resolved in serial slices and their 3D organization to be visualized as a continuum through large nuclear volumes in situ. ChromEMT stains and detects 30-nm fibers in nuclei purified from hypotonically lysed chicken erythrocytes and treated with MgCl2. However, we do not observe higher-order fibers in human interphase and mitotic cells in situ. Instead, we show that DNA and nucleosomes assemble into disordered chains that have diameters between 5 and 24 nm, with different particle arrangements, densities, and structural conformations. Chromatin has a more extended curvilinear structure in interphase nuclei and collapses into compact loops and interacting arrays in mitotic chromosome scaffolds. To analyze chromatin packing, we create 3D grid maps of chromatin volume concentrations (CVCs) in situ. We find that interphase nuclei have subvolumes with CVCs ranging from 12 to 52\% and distinct spatial distribution patterns, whereas mitotic chromosome subvolumes have CVCs {$>$}40\%.
CONCLUSIONWe conclude that chromatin is a flexible and disordered 5- to 24-nm-diameter granular chain that is packed together at different concentration densities in interphase nuclei and mitotic chromosomes. The overall primary structure of chromatin polymers does not change in mitotic chromosomes, which helps to explain the rapid dynamics of chromatin condensation and how epigenetic interactions and structures can be inherited through cell division. In contrast to rigid fibers that have longer fixed persistence lengths, disordered 5- to 24-nm-diameter chromatin chains are flexible and can bend at various lengths to achieve different levels of compaction and high packing densities. The diversity of chromatin structures is exciting and provides a structural basis for how different combinations of DNA sequences, interactions, linker lengths, histone variants, and modifications can be integrated to fine-tune the function of genomic DNA in the nucleus to specify cell fate. Our data also suggest that the assembly of 3D domains in the nucleus with different chromatin concentrations, rather than higher-order folding, determines the global accessibility and activity of DNA. {$<$}img class="fragment-image" aria-describedby="F1-caption" src="https://d2ufo47lrtsv5s.cloudfront.net/content/sci/357/6349/eaag0025/F1.medium.gif"/{$>$} Download high-res image Open in new tab Download Powerpoint ChromEMT reveals the in situ chromatin ultrastructure, 3D packing, and organization of DNA.EMT sample volume-DNA-nucleosome chains are black. Chromatin is a structurally disordered 5- to 24-nm granular chain that is packed together at different 3D CVC densities in human interphase nuclei and mitotic chromosomes (red, high density; yellow, medium density; blue, low density).
The chromatin structure of DNA determines genome compaction and activity in the nucleus. On the basis of in vitro structures and electron microscopy (EM) studies, the hierarchical model is that 11-nanometer DNA-nucleosome polymers fold into 30- and subsequently into 120- and 300- to 700-nanometer fibers and mitotic chromosomes. To visualize chromatin in situ, we identified a fluorescent dye that stains DNA with an osmiophilic polymer and selectively enhances its contrast in EM. Using ChromEMT (ChromEM tomography), we reveal the ultrastructure and three-dimensional (3D) organization of individual chromatin polymers, megabase domains, and mitotic chromosomes. We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis. Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.
A new technique reveals that chromatin is a disordered 5- to 24-nanometer chain that is packed at different concentration densities according to the cell cycle.
A new technique reveals that chromatin is a disordered 5- to 24-nanometer chain that is packed at different concentration densities according to the cell cycle.},
  language = {en},
  number = {6349},
  journal = {Science},
  doi = {10.1126/science.aag0025},
  author = {Ou, Horng D. and Phan, S\'ebastien and Deerinck, Thomas J. and Thor, Andrea and Ellisman, Mark H. and O'Shea, Clodagh C.},
  month = jul,
  year = {2017},
  pages = {eaag0025},
  file = {/home/bbeltr1/Documents/paper-collection/O’SheaC/Ou et al_2017_ChromEMT.pdf;/home/bbeltr1/Documents/zotero/storage/2BITBR9X/eaag0025.html},
  pmid = {28751582}
}

@article{voong2016,
  title = {Insights into {{Nucleosome Organization}} in {{Mouse Embryonic Stem Cells}} through {{Chemical Mapping}}},
  volume = {167},
  issn = {00928674},
  abstract = {Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Furthermore, we provide evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Taken together, we establish an accurate method for defining the nucleosome landscape and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.},
  language = {en},
  number = {6},
  journal = {Cell},
  doi = {10.1016/j.cell.2016.10.049},
  author = {Voong, Lilien N. and Xi, Liqun and Sebeson, Amy C. and Xiong, Bin and Wang, Ji-Ping and Wang, Xiaozhong},
  month = dec,
  year = {2016},
  pages = {1555-1570.e15},
  file = {/home/bbeltr1/Documents/paper-collection/WangX/Voong et al_2016_Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through.pdf}
}

@article{brogaard2012,
  title = {A Map of Nucleosome Positions in Yeast at Base-Pair Resolution},
  volume = {486},
  copyright = {2012 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function. However, existing methods for mapping nucleosomes do not provide the necessary single-base-pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centres on the basis of chemical modification of engineered histones. The resulting map locates nucleosome positions genome-wide in unprecedented detail and accuracy. It shows new aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing and the higher-order structure of the chromatin fibre.},
  language = {en},
  number = {7404},
  journal = {Nature},
  doi = {10.1038/nature11142},
  author = {Brogaard, Kristin and Xi, Liqun and Wang, Ji-Ping and Widom, Jonathan},
  month = jun,
  year = {2012},
  pages = {496-501},
  file = {/home/bbeltr1/Documents/paper-collection/WidomJ/Brogaard et al_2012_A map of nucleosome positions in yeast at base-pair resolution.pdf;/home/bbeltr1/Documents/zotero/storage/RTG9UVF6/nature11142.html}
}

@article{zhou2016,
  title = {A Computational Approach to Map Nucleosome Positions and Alternative Chromatin States with Base Pair Resolution},
  volume = {5},
  copyright = {\textcopyright{} 2016 Zhou et al.. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.},
  issn = {2050-084X},
  abstract = {Computational analysis of MNase-seq data reveals that alternatively positioned nucleosomes are prevalent in both yeast and human cells and create significant heterogeneity within cell populations.},
  language = {en},
  journal = {eLife Sciences},
  doi = {10.7554/eLife.16970},
  author = {Zhou, Xu and Blocker, Alexander W. and Airoldi, Edoardo M. and O'Shea, Erin K.},
  month = sep,
  year = {2016},
  pages = {e16970},
  file = {/home/bbeltr1/Documents/paper-collection/O'SheaE/Zhou et al_2016_A computational approach to map nucleosome positions and alternative chromatin.pdf;/home/bbeltr1/Documents/zotero/storage/2GJLVEFJ/16970.html}
}

@article{moyle-heyrman2013,
  title = {Chemical Map of {{Schizosaccharomyces}} Pombe Reveals Species-Specific Features in Nucleosome Positioning},
  volume = {110},
  copyright = {\textcopyright{}  . Freely available online through the PNAS open access option.},
  issn = {0027-8424, 1091-6490},
  abstract = {Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by {$\sim$}4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at {$\pm$}20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10- to 30-bp region from the dyad. S. pombe does not have a well-defined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.},
  language = {en},
  number = {50},
  journal = {PNAS},
  doi = {10.1073/pnas.1315809110},
  author = {{Moyle-Heyrman}, Georgette and Zaichuk, Tetiana and Xi, Liqun and Zhang, Quanwei and Uhlenbeck, Olke C. and Holmgren, Robert and Widom, Jonathan and Wang, Ji-Ping},
  month = dec,
  year = {2013},
  keywords = {heterochromatin,chromatin structure,gene regulation,sequence-specificity},
  pages = {20158-20163},
  file = {/home/bbeltr1/Documents/paper-collection/WangJ/Moyle-Heyrman et al_2013_Chemical map of Schizosaccharomyces pombe reveals species-specific features in.pdf;/home/bbeltr1/Documents/zotero/storage/E6BYP4ZC/20158.html},
  pmid = {24277842}
}

@article{sazer2018,
  title = {The Biology and Polymer Physics Underlying Large-Scale Chromosome Organization},
  volume = {19},
  issn = {13989219},
  language = {en},
  number = {2},
  journal = {Traffic},
  doi = {10.1111/tra.12539},
  author = {Sazer, Shelley and Schiessel, Helmut},
  month = feb,
  year = {2018},
  pages = {87-104},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Sazer_Schiessel_2018_The biology and polymer physics underlying large-scale chromosome organization.pdf}
}

