Organization of Chromatin by Intrinsic and Regulated Phase Separation

Allahverdi, 2011, The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association, Nucleic Acids Res., 39, 1680, 10.1093/nar/gkq900 Amendola, 2015, Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells, EMBO Rep., 16, 610, 10.15252/embr.201439789 Balleza, 2018, Systematic characterization of maturation time of fluorescent proteins in living cells, Nat. Methods, 15, 47, 10.1038/nmeth.4509 Banani, 2017, Biomolecular condensates: organizers of cellular biochemistry, Nat. Rev. Mol. Cell Biol., 18, 285, 10.1038/nrm.2017.7 Bass, 2019, Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays, J. Biol. Chem., 294, 4233, 10.1074/jbc.RA118.006412 Bednar, 2017, Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1, Mol. Cell, 66, 384, 10.1016/j.molcel.2017.04.012 Bintu, 2018, Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells, Science, 362, 10.1126/science.aau1783 Boija, 2018, Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains, Cell, 175, 1842, 10.1016/j.cell.2018.10.042 Brangwynne, 2009, Germline P granules are liquid droplets that localize by controlled dissolution/condensation, Science, 324, 1729, 10.1126/science.1172046 Brogaard, 2012, A map of nucleosome positions in yeast at base-pair resolution, Nature, 486, 496, 10.1038/nature11142 Brownell, 1996, Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation, Cell, 84, 843, 10.1016/S0092-8674(00)81063-6 Bulut-Karslioglu, 2014, Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells, Mol. Cell, 55, 277, 10.1016/j.molcel.2014.05.029 Cao, 2013, High-resolution mapping of h1 linker histone variants in embryonic stem cells, PLoS Genet., 9, e1003417, 10.1371/journal.pgen.1003417 Carruthers, 1998, Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding, Biochemistry, 37, 14776, 10.1021/bi981684e Chen, 2011, A general strategy for the evolution of bond-forming enzymes using yeast display, Proc. Natl. Acad. Sci. USA, 108, 11399, 10.1073/pnas.1101046108 Chen, 2016, Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo, Mol. Biol. Cell, 27, 3357, 10.1091/mbc.E16-07-0506 Cho, 2016, RNA Polymerase II cluster dynamics predict mRNA output in living cells, eLife, 5, 10.7554/eLife.13617 Cho, 2018, Mediator and RNA polymerase II clusters associate in transcription-dependent condensates, Science, 361, 412, 10.1126/science.aar4199 Chong, 2018, Imaging dynamic and selective low-complexity domain interactions that control gene transcription, Science, 361, 10.1126/science.aar2555 Cuylen, 2016, Ki-67 acts as a biological surfactant to disperse mitotic chromosomes, Nature, 535, 308, 10.1038/nature18610 Davey, 2002, Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution, J. Mol. Biol., 319, 1097, 10.1016/S0022-2836(02)00386-8 Di Pierro, 2016, Transferable model for chromosome architecture, Proc. Natl. Acad. Sci. USA, 113, 12168, 10.1073/pnas.1613607113 Dubochet, 1986, Cryo-electron microscopy of vitrified SV40 minichromosomes: the liquid drop model, EMBO J., 5, 519, 10.1002/j.1460-2075.1986.tb04241.x 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 Falk, 2019, Heterochromatin drives compartmentalization of inverted and conventional nuclei, Nature, 570, 395, 10.1038/s41586-019-1275-3 Fan, 2005, Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation, Cell, 123, 1199, 10.1016/j.cell.2005.10.028 Filion, 2010, Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, 143, 212, 10.1016/j.cell.2010.09.009 Filippakopoulos, 2010, Selective inhibition of BET bromodomains, Nature, 468, 1067, 10.1038/nature09504 Fletcher, 1995, Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms, J. Biol. Chem., 270, 25359, 10.1074/jbc.270.43.25359 Fujisawa, 2017, Functions of bromodomain-containing proteins and their roles in homeostasis and cancer, Nat. Rev. Mol. Cell Biol., 18, 246, 10.1038/nrm.2016.143 Grunstein, 1997, Histone acetylation in chromatin structure and transcription, Nature, 389, 349, 10.1038/38664 Hansen, 2002, Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions, Annu. Rev. Biophys. Biomol. Struct., 31, 361, 10.1146/annurev.biophys.31.101101.140858 Hergeth, 2015, The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle, EMBO Rep., 16, 1439, 10.15252/embr.201540749 Hihara, 2012, Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells, Cell Rep., 2, 1645, 10.1016/j.celrep.2012.11.008 Jenuwein, 2001, Translating the histone code, Science, 293, 1074, 10.1126/science.1063127 Kagey, 2010, Mediator and cohesin connect gene expression and chromatin architecture, Nature, 467, 430, 10.1038/nature09380 Kan, 2009, The H4 tail domain participates in intra- and internucleosome interactions with protein and DNA during folding and oligomerization of nucleosome arrays, Mol. Cell. Biol., 29, 538, 10.1128/MCB.01343-08 Kaplan, 2009, The DNA-encoded nucleosome organization of a eukaryotic genome, Nature, 458, 362, 10.1038/nature07667 Klinker, 2014, Rapid purification of recombinant histones, PLoS ONE, 9, e104029, 10.1371/journal.pone.0104029 Kornberg, 1974, Chromatin structure: a repeating unit of histones and DNA, Science, 184, 868, 10.1126/science.184.4139.868 Kundu, 2017, Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation, Mol. Cell, 65, 432, 10.1016/j.molcel.2017.01.009 