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      Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function

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          Abstract

          Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.

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          Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.

          William Marzluff, Eric Wagner, Robert Duronio (2008)
          The canonical histone proteins are encoded by replication-dependent genes and must rapidly reach high levels of expression during S phase. In metazoans the genes that encode these proteins produce mRNAs that, instead of being polyadenylated, contain a unique 3' end structure. By contrast, the synthesis of the variant, replication-independent histones, which are encoded by polyadenylated mRNAs, persists outside of S phase. Accurate positioning of both histone types in chromatin is essential for proper transcriptional regulation, the demarcation of heterochromatic boundaries and the epigenetic inheritance of gene expression patterns. Recent results suggest that the coordinated synthesis of replication-dependent and variant histone mRNAs is achieved by signals that affect formation of the 3' end of the replication-dependent histone mRNAs.
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            Nucleosome-interacting proteins regulated by DNA and histone methylation.

            Till Bartke, Michiel Vermeulen, Blerta Xhemalce … (2010)
            Modifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify "crosstalk" between these two distinct classes of modification. Our analysis reveals proteins whose binding to nucleosomes is regulated by methylation of CpGs, H3K4, H3K9, and H3K27 or a combination thereof. We identify the origin recognition complex (ORC), including LRWD1 as a subunit, to be a methylation-sensitive nucleosome interactor that is recruited cooperatively by DNA and histone methylation. Other interactors, such as the lysine demethylase Fbxl11/KDM2A, recognize nucleosomes methylated on histones, but their recruitment is disrupted by DNA methylation. These data establish SILAC nucleosome affinity purifications (SNAP) as a tool for studying the dynamics between different chromatin modifications and provide a modification binding "profile" for proteins regulated by DNA and histone methylation. Copyright © 2010 Elsevier Inc. All rights reserved.
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              Regulation of replication fork progression through histone supply and demand.

              Anja Groth, Armelle Corpet, Adam J L Cook … (2007)
              DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone chaperone Asf1 and MCM2-7, the putative replicative helicase, are connected through a histone H3-H4 bridge. Depletion of Asf1 by RNA interference impedes DNA unwinding at replication sites, and similar defects arise from overproduction of new histone H3-H4 that compromises Asf1 function. These data link Asf1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork progression and histone supply and demand.
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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): 28 September 2018
                Publication date (Electronic): 27 August 2018
                Publication date PMC-release: 27 August 2018
                Volume: 46
                Issue: 17
                Pages: 8665-8678
                Affiliations
                [1 ]Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
                [2 ]Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 614 292 6215; Fax: +1 614 292 6215; Email: parthun.1@ 123456osu.edu

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

                Article
                Publisher ID: gky768
                DOI: 10.1093/nar/gky768
                PMC ID: 6158624
                PubMed ID: 30165676
                SO-VID: bcb8e807-949b-444e-89be-301d0d384ff4
                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 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 : 24 August 2018
                Date revision received : 02 August 2018
                Date received : 25 May 2018
                Page count
                Pages: 14
                Funding
                Funded by: National Institute of General Medical Sciences 10.13039/100000057
                Award ID: GM062970
                Categories
                Subject: Survey and Summary

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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