Histone tails as signaling antennas of chromatin

Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, 389, 251, 10.1038/38444 Pilotto, 2015, Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation, Proc Natl Acad Sci U S A, 112, 2752, 10.1073/pnas.1419468112 Zhang, 2017, Histone acetylation regulates chromatin accessibility: role of H4K16 in inter-nucleosome interaction, Biophys J, 112, 450, 10.1016/j.bpj.2016.11.015 Morrison, 2018, The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome, eLife, 7, 10.7554/eLife.31481 Stutzer, 2016, Modulations of DNA contacts by linker histones and post-translational modifications determine the mobility and modifiability of nucleosomal H3 tails, Mol Cell, 61, 247, 10.1016/j.molcel.2015.12.015 Kirsch, 2020, Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper, Methods, 10.1016/j.ymeth.2020.01.012 Shaytan, 2016, Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions, J Mol Biol, 428, 221, 10.1016/j.jmb.2015.12.004 Weaver, 2018, Reading more than histones: the prevalence of nucleic acid binding among reader domains, Molecules, 23, 10.3390/molecules23102614 Zhao, 2019, Identification and characterization of ‘readers’ for novel histone modifications, Curr Opin Chem Biol, 51, 57, 10.1016/j.cbpa.2019.04.001 ww PDBc, 2019, Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Res, 47, D520, 10.1093/nar/gky949 Guo, 2015, Structural insight into autoinhibition and histone H3-induced activation of DNMT3A, Nature, 517, 640, 10.1038/nature13899 Ivic, 2019, Fuzzy interactions form and shape the histone transport complex, Mol Cell, 73, 1191, 10.1016/j.molcel.2019.01.032 Danilenko, 2019, Histone chaperone exploits intrinsic disorder to switch acetylation specificity, Nat Commun, 10, 10.1038/s41467-019-11410-7 Chakraborty, 2018, Molecular mechanism for the role of the H2A and H2B histone tails in nucleosome repositioning, J Phys Chem B, 122, 11827, 10.1021/acs.jpcb.8b07881 Gatchalian, 2017, Accessibility of the histone H3 tail in the nucleosome for binding of paired readers, Nat Commun, 8, 10.1038/s41467-017-01598-x Kale, 2019, Molecular recognition of nucleosomes by binding partners, Curr Opin Struct Biol, 56, 164, 10.1016/j.sbi.2019.03.010 Skrajna, 2020, Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding, Nucleic Acids Res, 48, 9415, 10.1093/nar/gkaa544 Shoemaker, 2000, Speeding molecular recognition by using the folding funnel: the fly-casting mechanism, Proc Natl Acad Sci U S A, 97, 8868, 10.1073/pnas.160259697 Erler, 2014, The role of histone tails in the nucleosome: a computational study, Biophys J, 107, 2911, 10.1016/j.bpj.2014.10.065 Parsons, 2019, Critical role of histone tail entropy in nucleosome unwinding, J Chem Phys, 150, 10.1063/1.5085663 Chakraborty, 2017, Asymmetric breathing motions of nucleosomal DNA and the role of histone tails, J Chem Phys, 147, 10.1063/1.4997573 Kenzaki, 2015, Partial unwrapping and histone tail dynamics in nucleosome revealed by coarse-grained molecular simulations, PLoS Comput Biol, 11, 10.1371/journal.pcbi.1004443 Fuxreiter, 2018, Fuzziness in protein interactions—a historical perspective, J Mol Biol, 430, 2278, 10.1016/j.jmb.2018.02.015 Borgia, 2018, Extreme disorder in an ultrahigh-affinity protein complex, Nature, 555, 61, 10.1038/nature25762 Langini, 2017, The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes, J Biol Chem, 292, 16734, 10.1074/jbc.M117.786350 Sridhar, 2020, Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1, Nucleic Acids Res, 48, 5318, 10.1093/nar/gkaa285 Hwang, 2014, Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA, Nature, 512, 213, 10.1038/nature13380 Longbotham, 2019, Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling, Nat Commun, 10, 94, 10.1038/s41467-018-07829-z Fenley, 2018, Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core, Epigenetics Chromatin, 11, 11, 10.1186/s13072-018-0181-5 Su, 2016, Reading the combinatorial histone language, ACS Chem Biol, 