Histone tail network and modulation in a nucleosome

Current Opinion in Structural Biology - Tập 75 - Trang 102436 - 2022
Yasuo Tsunaka1, Ayako Furukawa1, Yoshifumi Nishimura1,2
1Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
2Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, 739-8528, Japan

Tài liệu tham khảo

Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, 389, 251, 10.1038/38444 Suganuma, 2011, Signals and combinatorial functions of histone modifications, Annu Rev Biochem, 80, 473, 10.1146/annurev-biochem-061809-175347 Zentner, 2013, Regulation of nucleosome dynamics by histone modifications, Nat Struct Mol Biol, 20, 259, 10.1038/nsmb.2470 Stewart-Morgan, 2020, Chromatin replication and epigenetic cell memory, Nat Cell Biol, 22, 361, 10.1038/s41556-020-0487-y Furukawa, 2022, Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome, iScience, 25, 103937, 10.1016/j.isci.2022.103937 Morrison, 2021, Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility, Nucleic Acids Res, 49, 4750, 10.1093/nar/gkab246 Zhou, 2021, Distinct structures and dynamics of chromatosomes with different human linker histone isoforms, Mol Cell, 81, 166, 10.1016/j.molcel.2020.10.038 Furukawa, 2020, Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome, Proc Natl Acad Sci U S A, 117, 19661, 10.1073/pnas.2010506117 Tsunaka, 2020, Partial replacement of nucleosomal DNA with human FACT induces dynamic exposure and acetylation of histone H3 N-terminal tails, iScience, 23, 101641, 10.1016/j.isci.2020.101641 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 Liokatis, 2016, Differentially isotope-labeled nucleosomes to study asymmetric histone modification crosstalk by time-resolved nmr spectroscopy, Angew Chem Int Ed Engl, 55, 8262, 10.1002/anie.201601938 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 Zhou, 2012, Histone h4 k16q mutation, an acetylation mimic, causes structural disorder of its n-terminal basic patch in the nucleosome, J Mol Biol, 421, 30, 10.1016/j.jmb.2012.04.032 Peng, 2021, Histone tails as signaling antennas of chromatin, Curr Opin Struct Biol, 67, 153, 10.1016/j.sbi.2020.10.018 Bjarnason, 2021, Protein intrinsic disorder on a dynamic nucleosomal landscape, Prog Mol Biol Transl Sci, 183, 295, 10.1016/bs.pmbts.2021.06.006 Musselman, 2021, Characterization of functional disordered regions within chromatin associated proteins, iScience, 24, 10.1016/j.isci.2021.102070 Huertas, 2021, Breaths, twists, and turns of atomistic nucleosomes, J Mol Biol, 433, 10.1016/j.jmb.2020.166744 Dyson, 2021, NMR illuminates intrinsic disorder, Curr Opin Struct Biol, 70, 44, 10.1016/j.sbi.2021.03.015 Schneider, 2019, Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using nmr spectroscopy, Curr Opin Struct Biol, 54, 10, 10.1016/j.sbi.2018.09.007 Gatchalian, 2017, Accessibility of the histone H3 tail in the nucleosome for binding of paired readers, Nat Commun, 8, 1489, 10.1038/s41467-017-01598-x Lehmann, 2020, Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET, Nucleic Acids Res, 48, 1551, 10.1093/nar/gkz1186 Peng, 2021, Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails, Nat Commun, 12, 5280, 10.1038/s41467-021-25568-6 Ikebe, 2016, H3 histone tail conformation within the nucleosome and the impact of k14 acetylation studied using enhanced sampling simulation, PLoS Comput Biol, 12, 10.1371/journal.pcbi.1004788 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 Li, 2016, Distinct roles of histone h3 and h2a tails in nucleosome stability, Sci Rep, 6, 31437, 10.1038/srep31437 Zandian, 2021, Conformational dynamics of histone H3 tails in chromatin, J