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Larson, 2017, Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin, Nature, 547, 236, 10.1038/nature22822 Li, 2012, Phase transitions in the assembly of multivalent signalling proteins, Nature, 483, 336, 10.1038/nature10879 Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 Lohr, 1979, Organization of spacer DNA in chromatin, Proc. Natl. Acad. Sci. USA, 76, 6326, 10.1073/pnas.76.12.6326 Lowary, 1998, New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning, J. Mol. Biol., 276, 19, 10.1006/jmbi.1997.1494 Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, 389, 251, 10.1038/38444 Luger, 1999, Expression and purification of recombinant histones and nucleosome reconstitution, Methods Mol. Biol., 119, 1 Maeshima, 2016, Liquid-like behavior of chromatin, Curr. Opin. Genet. Dev., 37, 36, 10.1016/j.gde.2015.11.006 Maeshima, 2016, Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers, EMBO J., 35, 1115, 10.15252/embj.201592660 Meaburn, 2007, Cell biology: chromosome territories, Nature, 445, 379, 10.1038/445379a Mirny, 2019, Two major mechanisms of chromosome organization, Curr. Opin. Cell Biol., 58, 142, 10.1016/j.ceb.2019.05.001 Nikitina, 2017, DNA topology in chromatin is defined by nucleosome spacing, Sci. Adv., 3, e1700957, 10.1126/sciadv.1700957 Nishino, 2012, Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure, EMBO J., 31, 1644, 10.1038/emboj.2012.35 Nozaki, 2017, Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging, Mol. Cell, 67, 282, 10.1016/j.molcel.2017.06.018 Olins, 2003, Chromatin history: our view from the bridge, Nat. Rev. Mol. Cell Biol., 4, 809, 10.1038/nrm1225 Ou, 2017, ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells, Science, 357, eaag0025, 10.1126/science.aag0025 Peric-Hupkes, 2010, Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation, Mol. Cell, 38, 603, 10.1016/j.molcel.2010.03.016 Pettersen, 2004, UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Plys, 2019, Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2, Genes Dev., 33, 799, 10.1101/gad.326488.119 Quinlan, 2014, BEDTools: The Swiss-Army Tool for Genome Feature Analysis, Curr. Protoc. Bioinformatics, 47, 10.1002/0471250953.bi1112s47 Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 2013 Rao, 2017, Cohesin Loss Eliminates All Loop Domains, Cell, 171, 305, 10.1016/j.cell.2017.09.026 Rubinstein, 2003 Sabari, 2018, Coactivator condensation at super-enhancers links phase separation and gene control, Science, 361, 10.1126/science.aar3958 Saldanha, 2004, Java Treeview--extensible visualization of microarray data, Bioinformatics, 20, 3246, 10.1093/bioinformatics/bth349 Schalch, 2005, X-ray structure of a tetranucleosome and its implications for the chromatin fibre, Nature, 436, 138, 10.1038/nature03686 Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nat. Methods, 9, 676, 10.1038/nmeth.2019 Schneider, 2012, NIH Image to ImageJ: 25 years of image analysis, Nat. Methods, 9, 671, 10.1038/nmeth.2089 Schwarzer, 2017, Two independent modes of chromatin organization revealed by cohesin removal, Nature, 551, 51, 10.1038/nature24281 Shen, 1995, Linker histones are not essential and affect chromatin condensation in vivo, Cell, 82, 47, 10.1016/0092-8674(95)90051-9 Shin, 2017, Liquid phase condensation in cell physiology and disease, Science, 357, 10.1126/science.aaf4382 Shogren-Knaak, 2006, Histone H4-K16 acetylation controls chromatin structure and protein interactions, Science, 311, 844, 10.1126/science.1124000 Song, 2014, Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units, Science, 344, 376, 10.1126/science.1251413 Strom, 2017, Phase separation drives heterochromatin domain formation, Nature, 547, 241, 10.1038/nature22989 Struhl, 2013, Determinants of nucleosome positioning, Nat. Struct. Mol. Biol., 20, 267, 10.1038/nsmb.2506 Tóth, 2004, Trichostatin A-induced histone acetylation causes decondensation of interphase chromatin, J. Cell Sci., 117, 4277, 10.1242/jcs.01293 Turner, 2018, Highly disordered histone H1-DNA model complexes and their condensates, Proc. Natl. Acad. Sci. U.S.A., 115, 11964, 10.1073/pnas.1805943115 Uhlmann, 2016, SMC complexes: from DNA to chromosomes, Nat. Rev. Mol. Cell Biol., 17, 399, 10.1038/nrm.2016.30 Voong, 2016, Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping, Cell, 167, 1555, 10.1016/j.cell.2016.10.049 Whyte, 2013, Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, 153, 307, 10.1016/j.cell.2013.03.035 Widom, 1986, Physicochemical studies of the folding of the 100 A nucleosome filament into the 300 A filament. Cation dependence, J. Mol. Biol., 190, 411, 10.1016/0022-2836(86)90012-4 Williamson, 2014, Depsipeptide substrates for sortase-mediated N-terminal protein ligation, Nat. Protoc., 9, 253, 10.1038/nprot.2014.003 Wilson, 2016, The structural basis of modified nucleosome recognition by 53BP1, Nature, 536, 100, 10.1038/nature18951 Woodcock, 2006, Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length, Chromosome Res., 14, 17, 10.1007/s10577-005-1024-3 Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 Zhao, 2014, CrossMap: a versatile tool for coordinate conversion between genome assemblies, Bioinformatics, 30, 1006, 10.1093/bioinformatics/btt730