@article{buning2010,
  series = {Special Section "{{DNA}} and {{Chromosomes}}: {{Physical}} and {{Biological Approaches}}"},
  title = {Single-Pair {{FRET}} Experiments on Nucleosome Conformational Dynamics},
  volume = {92},
  issn = {0300-9084},
  abstract = {Nucleosomes, the basic units of DNA compaction in eukaryotes, play a crucial role in regulating all processes involving DNA, including transcription, replication and repair. Nucleosomes modulate DNA accessibility through conformational dynamics like DNA breathing \textendash{} the transient unwrapping of DNA from the nucleosome, repositioning of nucleosomes along the DNA, or partial dissociation. Single molecule techniques, in particular single-pair Fluorescence Resonance Energy Transfer (spFRET), have resolved such conformational dynamics in individual nucleosomes. Here, we review the results of FRET experiments on single nucleosomes, including fluorescence correlation spectroscopy (FCS), confocal single molecule microscopy on freely diffusing nucleosomes and widefield total internal reflection fluorescence (TIRF) microscopy on immobilized nucleosomes. The combined spFRET studies on single nucleosomes reveal a very dynamic organization of the nucleosome, that has been shown to be modulated by post-translational modifications of the histones and by DNA sequence.},
  number = {12},
  journal = {Biochimie},
  doi = {10.1016/j.biochi.2010.08.010},
  author = {Buning, Ruth and {van Noort}, John},
  month = dec,
  year = {2010},
  keywords = {Nucleosome,Conformational dynamics,DNA breathing,Single-pair FRET},
  pages = {1729-1740},
  file = {/home/bbeltr1/Documents/paper-collection/van NoortJ/Buning_van Noort_2010_Single-pair FRET experiments on nucleosome conformational dynamics.pdf;/home/bbeltr1/Documents/zotero/storage/C2N8HVHD/S0300908410002968.html}
}

@article{culkin2017,
  title = {The Role of {{DNA}} Sequence in Nucleosome Breathing},
  volume = {40},
  issn = {1292-8941, 1292-895X},
  abstract = {Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.},
  language = {en},
  number = {11},
  journal = {The European Physical Journal E},
  doi = {10.1140/epje/i2017-11596-2},
  author = {Culkin, Jamie and {de Bruin}, Lennart and Tompitak, Marco and Phillips, Rob and Schiessel, Helmut},
  month = nov,
  year = {2017},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Culkin et al_2017_The role of DNA sequence in nucleosome breathing.pdf}
}

@article{hughes2014a,
  title = {Mechanisms {{Underlying Nucleosome Positioning In Vivo}}},
  volume = {43},
  abstract = {It has been some 40 years since repeating subunits in eukaryotic chromatin, initially termed ``nu bodies,'' were described. Four decades of study have characterized the structural organization of the nucleosome, from multiple crystal structures of individual nucleosomes to genome-wide maps of nucleosome positions in scores of organisms. Nucleosome positioning can impact essentially all DNA-templated processes, making an appreciation of the forces shaping the nucleosomal landscape in eukaryotes key to fully understanding genomic regulation. Here, we review the factors impacting nucleosome positioning and the ways that nucleosomes can control the output of the genome.},
  number = {1},
  journal = {Annual Review of Biophysics},
  doi = {10.1146/annurev-biophys-051013-023114},
  author = {Hughes, Amanda L. and Rando, Oliver J.},
  year = {2014},
  pages = {41-63},
  file = {/home/bbeltr1/Documents/paper-collection/Rando, Oliver J./Hughes_Rando_2014_Mechanisms Underlying Nucleosome Positioning In Vivo.pdf},
  pmid = {24702039}
}

@article{eslami-mossallam2016,
  title = {Multiplexing {{Genetic}} and {{Nucleosome Positioning Codes}}: {{A Computational Approach}}},
  volume = {11},
  issn = {1932-6203},
  shorttitle = {Multiplexing {{Genetic}} and {{Nucleosome Positioning Codes}}},
  abstract = {Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.},
  language = {en},
  number = {6},
  journal = {PLOS ONE},
  doi = {10.1371/journal.pone.0156905},
  author = {{Eslami-Mossallam}, Behrouz and Schram, Raoul D. and Tompitak, Marco and van Noort, John and Schiessel, Helmut},
  month = jun,
  year = {2016},
  keywords = {Saccharomyces cerevisiae,Nucleosomes,Sequence motif analysis,Nucleosome mapping,Crystal structure,Monte Carlo method,Multiplexing,Phosphates},
  pages = {e0156905},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/Eslami-Mossallam et al_2016_Multiplexing Genetic and Nucleosome Positioning Codes.pdf;/home/bbeltr1/Documents/zotero/storage/X9D7KB5N/article.html}
}

@article{ngo2015,
  title = {Asymmetric {{Unwrapping}} of {{Nucleosomes}} under {{Tension Directed}} by {{DNA Local Flexibility}}},
  volume = {160},
  issn = {0092-8674, 1097-4172},
  abstract = {Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.},
  language = {English},
  number = {6},
  journal = {Cell},
  doi = {10.1016/j.cell.2015.02.001},
  author = {Ngo, Thuy T. M. and Zhang, Qiucen and Zhou, Ruobo and Yodh, Jaya G. and Ha, Taekjip},
  month = mar,
  year = {2015},
  pages = {1135-1144},
  file = {/home/bbeltr1/Documents/paper-collection/HaT/Ngo et al_2015_Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local.pdf;/home/bbeltr1/Documents/zotero/storage/QCTT9CBU/S0092-8674(15)00134-8.html},
  pmid = {25768909}
}

@article{drillon2016,
  title = {Evidence of Selection for an Accessible Nucleosomal Array in Human},
  volume = {17},
  issn = {1471-2164},
  abstract = {Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human ``master'' replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes.},
  journal = {BMC Genomics},
  doi = {10.1186/s12864-016-2880-2},
  author = {Drillon, Gu\'enola and Audit, Benjamin and Argoul, Fran{\c c}oise and Arneodo, Alain},
  month = jul,
  year = {2016},
  keywords = {GC content,Human genome,Mutation rates,Nucleosome depleted regions,Nucleosome ordering,Sequence evolution},
  pages = {526},
  file = {/home/bbeltr1/Documents/paper-collection/ArneodoA/Drillon et al_2016_Evidence of selection for an accessible nucleosomal array in human.pdf;/home/bbeltr1/Documents/zotero/storage/QIUJYMNA/s12864-016-2880-2.html}
}

@article{debruin2016,
  title = {Why {{Do Nucleosomes Unwrap Asymmetrically}}?},
  volume = {120},
  issn = {1520-6106},
  abstract = {Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic DNA and play a critical role in chromosomal processes, ranging from gene regulation, recombination, and replication to chromosome condensation. For more than a decade, micromanipulation experiments where nucleosomes are put under tension, as well as the theoretical interpretations of these experiments, have deepened our understanding of the stability and dynamics of nucleosomes. Here we give a theoretical explanation for a surprising new experimental finding: nucleosomes wrapped onto the 601 positioning sequence (the sequence used in most laboratories) respond highly asymmetrically to external forces by always unwrapping from the same end. Using a computational nucleosome model, we show that this asymmetry can be explained by differences in the DNA mechanics of two very short stretches on the wrapped DNA portion. Our finding suggests that the physical properties of nucleosomes, here the response to forces, can be tuned locally by the choice of the underlying base-pair sequence. This leads to a new view of nucleosomes: a physically highly varied set of DNA\textendash{}protein complexes whose properties can be tuned on evolutionary time scales to their specific function in the genomic context.},
  number = {26},
  journal = {J. Phys. Chem. B},
  doi = {10.1021/acs.jpcb.6b00391},
  author = {{de Bruin}, Lennart and Tompitak, Marco and {Eslami-Mossallam}, Behrouz and Schiessel, Helmut},
  month = jul,
  year = {2016},
  pages = {5855-5863},
  file = {/home/bbeltr1/Documents/paper-collection/SchiesselH/de Bruin et al_2016_Why Do Nucleosomes Unwrap Asymmetrically.pdf;/home/bbeltr1/Documents/zotero/storage/GB7ZUM6G/acs.jpcb.html}
}

@article{hall2009,
  title = {High-Resolution Dynamic Mapping of Histone-{{DNA}} Interactions in a Nucleosome},
  volume = {16},
  copyright = {2009 Nature Publishing Group},
  issn = {1545-9985},
  abstract = {The nature of the nucleosomal barrier that regulates access to the underlying DNA during many cellular processes is not fully understood. Here we present a detailed map of histone-DNA interactions along the DNA sequence to near base pair accuracy by mechanically unzipping single molecules of DNA, each containing a single nucleosome. This interaction map revealed a distinct {$\sim$}5-bp periodicity that was enveloped by three broad regions of strong interactions, with the strongest occurring at the dyad and the other two about {$\pm$}40-bp from the dyad. Unzipping up to the dyad allowed recovery of a canonical nucleosome upon relaxation of the DNA, but unzipping beyond the dyad resulted in removal of the histone octamer from its initial DNA sequence. These findings have important implications for how RNA polymerase and other DNA-based enzymes may gain access to DNA associated with a nucleosome.},
  language = {en},
  number = {2},
  journal = {Nature Structural \& Molecular Biology},
  doi = {10.1038/nsmb.1526},
  author = {Hall, Michael A. and Shundrovsky, Alla and Bai, Lu and Fulbright, Robert M. and Lis, John T. and Wang, Michelle D.},
  month = feb,
  year = {2009},
  pages = {124-129},
  file = {/home/bbeltr1/Documents/paper-collection/WangM/Hall et al_2009_High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.pdf;/home/bbeltr1/Documents/zotero/storage/5DBDL9WF/nsmb.html}
}

