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      SWI/SNF Chromatin-remodeling Factors: Multiscale Analyses and Diverse Functions*

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          Abstract

          Chromatin-remodeling enzymes play essential roles in many biological processes, including gene expression, DNA replication and repair, and cell division. Although one such complex, SWI/SNF, has been extensively studied, new discoveries are still being made. Here, we review SWI/SNF biochemistry; highlight recent genomic and proteomic advances; and address the role of SWI/SNF in human diseases, including cancer and viral infections. These studies have greatly increased our understanding of complex nuclear processes.

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          Structure and mechanism of helicases and nucleic acid translocases.

          Martin R. Singleton, Mark S Dillingham, Dale B Wigley (2007)
          Helicases and translocases are a ubiquitous, highly diverse group of proteins that perform an extraordinary variety of functions in cells. Consequently, this review sets out to define a nomenclature for these enzymes based on current knowledge of sequence, structure, and mechanism. Using previous definitions of helicase families as a basis, we delineate six superfamilies of enzymes, with examples of crystal structures where available, and discuss these structures in the context of biochemical data to outline our present understanding of helicase and translocase activity. As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized.
          Article 0 comments Cited 440 times – based on 0 reviews     Review now
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            Chromatin remodelling during development.

            Lena Ho, Gerald R Crabtree (2010)
            New methods for the genome-wide analysis of chromatin are providing insight into its roles in development and their underlying mechanisms. Current studies indicate that chromatin is dynamic, with its structure and its histone modifications undergoing global changes during transitions in development and in response to extracellular cues. In addition to DNA methylation and histone modification, ATP-dependent enzymes that remodel chromatin are important controllers of chromatin structure and assembly, and are major contributors to the dynamic nature of chromatin. Evidence is emerging that these chromatin-remodelling enzymes have instructive and programmatic roles during development. Particularly intriguing are the findings that specialized assemblies of ATP-dependent remodellers are essential for establishing and maintaining pluripotent and multipotent states in cells.
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              Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

              Andrew Flaus, David Martin, Geoffrey J. Barton … (2006)
              The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
              Article 0 comments Cited 233 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Biol Chem
                Journal ID (iso-abbrev): J. Biol. Chem
                Journal ID (hwp): jbc
                Journal ID (pmc): jbc
                Journal ID (publisher-id): JBC
                Title: The Journal of Biological Chemistry
                Publisher: American Society for Biochemistry and Molecular Biology (9650 Rockville Pike, Bethesda, MD 20814, U.S.A. )
                ISSN (Print): 0021-9258
                ISSN (Electronic): 1083-351X
                Publication date (Print): 7 September 2012
                Publication date (Electronic): 5 September 2012
                Publication date PMC-release: 5 September 2012
                Volume: 287
                Issue: 37
                Pages: 30897-30905
                Affiliations
                From the [‡ ]Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120 and
                the [§ ]Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
                Author notes
                [1 ] To whom correspondence should be addressed. E-mail: mpsnyder@ 123456stanford.edu .
                Article
                Publisher ID: R111.309302
                DOI: 10.1074/jbc.R111.309302
                PMC ID: 3438922
                PubMed ID: 22952240
                SO-VID: a319d8f3-7f22-4551-a6b5-ce97c7dc933d
                Copyright © © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.
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                Author's Choice—Final version full access.

                Creative Commons Attribution Non-Commercial License applies to Author Choice Articles

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                Subject: Minireviews

                ScienceOpen disciplines: Biochemistry
                Keywords: mass spectrometry (ms),chromatin,transcriptional regulation,chromatin immunoprecipitation (chip),dna sequencing,chromatin remodeling,hiv-1,swi/snf,viral transcription,cancer
                Data availability:
                ScienceOpen disciplines: Biochemistry
                Keywords: mass spectrometry (ms), chromatin, transcriptional regulation, chromatin immunoprecipitation (chip), dna sequencing, chromatin remodeling, hiv-1, swi/snf, viral transcription, cancer

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