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      DNA-mediated association of two histone-bound complexes of yeast Chromatin Assembly Factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication

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          Abstract

          Nucleosome assembly in the wake of DNA replication is a key process that regulates cell identity and survival. Chromatin assembly factor 1 (CAF-1) is a H3-H4 histone chaperone that associates with the replisome and orchestrates chromatin assembly following DNA synthesis. Little is known about the mechanism and structure of this key complex. Here we investigate the CAF-1•H3-H4 binding mode and the mechanism of nucleosome assembly. We show that yeast CAF-1 binding to a H3-H4 dimer activates the Cac1 winged helix domain interaction with DNA. This drives the formation of a transient CAF-1•histone•DNA intermediate containing two CAF-1 complexes, each associated with one H3-H4 dimer. Here, the (H3-H4) 2 tetramer is formed and deposited onto DNA. Our work elucidates the molecular mechanism for histone deposition by CAF-1, a reaction that has remained elusive for other histone chaperones, and it advances our understanding of how nucleosomes and their epigenetic information are maintained through DNA replication.

          DOI: http://dx.doi.org/10.7554/eLife.22799.001

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          Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.

          Liam Holt, Brian B. Tuch, Judit Villén … (2009)
          To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae. We combined specific chemical inhibition of Cdk1 with quantitative mass spectrometry to identify the positions of 547 phosphorylation sites on 308 Cdk1 substrates in vivo. Comparisons of these substrates with orthologs throughout the ascomycete lineage revealed that the position of most phosphorylation sites is not conserved in evolution; instead, clusters of sites shift position in rapidly evolving disordered regions. We propose that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions. The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.
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            Reconstitution of nucleosome core particles from recombinant histones and DNA.

            Pamela N Dyer, Raji S Edayathumangalam, Cindy L. White … (2004)
            Article 0 comments Cited 230 times – based on 0 reviews     Review now
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              Chromatin replication and epigenome maintenance.

              Constance Alabert, Anja Groth (2012)
              Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism.
              Article 0 comments Cited 194 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Paul D Kaufman: Role: Reviewing editor
                Journal
                Journal ID (nlm-ta): eLife
                Journal ID (iso-abbrev): Elife
                Journal ID (hwp): eLife
                Journal ID (publisher-id): eLife
                Title: eLife
                Publisher: eLife Sciences Publications, Ltd
                ISSN (Electronic): 2050-084X
                Publication date (Electronic, pub): 18 March 2017
                Publication date Collection: 2017
                Volume: 6
                Electronic Location Identifier: e22799
                Affiliations
                [1 ]deptDepartment of Chemistry and Biochemistry , Howard Hughes Medical Institute, University of Colorado Boulder , Boulder, United States
                [2 ]deptDepartment of Biochemistry and Molecular Biology , Colorado State University , Fort Collins, United States
                [3 ]Weill Cornell Graduate School of Medical Sciences , New York, United States
                [4 ]deptMolecular Biology Program , Memorial Sloan Kettering Cancer Center , New York, United States
                [5 ]deptDepartment of Chemistry and Biochemistry , University of Colorado Boulder , Boulder, United States
                [6 ]deptInstitute for Genome Architecture and Function , Colorado State University , Fort Collins, United States
                [7 ]deptBiofrontiers Institute , University of Colorado Boulder , Boulder, United States
                U. Massachusetts Medical School , United States
                U. Massachusetts Medical School , United States
                Author notes
                [†]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-1574-7217
                http://orcid.org/0000-0002-1514-1477
                http://orcid.org/0000-0003-0385-3116
                http://orcid.org/0000-0001-5136-5331
                Article
                Publisher ID: 22799
                DOI: 10.7554/eLife.22799
                PMC ID: 5404915
                PubMed ID: 28315523
                SO-VID: ef79d114-6b8c-4f06-93b9-028314b63c29
                Copyright © © 2017, Mattiroli et al
                License:

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                Date received : 29 October 2016
                Date accepted : 14 March 2017
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                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000011, Howard Hughes Medical Institute;
                Award ID: Investigator
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: GM067777
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004410, European Molecular Biology Organization;
                Award ID: ALTF 1267-2013
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004622, KWF Kankerbestrijding;
                Award ID: 2014-6649
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: MCB-1330019
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: GM114594
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: GM102253
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Subject: Research Article
                Subject: Biochemistry
                Subject: Biophysics and Structural Biology
                Custom metadata
                elife-xml-version 2.5
                Author impact statement After DNA replication, nucleosomes are assembled by two histone chaperone complexes each bound to an H3-H4 histone dimer, suggesting the feasibility for a semi-conservative mode of epigenome inheritance.

                ScienceOpen disciplines: Life sciences
                Keywords: chromatin assembly,dna replication,histone chaperones,s. cerevisiae
                Data availability:
                ScienceOpen disciplines: Life sciences
                Keywords: chromatin assembly, dna replication, histone chaperones, s. cerevisiae

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