11, 564, 10.1021/acschembio.5b00864 Nishi, 2015, Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites, J Mol Biol, 427, 511, 10.1016/j.jmb.2014.11.001 Aparicio Pelaz, 2020, Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes, Chem Sci, 11, 9218, 10.1039/D0SC03407J Winogradoff, 2015, The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects, J Am Chem Soc, 137, 6245, 10.1021/jacs.5b00235 Mishra, 2016, Acetylation mimics within a single nucleosome alter local DNA accessibility in compacted nucleosome arrays, Sci Rep, 6, 10.1038/srep34808 Draizen, 2016, HistoneDB 2.0: a histone database with variants—an integrated resource to explore histones and their variants, Database (Oxford), 2016, 10.1093/database/baw014 Chang, 2015, CHK1-driven histone H3.3 serine 31 phosphorylation is important for chromatin maintenance and cell survival in human ALT cancer cells, Nucleic Acids Res, 43, 2603, 10.1093/nar/gkv104 Ismail, 2008, The gamma-H2A.X: is it just a surrogate marker of double-strand breaks or much more?, Environ Mol Mutagen, 49, 73, 10.1002/em.20358 Churchill, 1989, ‘SPKK’ motifs prefer to bind to DNA at A/T-rich sites, EMBO J, 8, 4189, 10.1002/j.1460-2075.1989.tb08604.x Woods, 2020, Elucidating the influence of linker histone variants on chromatosome dynamics and energetics, Nucleic Acids Res, 48, 3591, 10.1093/nar/gkaa121 Osakabe, 2018, Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility, Nucleic Acids Res, 46, 7675, 10.1093/nar/gky540 Jiang, 2020, Short histone H2A variants: small in stature but not in function, Cells, 9, 10.3390/cells9040867 Martire, 2020, The roles of histone variants in fine-tuning chromatin organization and function, Nat Rev Mol Cell Biol, 21, 522, 10.1038/s41580-020-0262-8 Wakamori, 2015, Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation, Sci Rep, 5, 10.1038/srep17204 Yi, 2018, Histone tail cleavage as a novel epigenetic regulatory mechanism for gene expression, BMB Rep, 51, 211, 10.5483/BMBRep.2018.51.5.053 Azad, 2018, Modifying chromatin by histone tail clipping, J Mol Biol, 430, 3051, 10.1016/j.jmb.2018.07.013 Kim, 2016, MMP-9 facilitates selective proteolysis of the histone H3 tail at genes necessary for proficient osteoclastogenesis, Genes Dev, 30, 208, 10.1101/gad.268714.115 Shen, 2017, JMJD5 cleaves monomethylated histone H3 N-tail under DNA damaging stress, EMBO Rep, 18, 2131, 10.15252/embr.201743892 Allahverdi, 2015, Chromatin compaction under mixed salt conditions: opposite effects of sodium and potassium ions on nucleosome array folding, Sci Rep, 5, 10.1038/srep08512 Li, 2016, Distinct roles of histone H3 and H2A tails in nucleosome stability, Sci Rep, 6 Iwasaki, 2013, Contribution of histone N-terminal tails to the structure and stability of nucleosomes, FEBS Open Bio, 3, 363, 10.1016/j.fob.2013.08.007 Bilokapic, 2018, Cryo-EM of nucleosome core particle interactions in trans, Sci Rep, 8, 10.1038/s41598-018-25429-1 Berezhnoy, 2016, The influence of ionic environment and histone tails on columnar order of nucleosome core particles, Biophys J, 110, 1720, 10.1016/j.bpj.2016.03.016 Chen, 2017, Regulation of nucleosome stacking and chromatin compaction by the histone H4 N-terminal tail-H2A acidic patch interaction, J Mol Biol, 429, 2075, 10.1016/j.jmb.2017.03.016 Song, 2014, Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units, Science, 344, 376, 10.1126/science.1251413 Kim, 2015, Linker histone H1.2 establishes chromatin compaction and gene silencing through recognition of H3K27me3, Sci Rep, 5, 10.1038/srep16714 Shogren-Knaak, 2006, Histone H4-K16 acetylation controls chromatin structure and protein interactions, Science, 311, 844, 10.1126/science.1124000 Henikoff, 2015, Histone variants and epigenetics, Cold Spring Harb Perspect Biol, 7, 10.1101/cshperspect.a019364 Banerjee, 2019, Acetylation of the histone H3 tail domain regulates base excision repair on higher-order chromatin structures, Sci Rep, 9, 10.1038/s41598-019-52340-0