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      SAYP and Brahma are important for ‘repressive’ and ‘transient’ Pol II pausing

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          Abstract

          Drosophila SAYP, a homologue of human PHF10/BAF45a, is a metazoan coactivator associated with Brahma and essential for its recruitment on the promoter. The role of SAYP in DHR3 activator-driven transcription of the ftz-f1 gene, a member of the ecdysone cascade was studied. In the repressed state of ftz-f1 in the presence of DHR3, the Pol II complex is pre-recruited on the promoter; Pol II starts transcription but is paused 1.5 kb downstream of the promoter, with SAYP and Brahma forming a ‘nucleosomal barrier’ (a region of high nucleosome density) ahead of paused Pol II. SAYP depletion leads to the removal of Brahma, thereby eliminating the nucleosomal barrier. During active transcription, Pol II pausing at the same point correlates with Pol II CTD Ser2 phosphorylation. SAYP is essential for Ser2 phosphorylation and transcription elongation. Thus, SAYP as part of the Brahma complex participates in both ‘repressive’ and ‘transient’ Pol II pausing.

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          A chromatin landmark and transcription initiation at most promoters in human cells.

          Matthew Guenther, Stuart S. Levine, Laurie A. Boyer … (2007)
          We describe the results of a genome-wide analysis of human cells that suggests that most protein-coding genes, including most genes thought to be transcriptionally inactive, experience transcription initiation. We found that nucleosomes with H3K4me3 and H3K9,14Ac modifications, together with RNA polymerase II, occupy the promoters of most protein-coding genes in human embryonic stem cells. Only a subset of these genes produce detectable full-length transcripts and are occupied by nucleosomes with H3K36me3 modifications, a hallmark of elongation. The other genes experience transcription initiation but show no evidence of elongation, suggesting that they are predominantly regulated at postinitiation steps. Genes encoding most developmental regulators fall into this group. Our results also identify a class of genes that are excluded from experiencing transcription initiation, at which mechanisms that prevent initiation must predominate. These observations extend to differentiated cells, suggesting that transcription initiation at most genes is a general phenomenon in human cells.
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            The DNA-encoded nucleosome organization of a eukaryotic genome.

            Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf … (2009)
            Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.
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              Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter.

              Raphaël Métivier, Graziella Penot, Michael Hübner … (2003)
              Transcriptional activation of a gene involves an orchestrated recruitment of components of the basal transcription machinery and intermediate factors, concomitant with an alteration in local chromatin structure generated by posttranslational modifications of histone tails and nucleosome remodeling. We provide here a comprehensive picture of events resulting in transcriptional activation of a gene, through evaluating the estrogen receptor-alpha (NR3A1) target pS2 gene promoter in MCF-7 cells. This description integrates chromatin remodeling with a kinetic evaluation of cyclical networks of association of 46 transcription factors with the promoter, as determined by chromatin immunoprecipitation assays. We define the concept of a "transcriptional clock" that directs and achieves the sequential and combinatorial assembly of a transcriptionally productive complex on a promoter. Furthermore, the unanticipated findings of key roles for histone deacetylases and nucleosome-remodeling complexes in limiting transcription implies that transcriptional activation is a cyclical process that requires both activating and repressive epigenetic processes.
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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
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: August 2012
                Publication date (Print): August 2012
                Publication date (Electronic): 24 May 2012
                Publication date PMC-release: 24 May 2012
                Volume: 40
                Issue: 15
                Pages: 7319-7331
                Affiliations
                1Group of Transcription and mRNA Transport, 2Department of Regulation of Gene Expression, Institute of Gene Biology, Russian Academy of Sciences, 3University of Oslo, Centre for Medical Studies in Russia, Moscow 119334 and 4Department of Transcription Factors, Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
                Author notes
                *To whom correspondence should be addressed. Tel: +7 499 135 9731; Fax: +7 499 135 4105; Email: nvorobyova@ 123456gmail.com
                Correspondence may also be addressed to Yulii V. Shidlovskii. Tel: +7 499 135 9731; Fax: +7 499 135 4105; Email: yul@ 123456genebiology.ru
                Correspondence may also be addressed to Sofia G. Georgieva. Tel: +7 499 135 9729; Fax: +7 499 135 0541; Email: sonjag@ 123456molbiol.edu.ru
                Article
                Publisher ID: gks472
                DOI: 10.1093/nar/gks472
                PMC ID: 3424582
                PubMed ID: 22638575
                SO-VID: c464b920-76ef-44ca-9928-498b916bcce1
                Copyright © © The Author(s) 2012. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 12 December 2011
                Date revision received : 26 April 2012
                Date accepted : 2 May 2012
                Page count
                Pages: 13
                Categories
                Subject: Gene Regulation, Chromatin and Epigenetics

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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