@article{bondarenko2006,
  title = {Nucleosomes {{Can Form}} a {{Polar Barrier}} to {{Transcript Elongation}} by {{RNA Polymerase II}}},
  volume = {24},
  issn = {1097-2765},
  abstract = {Summary
Nucleosomes uniquely positioned on high-affinity DNA sequences present a polar barrier to transcription by human and yeast RNA polymerase II (Pol II). In one transcriptional orientation, these nucleosomes provide a strong, factor- and salt-insensitive barrier at~the entry into the H3/H4 tetramer that can be recapitulated without H2A/H2B dimers. The same nucleosomes transcribed in the opposite orientation form a weaker, more diffuse barrier that is largely relieved by higher salt, TFIIS, or FACT. Barrier properties are therefore dictated by both the local nucleosome structure (influenced by the strength of the histone-DNA interactions) and the location of the high-affinity DNA region within the nucleosome. Pol II transcribes DNA sequences at~the entry into the tetramer much less efficiently than the same sequences located distal to the nucleosome dyad. Thus, entry into the tetramer by Pol II facilitates further transcription, perhaps due to partial unfolding of the tetramer from DNA.},
  number = {3},
  journal = {Molecular Cell},
  doi = {10.1016/j.molcel.2006.09.009},
  author = {Bondarenko, Vladimir A. and Steele, Louise M. and \'Ujv\'ari, Andrea and Gaykalova, Daria A. and Kulaeva, Olga I. and Polikanov, Yury S. and Luse, Donal S. and Studitsky, Vasily M.},
  month = nov,
  year = {2006},
  keywords = {DNA},
  pages = {469-479},
  file = {/home/bbeltr1/Documents/paper-collection/StuditskyV/Bondarenko et al_2006_Nucleosomes Can Form a Polar Barrier to Transcript Elongation by RNA Polymerase.pdf;/home/bbeltr1/Documents/zotero/storage/ADU9QYKF/S109727650600637X.html}
}

@article{watson1953,
  title = {Molecular {{Structure}} of {{Nucleic Acids}}: {{A Structure}} for {{Deoxyribose Nucleic Acid}}},
  volume = {171},
  copyright = {1953 Nature Publishing Group},
  issn = {1476-4687},
  shorttitle = {Molecular {{Structure}} of {{Nucleic Acids}}},
  abstract = {Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid},
  language = {en},
  number = {4356},
  journal = {Nature},
  doi = {10.1038/171737a0},
  author = {Watson, J. D. and Crick, F. H. C.},
  month = apr,
  year = {1953},
  pages = {737-738},
  file = {/home/bbeltr1/Documents/paper-collection/CrickF/Watson_Crick_1953_Molecular Structure of Nucleic Acids.pdf;/home/bbeltr1/Documents/zotero/storage/BYMXK8ZY/171737a0.html}
}

@article{strom2017,
  title = {Phase Separation Drives Heterochromatin Domain Formation},
  volume = {547},
  copyright = {2017 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability1, and silencing of transposon and gene expression2. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA3. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments4. We show that Drosophila HP1a protein undergoes liquid\textendash{}liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.},
  language = {en},
  number = {7662},
  journal = {Nature},
  doi = {10.1038/nature22989},
  author = {Strom, Amy R. and Emelyanov, Alexander V. and Mir, Mustafa and Fyodorov, Dmitry V. and Darzacq, Xavier and Karpen, Gary H.},
  month = jul,
  year = {2017},
  pages = {241-245},
  file = {/home/bbeltr1/Documents/paper-collection/KarpenG/Strom et al_2017_Phase separation drives heterochromatin domain formation.pdf;/home/bbeltr1/Documents/zotero/storage/U5ETJ5WZ/nature22989.html}
}

@article{perez-rico2017,
  title = {Comparative Analyses of Super-Enhancers Reveal Conserved Elements in Vertebrate Genomes},
  volume = {27},
  issn = {1088-9051, 1549-5469},
  language = {en},
  number = {2},
  journal = {Genome Research},
  doi = {10.1101/gr.203679.115},
  author = {{P\'erez-Rico}, Yuvia A. and Boeva, Valentina and Mallory, Allison C. and Bitetti, Angelo and Majello, Sara and Barillot, Emmanuel and Shkumatava, Alena},
  month = feb,
  year = {2017},
  pages = {259-268},
  file = {/home/bbeltr1/Documents/paper-collection/ShkumatavaA/Pérez-Rico et al_2017_Comparative analyses of super-enhancers reveal conserved elements in vertebrate.pdf}
}

@article{buenrostro2013,
  title = {Transposition of Native Chromatin for Fast and Sensitive Epigenomic Profiling of Open Chromatin, {{DNA}}-Binding Proteins and Nucleosome Position},
  volume = {10},
  copyright = {2013 Nature Publishing Group},
  issn = {1548-7105},
  abstract = {We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500\textendash{}50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual's epigenome on a timescale compatible with clinical decision-making.},
  language = {en},
  number = {12},
  journal = {Nature Methods},
  doi = {10.1038/nmeth.2688},
  author = {Buenrostro, Jason D. and Giresi, Paul G. and Zaba, Lisa C. and Chang, Howard Y. and Greenleaf, William J.},
  month = dec,
  year = {2013},
  pages = {1213-1218},
  file = {/home/bbeltr1/Documents/paper-collection/GreenleafW/Buenrostro et al_2013_Transposition of native chromatin for fast and sensitive epigenomic profiling.pdf;/home/bbeltr1/Documents/zotero/storage/HF83B94H/nmeth.html}
}

@article{li2014,
  title = {Chromatin {{Interaction Analysis}} with {{Paired}}-{{End Tag}} ({{ChIA}}-{{PET}}) Sequencing Technology and Application},
  volume = {15},
  issn = {1471-2164},
  abstract = {Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.},
  number = {12},
  journal = {BMC Genomics},
  doi = {10.1186/1471-2164-15-S12-S11},
  author = {Li, Guoliang and Cai, Liuyang and Chang, Huidan and Hong, Ping and Zhou, Qiangwei and Kulakova, Ekaterina V. and Kolchanov, Nikolay A. and Ruan, Yijun},
  month = dec,
  year = {2014},
  keywords = {Chromatin Interaction,Distal Regulatory Element,Luciferase Reporter Gene Assay,Nonlinear Optimization Model,Transcription Regulation},
  pages = {S11},
  file = {/home/bbeltr1/Documents/paper-collection/RuanY/Li et al_2014_Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing.pdf;/home/bbeltr1/Documents/zotero/storage/XY54TFUP/1471-2164-15-S12-S11.html}
}

@article{fullwood2009,
  title = {Next-Generation {{DNA}} Sequencing of Paired-End Tags ({{PET}}) for Transcriptome and Genome Analyses},
  volume = {19},
  issn = {1088-9051, 1549-5469},
  abstract = {Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will require improvements in the throughputs and costs of DNA sequencing. Next-generation sequencing platforms have impressively low costs and high throughputs but are limited by short read lengths. An immediate and widely recognized solution to this critical limitation is the paired-end tag (PET) sequencing for various applications, collectively called the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing. The PET sequences can be accurately mapped to the reference genome, thus demarcating the genomic boundaries of PET-represented DNA fragments and revealing the identities of the target DNA elements. PET protocols have been developed for the analyses of transcriptomes, transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures. The exclusive advantage of the PET technology is its ability to uncover linkages between the two ends of DNA fragments. Using this unique feature, unconventional fusion transcripts, genome structural variations, and even molecular interactions between distant genomic elements can be unraveled by PET analysis. Extensive use of PET data could lead to efficient assembly of individual human genomes, transcriptomes, and interactomes, enabling new biological and clinical insights. With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead.},
  language = {en},
  number = {4},
  journal = {Genome Res.},
  doi = {10.1101/gr.074906.107},
  author = {Fullwood, Melissa J. and Wei, Chia-Lin and Liu, Edison T. and Ruan, Yijun},
  month = jan,
  year = {2009},
  pages = {521-532},
  file = {/home/bbeltr1/Documents/paper-collection/RuanY/Fullwood et al_2009_Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and.pdf;/home/bbeltr1/Documents/zotero/storage/A7GQTVXF/521.html},
  pmid = {19339662}
}

@article{belton2012,
  series = {{{3D}} Chromatin Architecture},
  title = {Hi\textendash{{C}}: {{A}} Comprehensive Technique to Capture the Conformation of Genomes},
  volume = {58},
  issn = {1046-2023},
  shorttitle = {Hi\textendash{{C}}},
  abstract = {We describe a method, Hi\textendash{}C, to comprehensively detect chromatin interactions in the mammalian nucleus. This method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. The ligation products contain the information of not only where they originated from in the genomic sequence but also where they reside, physically, in the 3D organization of the genome. In Hi\textendash{}C, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. The compatibility of Hi\textendash{}C with next generation sequencing platforms makes it possible to detect chromatin interactions on an unprecedented scale. This advance gives Hi\textendash{}C the power to both explore the biophysical properties of chromatin as well as the implications of chromatin structure for the biological functions of the nucleus. A massively parallel survey of chromatin interaction provides the previously missing dimension of spatial context to other genomic studies. This spatial context will provide a new perspective to studies of chromatin and its role in genome regulation in normal conditions and in disease.},
  number = {3},
  journal = {Methods},
  doi = {10.1016/j.ymeth.2012.05.001},
  author = {Belton, Jon-Matthew and McCord, Rachel Patton and Gibcus, Johan Harmen and Naumova, Natalia and Zhan, Ye and Dekker, Job},
  month = nov,
  year = {2012},
  keywords = {Genomics,Chromosome conformation,Nucleus},
  pages = {268-276},
  file = {/home/bbeltr1/Documents/paper-collection/DekkerJ/Belton et al_2012_Hi–C.pdf;/home/bbeltr1/Documents/zotero/storage/SNB97V7H/S1046202312001168.html}
}

