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      Histone sumoylation and chromatin dynamics

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

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          Abstract

          Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially thought that histone sumoylation exclusively suppressed gene transcription, but recent advances in proteomics and genomics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodeling, transcript elongation, and blocking cryptic initiation. Histone sumoylation is integral to complex signaling codes that prime additional histone PTMs as well as modifications of the RNA polymerase II carboxy-terminal domain (RNAPII-CTD) during transcription. In addition, sumoylation of histone variants is critical for the DNA double-strand break (DSB) response and for chromosome segregation during mitosis. This review describes recent findings on histone sumoylation and its coordination with other histone and RNAPII-CTD modifications in the regulation of chromatin dynamics.

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          High-resolution profiling of histone methylations in the human genome.

          Artem Barski, Suresh Cuddapah, Kairong Cui … (2007)
          Histone modifications are implicated in influencing gene expression. We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. Typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions are identified. The monomethylations of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylations of H3K27, H3K9, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Chromosome banding patterns are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.
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            Systematic and quantitative assessment of the ubiquitin-modified proteome.

            Woong Kim, Eric J. Bennett, Edward L. Huttlin … (2011)
            Despite the diverse biological pathways known to be regulated by ubiquitylation, global identification of substrates that are targeted for ubiquitylation has remained a challenge. To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides following trypsin digestion. We identify ~19,000 diGly-modified lysine residues within ~5000 proteins. Using quantitative proteomics we monitored temporal changes in diGly site abundance in response to both proteasomal and translational inhibition, indicating both a dependence on ongoing translation to observe alterations in site abundance and distinct dynamics of individual modified lysines in response to proteasome inhibition. Further, we demonstrate that quantitative diGly proteomics can be utilized to identify substrates for cullin-RING ubiquitin ligases. Interrogation of the ubiquitinome allows for not only a quantitative assessment of alterations in protein homeostasis fidelity, but also identification of substrates for individual ubiquitin pathway enzymes. Copyright © 2011 Elsevier Inc. All rights reserved.
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              The language of covalent histone modifications.

              B. D. Strahl, C Allis (2000)
              Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented. Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a 'histone code' that is, read by other proteins to bring about distinct downstream events.
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                Author and article information

                Contributors
                Hong-Yeoul Ryu:
                ORCID: https://orcid.org/0000-0002-3367-9887
                Mark Hochstrasser:
                ORCID: https://orcid.org/0000-0002-1131-5484
                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 Collection: 21 June 2021
                Publication date (Electronic): 22 April 2021
                Publication date PMC-release: 22 April 2021
                Volume: 49
                Issue: 11
                Pages: 6043-6052
                Affiliations
                School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University , Daegu 41566, Republic of Korea
                Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 203 432 5101; Email: mark.hochstrasser@ 123456yale.edu
                Correspondence may also be addressed to Hong-Yeoul Ryu. Tel: +82 53 950 6352; Fax: +82 53 943 6925; Email: rhr4757@ 123456knu.ac.kr
                Author information
                https://orcid.org/0000-0002-3367-9887
                https://orcid.org/0000-0002-1131-5484
                Article
                Publisher ID: gkab280
                DOI: 10.1093/nar/gkab280
                PMC ID: 8216275
                PubMed ID: 33885816
                SO-VID: b51345ee-2605-4c23-a73d-4f11512b16f6
                Copyright © © The Author(s) 2021. 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 License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 08 April 2021
                Date revision received : 28 March 2021
                Date received : 09 February 2021
                Page count
                Pages: 10
                Funding
                Funded by: NIH, DOI 10.13039/100000002;
                Award ID: GM053756
                Award ID: GM136325
                Funded by: National Research Foundation of Korea, DOI 10.13039/501100003725;
                Award ID: 2020R1C1C1009367
                Categories
                Subject: AcademicSubjects/SCI00010
                Subject: Survey and Summary

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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