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      Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics

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      Author(s): 1 , 2 , 3 , 2
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          DNA in nucleosomes has restricted nucleosome dynamics and is refractory to DNA-templated processes. Histone post-translational modifications play important roles in regulating DNA accessibility in nucleosomes. Whereas most histone modifications function either by mitigating the electrostatic shielding of histone tails or by recruiting ‘reader’ proteins, we show that ubiquitylation of H2B K34, which is located in a tight space protected by two coils of DNA superhelix, is able to directly influence the canonical nucleosome conformation via steric hindrances by ubiquitin groups. H2B K34 ubiquitylation significantly enhances nucleosome dynamics and promotes generation of hexasomes both with symmetrically or asymmetrically modified nucleosomes. Our results indicate a direct mechanism by which a histone modification regulates the chromatin structural states.

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          Histone H4-K16 acetylation controls chromatin structure and protein interactions.

          Michael A. Shogren-Knaak, Haruhiko Ishii, Jian-Min Sun … (2006)
          Acetylation of histone H4 on lysine 16 (H4-K16Ac) is a prevalent and reversible posttranslational chromatin modification in eukaryotes. To characterize the structural and functional role of this mark, we used a native chemical ligation strategy to generate histone H4 that was homogeneously acetylated at K16. The incorporation of this modified histone into nucleosomal arrays inhibits the formation of compact 30-nanometer-like fibers and impedes the ability of chromatin to form cross-fiber interactions. H4-K16Ac also inhibits the ability of the adenosine triphosphate-utilizing chromatin assembly and remodeling enzyme ACF to mobilize a mononucleosome, indicating that this single histone modification modulates both higher order chromatin structure and functional interactions between a nonhistone protein and the chromatin fiber.
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            Histone exchange, chromatin structure and the regulation of transcription.

            Swaminathan Venkatesh, Jerry L Workman (2015)
            The packaging of DNA into strings of nucleosomes is one of the features that allows eukaryotic cells to tightly regulate gene expression. The ordered disassembly of nucleosomes permits RNA polymerase II (Pol II) to access the DNA, whereas nucleosomal reassembly impedes access, thus preventing transcription and mRNA synthesis. Chromatin modifications, chromatin remodellers, histone chaperones and histone variants regulate nucleosomal dynamics during transcription. Disregulation of nucleosome dynamics results in aberrant transcription initiation, producing non-coding RNAs. Ongoing research is elucidating the molecular mechanisms that regulate chromatin structure during transcription by preventing histone exchange, thereby limiting non-coding RNA expression.
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              Histone core modifications regulating nucleosome structure and dynamics.

              Peter Tessarz, Tony Kouzarides (2014)
              Post-translational modifications of histones regulate all DNA-templated processes, including replication, transcription and repair. These modifications function as platforms for the recruitment of specific effector proteins, such as transcriptional regulators or chromatin remodellers. Recent data suggest that histone modifications also have a direct effect on nucleosomal architecture. Acetylation, methylation, phosphorylation and citrullination of the histone core may influence chromatin structure by affecting histone-histone and histone-DNA interactions, as well as the binding of histones to chaperones.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 06 September 2018
                Publication date (Electronic): 21 June 2018
                Publication date PMC-release: 21 June 2018
                Volume: 46
                Issue: 15
                Pages: 7631-7642
                Affiliations
                [1 ]N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow, 119334, Russia
                [2 ]Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
                [3 ]School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
                Author notes
                To whom correspondence should be addressed. Tel: +1 734 615 1315; Fax: +1 734 615 4503; Email: yalid@ 123456med.umich.edu . Correspondence may also be addressed to Wladyslaw A. Krajewski. Tel: +7 499 135 88 47; Email: wkrajewski@ 123456hotmail.com
                Article
                Publisher ID: gky526
                DOI: 10.1093/nar/gky526
                PMC ID: 6125632
                PubMed ID: 29931239
                SO-VID: bde5591d-a449-454f-95cc-9fdedcb36828
                Copyright © © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 25 May 2018
                Date revision received : 23 May 2018
                Date received : 19 January 2018
                Page count
                Pages: 12
                Funding
                Funded by: National Computational Infrastructure 10.13039/100010582
                Award ID: CA190911A
                Funded by: IDB RAS government programs of basic research 10.13039/100009977
                Award ID: 0108-2018-0001
                Categories
                Subject: Gene regulation, Chromatin and Epigenetics

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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