@article{zhang2018,
  title = {Enhancing {{Hi}}-{{C}} Data Resolution with Deep Convolutional Neural Network {{HiCPlus}}},
  volume = {9},
  copyright = {2018 The Author(s)},
  issn = {2041-1723},
  abstract = {Despite its popularity for measuring the spatial organization of mammalian genomes, the resolution of most Hi-C datasets is coarse due to sequencing cost. Here, Zhang et al. develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data.},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-018-03113-2},
  author = {Zhang, Yan and An, Lin and Xu, Jie and Zhang, Bo and Zheng, W. Jim and Hu, Ming and Tang, Jijun and Yue, Feng},
  month = feb,
  year = {2018},
  pages = {750},
  file = {/home/bbeltr1/Documents/paper-collection/YueF/Zhang et al_2018_Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus.pdf;/home/bbeltr1/Documents/zotero/storage/G94GGNF2/s41467-018-03113-2.html}
}

@article{ramani2017,
  title = {Massively Multiplex Single-Cell {{Hi}}-{{C}}},
  volume = {14},
  copyright = {2017 Nature Publishing Group},
  issn = {1548-7105},
  abstract = {We present single-cell combinatorial indexed Hi-C (sciHi-C), a method that applies combinatorial cellular indexing to chromosome conformation capture. In this proof of concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells. We use sciHi-C data to separate cells by karyotypic and cell-cycle state differences and identify cell-to-cell heterogeneity in mammalian chromosomal conformation. Our results demonstrate that combinatorial indexing is a generalizable strategy for single-cell genomics.},
  language = {en},
  number = {3},
  journal = {Nature Methods},
  doi = {10.1038/nmeth.4155},
  author = {Ramani, Vijay and Deng, Xinxian and Qiu, Ruolan and Gunderson, Kevin L. and Steemers, Frank J. and Disteche, Christine M. and Noble, William S. and Duan, Zhijun and Shendure, Jay},
  month = mar,
  year = {2017},
  pages = {263-266},
  file = {/home/bbeltr1/Documents/paper-collection/ShendureJ/Ramani et al_2017_Massively multiplex single-cell Hi-C.pdf;/home/bbeltr1/Documents/zotero/storage/WDBT3S5T/nmeth.html}
}

@article{stevens2017,
  title = {{{3D}} Structures of Individual Mammalian Genomes Studied by Single-Cell {{Hi}}-{{C}}},
  volume = {544},
  copyright = {2017 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated. The structures of individual topological-associated domains and loops vary substantially from cell to cell. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes.},
  language = {en},
  number = {7648},
  journal = {Nature},
  doi = {10.1038/nature21429},
  author = {Stevens, Tim J. and Lando, David and Basu, Srinjan and Atkinson, Liam P. and Cao, Yang and Lee, Steven F. and Leeb, Martin and Wohlfahrt, Kai J. and Boucher, Wayne and {O'Shaughnessy-Kirwan}, Aoife and Cramard, Julie and Faure, Andre J. and Ralser, Meryem and Blanco, Enrique and Morey, Lluis and Sans\'o, Miriam and Palayret, Matthieu G. S. and Lehner, Ben and Croce, Luciano Di and Wutz, Anton and Hendrich, Brian and Klenerman, Dave and Laue, Ernest D.},
  month = apr,
  year = {2017},
  pages = {59-64},
  file = {/home/bbeltr1/Documents/paper-collection/LaueE/Stevens et al_2017_3D structures of individual mammalian genomes studied by single-cell Hi-C.pdf;/home/bbeltr1/Documents/zotero/storage/UEURMBAV/nature21429.html}
}

@article{nagano2017,
  title = {Cell-Cycle Dynamics of Chromosomal Organization at Single-Cell Resolution},
  volume = {547},
  copyright = {2017 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Chromosomes in proliferating metazoan cells undergo marked structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures that facilitate chromosome segregation, and decondensed interphase structures that accommodate transcription, gene silencing and DNA replication. Here we use single-cell Hi-C (high-resolution chromosome conformation capture) analysis to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological-associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with a build-up of compartments and a reduction in TAD insulation, while loops are generally stable from G1 to S and G2 phase. Whole-genome three-dimensional structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data therefore allow re-interpretation of chromosome conformation maps through the prism of the cell cycle.},
  language = {en},
  number = {7661},
  journal = {Nature},
  doi = {10.1038/nature23001},
  author = {Nagano, Takashi and Lubling, Yaniv and V\'arnai, Csilla and Dudley, Carmel and Leung, Wing and Baran, Yael and Cohen, Netta Mendelson and Wingett, Steven and Fraser, Peter and Tanay, Amos},
  month = jul,
  year = {2017},
  pages = {61-67},
  file = {/home/bbeltr1/Documents/paper-collection/TanayA/Nagano et al_2017_Cell-cycle dynamics of chromosomal organization at single-cell resolution.pdf;/home/bbeltr1/Documents/zotero/storage/VZ9SXMM9/nature23001.html}
}

@article{chen2017,
  title = {Direct Visualization of Transcriptional Activation by Physical Enhancer-Promoter Proximity},
  abstract = {A long-standing question in metazoan gene regulation is how remote enhancers communicate with their target promoters over long distances. Combining genome editing and quantitative live imaging we simultaneously visualize physical enhancer-promoter communication and transcription in Drosophila embryos. Enhancers regulating pair rule stripes of even-skipped expression activate transcription of a reporter gene over a distance of 150 kb. We show in individual cells that activation only occurs after the enhancer comes into close proximity with its regulatory target and that upon dissociation transcription ceases almost immediately. We further observe distinct topological conformations of the eve locus, depending on the spatial identity of the activating stripe enhancer. In addition, long-range activation results in transcriptional competition at the endogenous eve locus, causing corresponding developmental defects. Overall, we demonstrate that sustained physical proximity and enhancer-promoter engagement are required for enhancer action, and we provide a path to probe the implications of long-range regulation on cellular fates.},
  language = {en},
  doi = {10.1101/099523},
  author = {Chen, Hongtao and Fujioka, Miki and Jaynes, James B and Gregor, Thomas},
  month = jan,
  year = {2017},
  file = {/home/bbeltr1/Documents/paper-collection/GregorT/Chen et al_2017_Direct visualization of transcriptional activation by physical.pdf}
}

@article{phanstiel2017,
  title = {Static and {{Dynamic DNA Loops}} Form {{AP}}-1-{{Bound Activation Hubs}} during {{Macrophage Development}}},
  volume = {67},
  issn = {1097-2765},
  language = {English},
  number = {6},
  journal = {Molecular Cell},
  doi = {10.1016/j.molcel.2017.08.006},
  author = {Phanstiel, Douglas H. and Bortle, Kevin Van and Spacek, Damek and Hess, Gaelen T. and Shamim, Muhammad Saad and Machol, Ido and Love, Michael I. and Aiden, Erez Lieberman and Bassik, Michael C. and Snyder, Michael P.},
  month = sep,
  year = {2017},
  keywords = {AP-1,cellular differentiation,CTCF,DNA looping,Hi-C,TAD},
  pages = {1037-1048.e6},
  file = {/home/bbeltr1/Documents/paper-collection/SnyderM/Phanstiel et al_2017_Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage.pdf;/home/bbeltr1/Documents/zotero/storage/RFQNQXWV/S1097-2765(17)30603-2.html},
  pmid = {28890333}
}

@article{acemel2017,
  title = {Topologically Associated Domains: A Successful Scaffold for the Evolution of Gene Regulation in Animals: {{Topologically}} Associated Domains},
  volume = {6},
  issn = {17597684},
  shorttitle = {Topologically Associated Domains},
  language = {en},
  number = {3},
  journal = {Wiley Interdisciplinary Reviews: Developmental Biology},
  doi = {10.1002/wdev.265},
  author = {Acemel, Rafael D. and Maeso, Ignacio and {G\'omez-Skarmeta}, Jos\'e Luis},
  month = may,
  year = {2017},
  pages = {e265},
  file = {/home/bbeltr1/Documents/paper-collection/Gómez-SkarmetaJ/Acemel et al_2017_Topologically associated domains.pdf}
}

@article{dultz2018,
  title = {Quantitative Imaging of Chromatin Decompaction in Living Cells},
  issn = {1059-1524},
  abstract = {Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as ``open'', but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high-resolution microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by {$>$}100 nm. This decompaction is linked to active transcription but is not sensitive to the histone deacetylase inhibitor trichostatin A or to deletion of the histone acetyl transferase Gcn5. By contrast, the deletion of SNF2 (encoding the ATPase of the SWI/SNF chromatin remodeling complex) or the deactivation of the histone chaperone complex FACT lead to a strongly reduced decompaction without significant effects on transcriptional induction. Our findings are consistent with nucleosome remodeling and eviction activities being major contributors to chromatin reorganization during transcription but also suggest that transcription can occur in the absence of detectable decompaction.},
  journal = {MBoC},
  doi = {10.1091/mbc.E17-11-0648},
  author = {Dultz, Elisa and Mancini, Roberta and Polles, Guido and Vallotton, Pascal and Alber, Frank and Weis, Karsten and {Cohen-Fix}, Orna},
  month = may,
  year = {2018},
  pages = {mbc.E17-11-0648},
  file = {/home/bbeltr1/Documents/paper-collection/Cohen-FixO/Dultz et al_2018_Quantitative imaging of chromatin decompaction in living cells.pdf;/home/bbeltr1/Documents/zotero/storage/SEAJCLKZ/mbc.html}
}

