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      A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation

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          Summary

          Lysine acetylation of histones defines the epigenetic status of human embryonic stem cells and orchestrates DNA replication, chromosome condensation, transcription, telomeric silencing, and DNA repair. A detailed mechanistic explanation of these phenomena is impeded by the limited availability of homogeneously acetylated histones. We report a general method for the production of homogeneously and site-specifically acetylated recombinant histones by genetically encoding acetyl-lysine. We reconstitute histone octamers, nucleosomes, and nucleosomal arrays bearing defined acetylated lysine residues. With these designer nucleosomes, we demonstrate that, in contrast to the prevailing dogma, acetylation of H3 K56 does not directly affect the compaction of chromatin and has modest effects on remodeling by SWI/SNF and RSC. Single-molecule FRET experiments reveal that H3 K56 acetylation increases DNA breathing 7-fold. Our results provide a molecular and mechanistic underpinning for cellular phenomena that have been linked with K56 acetylation.

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          Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.

          A Bannister, P Zegerman, J F Partridge … (2001)
          Heterochromatin protein 1 (HP1) is localized at heterochromatin sites where it mediates gene silencing. The chromo domain of HP1 is necessary for both targeting and transcriptional repression. In the fission yeast Schizosaccharomyces pombe, the correct localization of Swi6 (the HP1 equivalent) depends on Clr4, a homologue of the mammalian SUV39H1 histone methylase. Both Clr4 and SUV39H1 methylate specifically lysine 9 of histone H3 (ref. 6). Here we show that HP1 can bind with high affinity to histone H3 methylated at lysine 9 but not at lysine 4. The chromo domain of HP1 is identified as its methyl-lysine-binding domain. A point mutation in the chromo domain, which destroys the gene silencing activity of HP1 in Drosophila, abolishes methyl-lysine-binding activity. Genetic and biochemical analysis in S. pombe shows that the methylase activity of Clr4 is necessary for the correct localization of Swi6 at centromeric heterochromatin and for gene silencing. These results provide a stepwise model for the formation of a transcriptionally silent heterochromatin: SUV39H1 places a 'methyl marker' on histone H3, which is then recognized by HP1 through its chromo domain. This model may also explain the stable inheritance of the heterochromatic state.
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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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              How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.

              Sean Taverna, Haitao Li, Alexander Ruthenburg … (2007)
              Histones comprise the major protein component of chromatin, the scaffold in which the eukaryotic genome is packaged, and are subject to many types of post-translational modifications (PTMs), especially on their flexible tails. These modifications may constitute a 'histone code' and could be used to manage epigenetic information that helps extend the genetic message beyond DNA sequences. This proposed code, read in part by histone PTM-binding 'effector' modules and their associated complexes, is predicted to define unique functional states of chromatin and/or regulate various chromatin-templated processes. A wealth of structural and functional data show how chromatin effector modules target their cognate covalent histone modifications. Here we summarize key features in molecular recognition of histone PTMs by a diverse family of 'reader pockets', highlighting specific readout mechanisms for individual marks, common themes and insights into the downstream functional consequences of the interactions. Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mol Cell
                Journal ID (iso-abbrev): Mol. Cell
                Title: Molecular Cell
                Publisher: Cell Press
                ISSN (Print): 1097-2765
                ISSN (Electronic): 1097-4164
                Publication date PMC-release: 09 October 2009
                Publication date (Print): 09 October 2009
                Volume: 36
                Issue: 1
                Pages: 153-163
                Affiliations
                [1 ]Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, England, UK
                [2 ]Physics of Life Processes, Leiden Institute of Physics, Leiden University, The Netherlands
                [3 ]Wellcome Trust Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
                Author notes
                [∗ ]Corresponding author chin@ 123456mrc-lmb.cam.ac.uk
                Article
                Publisher ID: MOLCEL3205
                DOI: 10.1016/j.molcel.2009.07.027
                PMC ID: 2856916
                PubMed ID: 19818718
                SO-VID: 5d3bacad-9e48-41f9-ae0c-78f011480c59
                Copyright © © 2009 ELL & Excerpta Medica.
                License:

                This document may be redistributed and reused, subject to certain conditions.

                History
                Date received : 1 April 2009
                Date revision received : 23 June 2009
                Date accepted : 31 July 2009
                Categories
                Subject: Resource

                ScienceOpen disciplines: Molecular biology
                Keywords: proteins,dna
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: proteins, dna

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