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      A base pair resolution map of nucleosome positions in yeast

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      Author(s): 1 , 2 , 2 , 1
      Publication date PMC-release:
      Journal: Nature

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          Abstract

          The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber.

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          A genomic code for nucleosome positioning.

          Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen … (2006)
          Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approximately 50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.
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            The structure of DNA in the nucleosome core.

            Timothy Richmond, Curt Davey (2003)
            The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.
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              Nascent transcript sequencing visualizes transcription at nucleotide resolution.

              L Stirling Churchman, Jonathan S Weissman (2011)
              Recent studies of transcription have revealed a level of complexity not previously appreciated even a few years ago, both in the intricate use of post-initiation control and the mass production of rapidly degraded transcripts. Dissection of these pathways requires strategies for precisely following transcripts as they are being produced. Here we present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3' ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that although promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus, nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 0410462
                Journal ID (pubmed-jr-id): 6011
                Journal ID (nlm-ta): Nature
                Journal ID (iso-abbrev): Nature
                Title: Nature
                ISSN (Print): 0028-0836
                ISSN (Electronic): 1476-4687
                Publication date Nihms-submitted: 16 September 2013
                Publication date (Print): 28 June 2012
                Publication date PMC-release: 30 September 2013
                Volume: 486
                Issue: 7404
                Pages: 496-501
                Affiliations
                [1 ]Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
                [2 ]Department of Statistics, Northwestern University, Evanston, IL, 60208, USA
                Author notes
                [* ]Correspondence should be addressed to J. Wang ( jzwang@ 123456northwestern.edu )
                Article
                Manuscript ID: NIHMS370046
                DOI: 10.1038/nature11142
                PMC ID: 3786739
                PubMed ID: 22722846
                SO-VID: 414a05bb-8cb9-4ce8-83b2-295af8f30f95
                History
                Funding
                Funded by: National Cancer Institute : NCI
                Award ID: U54 CA143869 || CA
                Funded by: National Cancer Institute : NCI
                Award ID: U54 CA143869 || CA
                Funded by: National Institute of General Medical Sciences : NIGMS
                Award ID: R01 GM058617 || GM
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                Subject: Article

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