@article{huang2018,
  title = {Dissecting Super-Enhancer Hierarchy Based on Chromatin Interactions},
  volume = {9},
  copyright = {2018 The Author(s)},
  issn = {2041-1723},
  abstract = {Super-enhancers (SEs) are important regulatory elements for gene expression, but their intrinsic properties remain poorly understood. Here the authors analyse Hi-C and ChIP-seq data and find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers.},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-018-03279-9},
  author = {Huang, Jialiang and Li, Kailong and Cai, Wenqing and Liu, Xin and Zhang, Yuannyu and Orkin, Stuart H. and Xu, Jian and Yuan, Guo-Cheng},
  month = mar,
  year = {2018},
  pages = {943},
  file = {/home/bbeltr1/Documents/paper-collection/YuanG/Huang et al_2018_Dissecting super-enhancer hierarchy based on chromatin interactions.pdf;/home/bbeltr1/Documents/zotero/storage/FNXCDA42/s41467-018-03279-9.html}
}

@article{flyamer2017,
  title = {Single-Nucleus {{Hi}}-{{C}} Reveals Unique Chromatin Reorganization at Oocyte-to-Zygote Transition},
  volume = {544},
  copyright = {2017 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism1. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods2,3,4,5 are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method2. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin `ground state' could potentially provide insights into reprogramming cells to a state of totipotency.},
  language = {en},
  number = {7648},
  journal = {Nature},
  doi = {10.1038/nature21711},
  author = {Flyamer, Ilya M. and Gassler, Johanna and Imakaev, Maxim and Brand\~ao, Hugo B. and Ulianov, Sergey V. and Abdennur, Nezar and Razin, Sergey V. and Mirny, Leonid A. and {Tachibana-Konwalski}, Kiku\"e},
  month = apr,
  year = {2017},
  pages = {110-114},
  file = {/home/bbeltr1/Documents/paper-collection/Tachibana-KonwalskiK/Flyamer et al_2017_Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote.pdf;/home/bbeltr1/Documents/zotero/storage/HJ2XSEER/nature21711.html}
}

@article{kubo2017,
  title = {Preservation of {{Chromatin Organization}} after {{Acute Loss}} of {{CTCF}} in {{Mouse Embryonic Stem Cells}}},
  copyright = {\textcopyright{} 2017, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
  abstract = {The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of the impact of loss of CTCF on genome architecture has been difficult due to its essential role in cell proliferation and early embryogenesis. Here, using auxin-inducible degron techniques to acutely deplete CTCF in mouse embryonic stem cells, we show that cell growth is severely slowed yet chromatin organization remains largely intact after loss of CTCF. Depletion of CTCF reduces interactions between chromatin loop anchors, diminishes occupancy of cohesin complex genome-wide, and slightly weakens topologically associating domain (TAD) structure, but the active and inactive chromatin compartments are maintained and the vast majority of TAD boundaries persist. Furthermore, transcriptional regulation and histone marks associated with enhancers are broadly unchanged upon CTCF depletion. Our results suggest CTCF-independent mechanisms in maintenance of chromatin organization.},
  language = {en},
  journal = {bioRxiv},
  doi = {10.1101/118737},
  author = {Kubo, Naoki and Ishii, Haruhiko and Gorkin, David and Meitinger, Franz and Xiong, Xiong and Fang, Rongxin and Liu, Tristin and Ye, Zhen and Li, Bin and Dixon, Jesse and Desai, Arshad and Zhao, Huimin and Ren, Bing},
  month = mar,
  year = {2017},
  pages = {118737},
  file = {/home/bbeltr1/Documents/paper-collection/RenB/Kubo et al_2017_Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse.pdf;/home/bbeltr1/Documents/zotero/storage/Y39FKR5V/118737.html}
}

@article{doyle2014,
  title = {Chromatin {{Loops}} as {{Allosteric Modulators}} of {{Enhancer}}-{{Promoter Interactions}}},
  volume = {10},
  issn = {1553-7358},
  abstract = {The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.},
  language = {en},
  number = {10},
  journal = {PLOS Computational Biology},
  doi = {10.1371/journal.pcbi.1003867},
  author = {Doyle, Boryana and Fudenberg, Geoffrey and Imakaev, Maxim and Mirny, Leonid A.},
  month = oct,
  year = {2014},
  keywords = {Gene expression,Polymers,Simulation and modeling,Chromatin,Allosteric regulation,Enhancer elements,Fibers,Stiffness},
  pages = {e1003867},
  file = {/home/bbeltr1/Documents/paper-collection/MirnyL/Doyle et al_2014_Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions.pdf;/home/bbeltr1/Documents/zotero/storage/8UBKDX3T/article.html}
}

@article{stack1977,
  title = {Visualization of Interphase Chromosomes},
  volume = {26},
  issn = {0021-9533},
  abstract = {Using a modified Giemsa-banding technique we have observed what appear to be chromosomes during interphase in nuclei from Allium cepa root tips and Chinese hamster cells (CHO line). During telophase through G1 chromosomes progressively uncoil and decondense. During S chromosomes are comparatively decondensed, but some segments have structure similar to chromosomes in G1 and G2. During G2 the chromosomes progressively recondense and coil in apparent preparation for prophase. Although specific structural modifications of chromosomes occur in G1, Sand G2 nuclei, chromosomes appear never to decondense to the point that they lose their 3-dimensional integrity, but remain in distinct domains throughout interphase.},
  language = {eng},
  journal = {J. Cell. Sci.},
  author = {Stack, S. M. and Brown, D. B. and Dewey, W. C.},
  month = aug,
  year = {1977},
  keywords = {Animals,Cell Cycle,Chromosomes,Azure Stains,Cell Line,Cell Nucleus,Cricetinae,Cricetulus,Interphase,Plants},
  pages = {281-299},
  file = {/home/bbeltr1/Documents/paper-collection/DeweyW/Stack et al_1977_Visualization of interphase chromosomes.pdf},
  pmid = {562895}
}

@article{zorn1979,
  title = {Unscheduled {{DNA}} Synthesis after Partial {{UV}} Irradiation of the Cell Nucleus. {{Distribution}} in Interphase and Metaphase},
  volume = {124},
  issn = {0014-4827},
  language = {eng},
  number = {1},
  journal = {Exp. Cell Res.},
  author = {Zorn, C. and Cremer, C. and Cremer, T. and Zimmer, J.},
  month = nov,
  year = {1979},
  keywords = {Animals,Cells; Cultured,Chromosomes,DNA,Cell Nucleus,Cricetinae,Interphase,DNA Repair,Metaphase,Ultraviolet Rays},
  pages = {111-119},
  file = {/home/bbeltr1/Documents/paper-collection/ZimmerJ/Zorn et al_1979_Unscheduled DNA synthesis after partial UV irradiation of the cell nucleus.pdf},
  pmid = {499376}
}

@article{cremer1993,
  title = {Role of {{Chromosome Territories}} in the {{Functional Compartmentalization}} of the {{Cell Nucleus}}},
  volume = {58},
  issn = {0091-7451, 1943-4456},
  abstract = {Detailed reviews describing work presented at the annual Cold Spring Harbor Symposia on Quantitative Biology},
  language = {en},
  journal = {Cold Spring Harb Symp Quant Biol},
  doi = {10.1101/SQB.1993.058.01.085},
  author = {Cremer, T. and Kurz, A. and Zirbel, R. and Dietzel, S. and Rinke, B. and Schr\"ock, E. and Speicher, M. R. and Mathieu, U. and Jauch, A. and Emmerich, P. and Scherthan, H. and Ried, T. and Cremer, C. and Lichter, P.},
  month = jan,
  year = {1993},
  pages = {777-792},
  file = {/home/bbeltr1/Documents/paper-collection/LichterP/Cremer et al_1993_Role of Chromosome Territories in the Functional Compartmentalization of the.pdf;/home/bbeltr1/Documents/zotero/storage/S6BDM6CC/777.html},
  pmid = {7525149}
}

@article{rabl1885,
  title = {\"Uber {{Zelltheilung}}},
  volume = {10},
  journal = {Morphologisches Jahrbuch},
  author = {Rabl, Carl},
  year = {1885}
}

@article{boveri1909,
  title = {Die {{Blastomerenkerne}} von {{Ascaris}} Megalocephala Und Die {{Theorie}} Der {{Chromosomenindividualit\"at}}},
  volume = {3},
  author = {Boveri, Theodor},
  year = {1909},
  booktitle = {Arch. Zellforch.}
}