Phys Chem Lett, 12, 6174, 10.1021/acs.jpclett.1c01187 Arimura, 2021, Structural features of nucleosomes in interphase and metaphase chromosomes, Mol Cell, 81, 4377, 10.1016/j.molcel.2021.08.010 Tsunaka, 2016, Integrated molecular mechanism directing nucleosome reorganization by human FACT, Genes Dev, 30, 673, 10.1101/gad.274183.115 Mayanagi, 2019, Structural visualiza ion of key steps in nucleosome reorganization by human FACT, Sci Rep, 9, 10183, 10.1038/s41598-019-46617-7 Liu, 2020, FACT caught in the act of manipulating the nucleosome, Nature, 577, 426, 10.1038/s41586-019-1820-0 Wang, 2022, H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly, Nucleic Acids Res, 50, 833, 10.1093/nar/gkab1271 Sivkina, 2022, Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT, Commun Biol, 5, 2, 10.1038/s42003-021-02948-8 Safaric, 2022, The fork protection complex recruits FACT to reorganize nucleosomes during replication, Nucleic Acids Res, 50, 1317, 10.1093/nar/gkac005 Farnung, 2021, Structural basis of nucleosome transcription mediated by Chd1 and FACT, Nat Struct Mol Biol, 28, 382, 10.1038/s41594-021-00578-6 Jeronimo, 2021, FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner, Mol Cell, 81, 3542, 10.1016/j.molcel.2021.07.010 Bilokapic, 2019, Nucleosome and ubiquitin position Set2 to methylate H3K36, Nat Commun, 10, 3795, 10.1038/s41467-019-11726-4 Li, 2021, Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases, Nature, 590, 498, 10.1038/s41586-020-03069-8 Sato, 2021, Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2, Nat Commun, 12, 6605, 10.1038/s41467-021-26913-5 Zhou, 2021, Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2, EMBO J, 40, 10.15252/embj.2020105907 Yan, 2019, Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome, Nature, 574, 278, 10.1038/s41586-019-1609-1 Farnung, 2017, Nucleosome–Chd1 structure and implications for chromatin remodelling, Nature, 550, 539, 10.1038/nature24046 Eustermann, 2018, Structural basis for ATP-dependent chromatin remodelling by the INO80 complex, Nature, 556, 386, 10.1038/s41586-018-0029-y Willhoft, 2018, Structure and dynamics of the yeast SWR1-nucleosome complex, Science, 362, eaat7716, 10.1126/science.aat7716 Michael, 2020, Mechanisms of OCT4-SOX2 motif readout on nucleosomes, Science, 368, 1460, 10.1126/science.abb0074 Kujirai, 2018, Structural basis of the nucleosome transition during RNA polymerase II passage, Science, 362, 595, 10.1126/science.aau9904 Ehara, 2019, Structural insight into nucleosome transcription by RNA polymerase II with elongation factors, Science, 363, 744, 10.1126/science.aav8912 Ohtomo, 2021, The N-terminal tails of histones H2A and H2B adopt two distinct conformations in the nucleosome with contact and reduced contact to DNA, J Mol Biol, 433, 10.1016/j.jmb.2021.167110 Wilson, 2019, Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer, Nat Commun, 10, 4189, 10.1038/s41467-019-12007-w Kasinath, 2021, JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications, Science, 371, 10.1126/science.abc3393 Okuda, 2021, Structural and dynamical insights into the PH domain of p62 in human TFIIH, Nucleic Acids Res, 49, 2916, 10.1093/nar/gkaa1045 Okuda, 2022, Three human RNA polymerases interact with TFIIH via a common RPB6 subunit, Nucleic Acids Res, 50, 1, 10.1093/nar/gkab612 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, 17204, 10.1038/srep17204 Taylor, 2021, Combinations of histone post-translational modifications, Biochem J, 478, 511, 10.1042/BCJ20200170 Tsunaka, 2005, Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle, Nucleic Acids Res, 33, 3424, 10.1093/nar/gki663