@article{cremer2010,
  title = {Chromosome {{Territories}}},
  volume = {2},
  issn = {1943-0264},
  abstract = {Chromosome territories (CTs) constitute a major feature of nuclear architecture. In a brief statement, the possible contribution of nuclear architecture studies to the field of epigenomics is considered, followed by a historical account of the CT concept and the final compelling experimental evidence of a territorial organization of chromosomes in all eukaryotes studied to date. Present knowledge of nonrandom CT arrangements, of the internal CT architecture, and of structural interactions with other CTs is provided as well as the dynamics of CT arrangements during cell cycle and postmitotic terminal differentiation. The article concludes with a discussion of open questions and new experimental strategies to answer them., Chromosomes occupy distinct territories in the cell nucleus. The major components of chromosome territories are chromatin domains separated by an interchromatin compartment.},
  number = {3},
  journal = {Cold Spring Harb Perspect Biol},
  doi = {10.1101/cshperspect.a003889},
  author = {Cremer, Thomas and Cremer, Marion},
  month = mar,
  year = {2010},
  file = {/home/bbeltr1/Documents/paper-collection/CremerM/Cremer_Cremer_2010_Chromosome Territories.pdf},
  pmid = {20300217},
  pmcid = {PMC2829961}
}

@article{barutcu2018,
  title = {A {{TAD}} Boundary Is Preserved upon Deletion of the {{CTCF}}-Rich {{Firre}} Locus},
  volume = {9},
  copyright = {2018 The Author(s)},
  issn = {2041-1723},
  abstract = {Although CTCF binding has been implicated in the formation of topologically associated domains (TADs) the mechanisms folding the genome into TADs are not fully understood. Here the authors investigate the TAD boundary on lncRNA locus Firre, which has \textasciitilde\,15 CTCF binding sites, and its organization.},
  language = {en},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-018-03614-0},
  author = {Barutcu, A. Rasim and Maass, Philipp G. and Lewandowski, Jordan P. and Weiner, Catherine L. and Rinn, John L.},
  month = apr,
  year = {2018},
  pages = {1444},
  file = {/home/bbeltr1/Documents/paper-collection/RinnJ/Barutcu et al_2018_A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.pdf;/home/bbeltr1/Documents/zotero/storage/3QSTKLQU/s41467-018-03614-0.html}
}

@article{weintraub2017,
  title = {{{YY1 Is}} a {{Structural Regulator}} of {{Enhancer}}-{{Promoter Loops}}},
  volume = {171},
  issn = {0092-8674},
  abstract = {Summary
There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not employ this structural protein. Here, we show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements and forms dimers that facilitate the interaction of these DNA elements. Deletion of YY1 binding sites or depletion of YY1 protein disrupts enhancer-promoter looping and gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.},
  number = {7},
  journal = {Cell},
  doi = {10.1016/j.cell.2017.11.008},
  author = {Weintraub, Abraham S. and Li, Charles H. and Zamudio, Alicia V. and Sigova, Alla A. and Hannett, Nancy M. and Day, Daniel S. and Abraham, Brian J. and Cohen, Malkiel A. and Nabet, Behnam and Buckley, Dennis L. and Guo, Yang Eric and Hnisz, Denes and Jaenisch, Rudolf and Bradner, James E. and Gray, Nathanael S. and Young, Richard A.},
  month = dec,
  year = {2017},
  keywords = {chromosome structure,gene regulation,enhancers,promoters},
  pages = {1573-1588.e28},
  file = {/home/bbeltr1/Documents/paper-collection/YoungR/Weintraub et al_2017_YY1 Is a Structural Regulator of Enhancer-Promoter Loops.pdf;/home/bbeltr1/Documents/zotero/storage/LR6GMI45/S009286741731317X.html}
}

@article{jin2013,
  title = {A High-Resolution Map of the Three-Dimensional Chromatin Interactome in Human Cells},
  volume = {503},
  copyright = {2013 Nature Publishing Group},
  issn = {1476-4687},
  abstract = {A large number of cis-regulatory sequences have been annotated in the human genome1,2, but defining their target genes remains a challenge3. One strategy is to identify the long-range looping interactions at these elements with the use of chromosome conformation capture (3C)-based techniques4. However, previous studies lack either the resolution or coverage to permit a whole-genome, unbiased view of chromatin interactions. Here we report a comprehensive chromatin interaction map generated in human fibroblasts using a genome-wide 3C analysis method (Hi-C)5. We determined over one million long-range chromatin interactions at 5\textendash{}10-kb resolution, and uncovered general principles of chromatin organization at different types of genomic features. We also characterized the dynamics of promoter\textendash{}enhancer contacts after TNF-{$\alpha$} signalling in these cells. Unexpectedly, we found that TNF-{$\alpha$}-responsive enhancers are already in contact with their target promoters before signalling. Such pre-existing chromatin looping, which also exists in other cell types with different extracellular signalling, is a strong predictor of gene induction. Our observations suggest that the three-dimensional chromatin landscape, once established in a particular cell type, is relatively stable and could influence the selection or activation of target genes by a ubiquitous transcription activator in a cell-specific manner.},
  language = {en},
  number = {7475},
  journal = {Nature},
  doi = {10.1038/nature12644},
  author = {Jin, Fulai and Li, Yan and Dixon, Jesse R. and Selvaraj, Siddarth and Ye, Zhen and Lee, Ah Young and Yen, Chia-An and Schmitt, Anthony D. and Espinoza, Celso A. and Ren, Bing},
  month = nov,
  year = {2013},
  pages = {290-294},
  file = {/home/bbeltr1/Documents/paper-collection/RenB/Jin et al_2013_A high-resolution map of the three-dimensional chromatin interactome in human.pdf;/home/bbeltr1/Documents/zotero/storage/PJASCFXZ/nature12644.html}
}

@article{polikanov2007,
  title = {Probability of the {{Site Juxtaposition Determines}} the {{Rate}} of {{Protein}}-{{Mediated DNA Looping}}},
  volume = {93},
  issn = {0006-3495},
  abstract = {Numerous biological processes are regulated by DNA elements that communicate with their targets over a distance via formation of protein-bridged DNA loops. One of the first questions arising in studies of DNA looping is whether the rate of loop formation is limited by diffusion of the DNA sites. We addressed this question by comparing the in vitro measured rates of transcription initiation in the NtrC-glnAp2 enhancer-dependent transcription initiation system with predictions of two different theoretical models. The promoter and enhancer were in a 7.6-kb plasmid and separated by 2.5 kb. The measurements were performed for different values of the plasmid superhelix density, from 0 to -0.07. Earlier theoretical analysis, based on the Monte Carlo simulation of DNA conformations, showed that if the rate of loop formation is determined by the equilibrium probability of juxtaposition of the DNA sites, the rate should be {$\sim$}100 times higher in supercoiled than in relaxed DNA. On the other hand, Brownian dynamics simulation showed that if the rate of loop formation is limited by the site diffusion, it should be nearly independent of DNA supercoiling. We found that efficiency of the transcription initiation increases by nearly two orders of magnitude as a result of the corresponding increase of the template supercoiling. This clearly shows that the rate of bridging in the enhancer-promoter system is not limited by diffusion of the DNA sites to one another. We argue that this conclusion derived for the specific system is likely to be valid for the great majority of biological processes involving protein-mediated DNA looping.},
  number = {8},
  journal = {Biophys J},
  doi = {10.1529/biophysj.107.111245},
  author = {Polikanov, Yury S. and Bondarenko, Vladimir A. and Tchernaenko, Vladimir and Jiang, Yong I. and Lutter, Leonard C. and Vologodskii, Alexander and Studitsky, Vasily M.},
  month = oct,
  year = {2007},
  pages = {2726-2731},
  file = {/home/bbeltr1/Documents/paper-collection/StuditskyV/Polikanov et al_2007_Probability of the Site Juxtaposition Determines the Rate of Protein-Mediated.pdf},
  pmid = {17573434},
  pmcid = {PMC1989718}
}

@article{grigoryev2018,
  title = {Chromatin {{Higher}}-{{Order Folding}}: {{A Perspective}} with {{Linker DNA Angles}}},
  volume = {114},
  issn = {0006-3495},
  shorttitle = {Chromatin {{Higher}}-{{Order Folding}}},
  language = {English},
  number = {10},
  journal = {Biophysical Journal},
  doi = {10.1016/j.bpj.2018.03.009},
  author = {Grigoryev, Sergei A.},
  month = may,
  year = {2018},
  pages = {2290-2297},
  file = {/home/bbeltr1/Documents/paper-collection/GrigoryevS/Grigoryev_2018_Chromatin Higher-Order Folding.pdf;/home/bbeltr1/Documents/zotero/storage/BW5FR9YD/S0006-3495(18)30346-1.html},
  pmid = {29628212}
}

@article{collepardo-guevara2014,
  title = {Chromatin Fiber Polymorphism Triggered by Variations of {{DNA}} Linker Lengths},
  volume = {111},
  issn = {0027-8424, 1091-6490},
  abstract = {Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin's diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.},
  language = {en},
  number = {22},
  journal = {PNAS},
  doi = {10.1073/pnas.1315872111},
  author = {{Collepardo-Guevara}, Rosana and Schlick, Tamar},
  month = jun,
  year = {2014},
  keywords = {chromatin bending and looping,chromatin polymorphism,coarse-grained modeling,nonuniform NRL},
  pages = {8061-8066},
  file = {/home/bbeltr1/Documents/paper-collection/SchlickT/Collepardo-Guevara_Schlick_2014_Chromatin fiber polymorphism triggered by variations of DNA linker lengths.pdf;/home/bbeltr1/Documents/zotero/storage/GFEIQV4I/8061.html},
  pmid = {24847063}
}

@article{grigoryev1981,
  title = {The Dependence of the Linking Number of a Circular Minichromosome upon the Shape and the Orientation of Its Nucleosomes},
  volume = {130},
  issn = {00145793},
  language = {en},
  number = {1},
  journal = {FEBS Letters},
  doi = {10.1016/0014-5793(81)80661-8},
  author = {Grigoryev, Sergei A. and Ioffe, Lev B.},
  month = jul,
  year = {1981},
  pages = {43-46},
  file = {/home/bbeltr1/Documents/paper-collection/IoffeL/Grigoryev_Ioffe_1981_The dependence of the linking number of a circular minichromosome upon the.pdf}
}

@article{schiessel2001,
  title = {{{DNA}} Folding: Structural and Mechanical Properties of the Two-Angle Model for Chromatin.},
  volume = {80},
  issn = {0006-3495},
  shorttitle = {{{DNA}} Folding},
  abstract = {We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N. Whitaker. 1993. Proc. Natl. Acad. Sci. USA. 90:9021-9025) that describes the chromatin fiber geometry in terms of the entry-exit angle of the nucleosomal DNA and the rotational setting of the neighboring nucleosomes with respect to each other. We analytically explore the different structures that arise from this building principle, and demonstrate that the geometry with the highest density is close to the one found in native chromatin fibers under physiological conditions. On the basis of this model we calculate mechanical properties of the fiber under stretching. We obtain expressions for the stress-strain characteristics that show good agreement with the results of recent stretching experiments (Cui, Y., and C. Bustamante. 2000. Proc. Natl. Acad. Sci. USA. 97:127-132) and computer simulations (Katritch, V., C. Bustamante, and W. K. Olson. 2000. J. Mol. Biol. 295:29-40), and which provide simple physical insights into correlations between the structural and elastic properties of chromatin.},
  number = {4},
  journal = {Biophys J},
  author = {Schiessel, H and Gelbart, W M and Bruinsma, R},
  month = apr,
  year = {2001},
  pages = {1940-1956},
  file = {/home/bbeltr1/Documents/paper-collection/BruinsmaR/Schiessel et al_2001_DNA folding.pdf},
  pmid = {11259307},
  pmcid = {PMC1301383}
}

@article{langowski2007,
  series = {Membrane {{Lipid Microdomains}}: {{Roles}} in {{Signalling}} and {{Disease}} and {{3D Chromatin}}},
  title = {Computational Modeling of the Chromatin Fiber},
  volume = {18},
  issn = {1084-9521},
  abstract = {The packing of the genomic DNA in the living cell is essential for its biological function. While individual aspects of the genome architecture, such as DNA and nucleosome structure or the arrangement of chromosome territories are well studied, much information is missing for a unified description of cellular DNA at all its structural levels. Computer modeling can contribute to such a description. We present here some typical approaches to models of the chromatin fiber, including different amounts of detail in the description of the local nucleosome structure. The main results from our simulations are that the physical properties of the chromatin fiber can be well described by a simplified model consisting of cylinder-like nucleosomes connected by flexible DNA segments, with a geometry determined by the bending and twisting angles between nucleosomes. Randomness in the local geometry \textendash{} such as random absence of linker histone H1 \textendash{} leads to a dramatic increase in the chromatin fiber flexibility. Furthermore, we show that chromatin is much more flexible to bending than to stretching, and that the structure of the chromatin fiber favors the formation of sharp bends.},
  number = {5},
  journal = {Seminars in Cell \& Developmental Biology},
  doi = {10.1016/j.semcdb.2007.08.011},
  author = {Langowski, J\"org and Heermann, Dieter W.},
  month = oct,
  year = {2007},
  keywords = {Nucleosomes,Chromatin fiber,Linker histone,Modeling},
  pages = {659-667},
  file = {/home/bbeltr1/Documents/paper-collection/HeermannD/Langowski_Heermann_2007_Computational modeling of the chromatin fiber.pdf;/home/bbeltr1/Documents/zotero/storage/9DZ2IRT6/S1084952107001267.html}
}

@article{katritch2000,
  title = {Pulling Chromatin Fibers: Computer Simulations of Direct Physical {{micromanipulations11Edited}} by {{I}}. {{Tinoco}}},
  volume = {295},
  issn = {0022-2836},
  shorttitle = {Pulling Chromatin Fibers},
  abstract = {A low-resolution molecular model, which combines the known mechanical properties of protein-free DNA with the accumulating picture of chromatosome structure, has been developed to account for the stretching of single chromatin fibers by an imposed external force. Force-extension characteristics of sets of chains accumulated by Monte Carlo sampling are consistent with recently observed findings in the non-destructive regime ({$<$}20 pN imposed force), where the structure of the chromatosome remains intact. The correspondence between simulation and the relaxation phase of the experiment limits the equilibrium entry-exit angle of linker DNA on the chromatosome to W=50({$\pm$}10)\textdegree{} and the effective DNA linker length to Leff=40({$\pm$}5) bp. The computed force-extension characteristics are relatively insensitive to other parameters of the model, precluding their accurate estimation. The introduction of an attractive potential between closely spaced nucleosomes reproduces the added initial resistance of single fibers to extension at high salt conditions. The consideration of elastic linkers also improves the fitting of assorted classical measurements of unstressed chromatin structure in solution. The overall picture of chromatin that emerges is an irregular, fluctuating, three-dimensional, zig-zag structure with intact, mechanically stable chromatosome units and deformable linkers. The modeled fiber undergoes large-scale configurational rearrangements without significant perturbation of the constituent chromatosome beads, collapsing into a highly condensed form in response to small ({$<$}2kT) inter-nucleosomal attractions.},
  number = {1},
  journal = {Journal of Molecular Biology},
  doi = {10.1006/jmbi.1999.3021},
  author = {Katritch, Vsevolod and Bustamante, Carlos and Olson, Wilma K.},
  month = jan,
  year = {2000},
  keywords = {chromatin fiber,Monte Carlo simulations,single-fiber stretching},
  pages = {29-40},
  file = {/home/bbeltr1/Documents/paper-collection/OlsonW/Katritch et al_2000_Pulling chromatin fibers.pdf;/home/bbeltr1/Documents/zotero/storage/72RIMCG4/S0022283699930218.html}
}

@article{smith1996,
  title = {Overstretching {{B}}-{{DNA}}: {{The Elastic Response}} of {{Individual Double}}-{{Stranded}} and {{Single}}-{{Stranded DNA Molecules}}},
  volume = {271},
  copyright = {\textcopyright{} 1996 American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  shorttitle = {Overstretching {{B}}-{{DNA}}},
  abstract = {Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of {$\sim$}65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70\% longer than B-form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.},
  language = {en},
  number = {5250},
  journal = {Science},
  doi = {10.1126/science.271.5250.795},
  author = {Smith, Steven B. and Cui, Yujia and Bustamante, Carlos},
  month = feb,
  year = {1996},
  pages = {795-799},
  file = {/home/bbeltr1/Documents/paper-collection/BustamanteC/Smith et al_1996_Overstretching B-DNA.pdf;/home/bbeltr1/Documents/zotero/storage/FUU3W97H/795.html},
  pmid = {8628994}
}

@article{cui2000,
  title = {Pulling a Single Chromatin Fiber Reveals the Forces That Maintain Its Higher-Order Structure},
  volume = {97},
  copyright = {Copyright \textcopyright{} 2000, The National Academy of Sciences},
  issn = {0027-8424, 1091-6490},
  abstract = {Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of {$\approx$}5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40\textendash{}150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of {$\approx$}2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between ``open'' and ``closed'' states because of thermal fluctuations.},
  language = {en},
  number = {1},
  journal = {PNAS},
  doi = {10.1073/pnas.97.1.127},
  author = {Cui, Yujia and Bustamante, Carlos},
  month = jan,
  year = {2000},
  pages = {127-132},
  file = {/home/bbeltr1/Documents/paper-collection/BustamanteC/Cui_Bustamante_2000_Pulling a single chromatin fiber reveals the forces that maintain its.pdf;/home/bbeltr1/Documents/zotero/storage/IM5KVKWU/127.html},
  pmid = {10618382}
}

@article{beard2001,
  title = {Modeling Salt-Mediated Electrostatics of Macromolecules: The Discrete Surface Charge Optimization Algorithm and Its Application to the Nucleosome},
  volume = {58},
  issn = {0006-3525},
  shorttitle = {Modeling Salt-Mediated Electrostatics of Macromolecules},
  abstract = {Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-H\"uckel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-H\"uckel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels.},
  language = {eng},
  number = {1},
  journal = {Biopolymers},
  doi = {10.1002/1097-0282(200101)58:1<106::AID-BIP100>3.0.CO;2-\#},
  author = {Beard, D. A. and Schlick, T.},
  month = jan,
  year = {2001},
  keywords = {Algorithms,Chromatin,Nucleosomes,DNA,Models; Molecular,Models; Structural,Nucleic Acid Conformation,Nuclear Proteins,Poisson Distribution,Protein Conformation,Static Electricity},
  pages = {106-115},
  file = {/home/bbeltr1/Documents/paper-collection/SchlickT/Beard_Schlick_2001_Modeling salt-mediated electrostatics of macromolecules.pdf},
  pmid = {11072233}
}

@article{zhang2003,
  title = {{Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm}},
  volume = {24},
  copyright = {Copyright \textcopyright{} 2003 Wiley Periodicals, Inc.},
  issn = {1096-987X},
  abstract = {Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-H\"uckel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle ({$>$}12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a {$\sim$}5.5\% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level. \textcopyright{} 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2063\textendash{}2074, 2003},
  language = {de},
  number = {16},
  journal = {Journal of Computational Chemistry},
  doi = {10.1002/jcc.10337},
  author = {Zhang, Qing and Beard, Daniel A. and Schlick, Tamar},
  month = sep,
  year = {2003},
  keywords = {Debye-Hückel approximation,discrete surface charges,electric field refinement,electrostatic potential refinement,electrostatics,nonlinear Poisson-Boltzmann equation,nucleosome core particle},
  pages = {2063-2074},
  file = {/home/bbeltr1/Documents/zotero/storage/L82HWWLV/jcc.html}
}

@incollection{bascom2018,
  address = {Boston},
  series = {Translational {{Epigenetics}}},
  title = {5 - {{Mesoscale Modeling}} of {{Chromatin Fibers}}},
  volume = {2},
  abstract = {Although many computational approaches for treating general nucleic acids exist, there are few available for treating the nucleic-acid/protein complex which packages eukaryotic DNA, namely the chromatin fiber. Understanding chromatin structure and its relation to function has been an enduring challenge for biology. Here we describe the evolution, mechanics, and analysis of a computational model on the mesoscale level to investigate chromatin fibers up to several hundred nucleosomes. The rigid nucleosome core particle is considered the basic subunit for modeling, and histone tails, DNA linkers, and linker histones are treated as flexible beads. Following a description of the structure and function of chromatin constituents, including histone core proteins and their protruding tails, we review chromatin secondary and tertiary structures up to the gene level. We briefly describe the evolution of our mesoscale model and its application to a variety of chromatin structure/function problems. Details of all energy functions, model mechanics, sampling methods, and model parameters are given, along with analytical techniques for quantifying both local and global properties of chromatin fibers. Future developments and applications are outlined.},
  booktitle = {Nuclear {{Architecture}} and {{Dynamics}}},
  publisher = {{Academic Press}},
  author = {Bascom, Gavin D. and Schlick, Tamar},
  editor = {Lavelle, Christophe and Victor, Jean-Marc},
  year = {2018},
  keywords = {coarse-grained modeling,Chromatin architecture,chromatin fibers,contact maps,Equlilibrium sampling,gene elements,multiscale modeling},
  pages = {123-147},
  file = {/home/bbeltr1/Documents/paper-collection/VictorJ/D. Bascom_Schlick_2018_5 - Mesoscale Modeling of Chromatin Fibers.pdf;/home/bbeltr1/Documents/zotero/storage/FZ4NDELD/B9780128034804000053.html},
  doi = {10.1016/B978-0-12-803480-4.00005-3}
}

@article{finch1976,
  title = {Solenoidal Model for Superstructure in Chromatin},
  volume = {73},
  issn = {0027-8424},
  abstract = {Chromatin prepared by brief digestion of nuclei with micrococcal nuclease, and extracted in 0.2 mM EDTA, appears in the electron microscope as filaments of about 100 A diameter which coil loosely. In 0.2 mM Mg++ these "nucleofilaments" condense into a supercoil or solenoidal structure of pitch about 110 A corresponding to the diameter of a nucleofilament. It is proposed that the x-ray reflections at orders of 110 A observed in chromatin originate in the spacing between turns of the solenoid rather than that between nucleosomes along the nucleofilament. The solenoidal structure appears to need histone H1 for its stabilization. Under certain conditions, isolated nucleosomes can also aggregate into a similar structure. The solenoidal structure can be correlated with the "thread" of diameter about 300 A observed by other workers in nuclei.},
  language = {eng},
  number = {6},
  journal = {Proc. Natl. Acad. Sci. U.S.A.},
  author = {Finch, J. T. and Klug, A.},
  month = jun,
  year = {1976},
  keywords = {Models; Biological,Animals,Chromatin,Histones,Microscopy; Electron,Freeze Etching,Rats,X-Ray Diffraction},
  pages = {1897-1901},
  file = {/home/bbeltr1/Documents/paper-collection/KlugA/Finch_Klug_1976_Solenoidal model for superstructure in chromatin.pdf},
  pmid = {1064861},
  pmcid = {PMC430414}
}

@article{gerchman1987,
  title = {Chromatin {{Higher}}-{{Order Structure Studied}} by {{Neutron Scattering}} and {{Scanning Transmission Electron Microscopy}}},
  volume = {84},
  issn = {0027-8424},
  abstract = {Neutron scattering in solution and scanning transmission electron microscopy were simultaneously done on chicken erythrocyte chromatin at various salt and magnesium concentrations. We show that chromatin is organized into a higher-order structure even at low ionic strength and that the mass per unit length increases continuously as a function of salt concentration, reaching a limiting value of between six and seven nucleosomes per 11 nm. There is no evidence of a transition from a 10-nm to a 30-nm fiber. Fiber diameter is correlated with mass per unit length, showing that both increase during condensation. We also find that there is no essential difference between the mass per unit length measured by scanning transmission electron microscopy and neutron scattering in solution, showing that the ordered regions seen in micrographs are representative of chromatin in solution.},
  number = {22},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  author = {Gerchman, S. E. and Ramakrishnan, V.},
  year = {1987},
  pages = {7802-7806}
}

@book{holde1989,
  address = {New York},
  series = {Springer {{Series}} in {{Molecular}} and {{Cell Biology}}},
  title = {Chromatin},
  isbn = {978-1-4612-8123-8},
  abstract = {Contemporary views on the structure and function of chromatin are presented and the history of the development of these ideas as well as the nature of the nucleic acid and protein components of chromatin are reviewed. The structure of chromatin is studied at several levels, and its modes of transcription and replication are analyzed. Chromatin provides researchers with a critical evaluation of current knowledge. It combines much information that has never before been assembled, and evaluates and interrelates it in a critical way. This has not been done before so that readers are not only provided with an overview, but with extensive references to the literature (there are about 2000 references in all).},
  language = {en},
  publisher = {{Springer-Verlag}},
  author = {van Holde, Kensal E.},
  year = {1989},
  file = {/home/bbeltr1/Documents/zotero/storage/9ZL76E3Z/9781461281238.html}
}

@article{engh1992,
  title = {Estimating Genomic Distance from {{DNA}} Sequence Location in Cell Nuclei by a Random Walk Model},
  volume = {257},
  copyright = {\textcopyright{} 1992},
  issn = {0036-8075, 1095-9203},
  abstract = {The folding of chromatin in interphase cell nuclei was studied by fluorescent in situ sequences chromatin according to a random walk model. This model provides the basis for calculating the spacing of sequences along the linear DNA molecule from interphase distance measurements. An interphase mapping strategy based on this model was tested with 13 probes from a 4-megabase pair (Mbp) region of chromosome 4 containing the Huntington disease locus. The results confirmed the locations of the probes and showed that the remaining gap in the published maps of this region is negligible in size. Interphase distance measurements should facilitate construction of chromosome maps with an average marker density of one per 100 kbp, approximately ten times greater than that achieved by hybridization to metaphase chromosome. achieved by hybridization to metaphase chromosomes.},
  language = {en},
  number = {5075},
  journal = {Science},
  doi = {10.1126/science.1388286},
  author = {van den Engh, G. and Sachs, R. and Trask, B. J.},
  month = sep,
  year = {1992},
  pages = {1410-1412},
  file = {/home/bbeltr1/Documents/paper-collection/TraskB/Engh et al_1992_Estimating genomic distance from DNA sequence location in cell nuclei by a.pdf;/home/bbeltr1/Documents/zotero/storage/IJ2YR7ER/1410.html},
  pmid = {1388286}
}

@article{yokota1995,
  title = {Evidence for the Organization of Chromatin in Megabase Pair-Sized Loops Arranged along a Random Walk Path in the Human {{G0}}/{{G1}} Interphase Nucleus},
  volume = {130},
  issn = {0021-9525},
  abstract = {We determined the folding of chromosomes in interphase nuclei by measuring the distance between points on the same chromosome. Over 25,000 measurements were made in G0/G1 nuclei between DNA sequences separated by 0.15-190 megabase pairs (Mbp) on three human chromosomes. The DNA sequences were specifically labeled by fluorescence in situ hybridization. The relationship between mean-square interphase distance and genomic separation has two linear phases, with a transition at approximately 2 Mbp. This biphasic relationship indicates the existence of two organizational levels at scales {$>$} 100 kbp. On one level, chromatin appears to be arranged in large loops several Mbp in size. Within each loop, chromatin is randomly folded. On the second level, specific loop-attachment sites are arranged to form a supple, backbonelike structure, which also shows characteristic random walk behavior. This random walk/giant loop model is the simplest model that fully describes the observed large-scale spatial relationships. Additional evidence for large loops comes from measurements among probes in Xq28, where interphase distance increases and then locally decreases with increasing genomic separation.},
  language = {eng},
  number = {6},
  journal = {J. Cell Biol.},
  author = {Yokota, H. and {van den Engh}, G. and Hearst, J. E. and Sachs, R. K. and Trask, B. J.},
  month = sep,
  year = {1995},
  keywords = {Humans,Cell Cycle,Cells; Cultured,Chromosomes,Chromatin,DNA,Cell Nucleus,Female,F