A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

被引：180

作者：

Jiang, Cizhong ^{[1
]}

Pugh, B. Franklin ^{[1
]}

机构：

[1] Penn State Univ, Ctr Eukaryot Gene Regulat, N Frear Lab 456, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 10期

关键词：

HIGH-RESOLUTION; DNA; TRANSCRIPTION; YEAST; ORGANIZATION; POLY(DA-DT); PARTICLE; CORE;

D O I：

10.1186/gb-2009-10-10-r109

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/.

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页数：11

相关论文

共 28 条

[1] GeneTrack - a genomic data processing and visualization framework [J].

Albert, Istvan ;

Wachi, Shinichiro ;

Jiang, Cizhong ;

Pugh, Franklin .

BIOINFORMATICS, 2008, 24 (10) :1305-1306

[2] Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome [J].

Albert, Istvan ;

Mavrich, Travis N. ;

Tomsho, Lynn P. ;

Qi, Ji ;

Zanton, Sara J. ;

Schuster, Stephan C. ;

Pugh, B. Franklin .

NATURE, 2007, 446 (7135) :572-576

[3] Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites [J].

Anderson, JD ;

Widom, J .

MOLECULAR AND CELLULAR BIOLOGY, 2001, 21 (11) :3830-3839

[4]

[Anonymous], 2007, SACCHAROMYCES GENOME

[5] Chromatin dynamics at DNA replication, transcription and repair [J].

Ehrenhofer-Murray, AE .

EUROPEAN JOURNAL OF BIOCHEMISTRY, 2004, 271 (12) :2335-2349

[6] Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals [J].

Field, Yair ;

Kaplan, Noam ;

Fondufe-Mittendorf, Yvonne ;

Moore, Irene K. ;

Sharon, Eilon ;

Lubling, Yaniv ;

Widom, Jonathan ;

Segal, Eran .

PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (11)

[7] Mechanisms that Specify Promoter Nucleosome Location and Identity [J].

Hartley, Paul D. ;

Madhani, Hiten D. .

CELL, 2009, 137 (03) :445-458

[8] POLY(DA-DT), A UBIQUITOUS PROMOTER ELEMENT THAT STIMULATES TRANSCRIPTION VIA ITS INTRINSIC DNA-STRUCTURE [J].

IYER, V ;

STRUHL, K .

EMBO JOURNAL, 1995, 14 (11) :2570-2579

[9] The DNA-encoded nucleosome organization of a eukaryotic genome [J].

Kaplan, Noam ;

Moore, Irene K. ;

Fondufe-Mittendorf, Yvonne ;

Gossett, Andrea J. ;

Tillo, Desiree ;

Field, Yair ;

LeProust, Emily M. ;

Hughes, Timothy R. ;

Lieb, Jason D. ;

Widom, Jonathan ;

Segal, Eran .

NATURE, 2009, 458 (7236) :362-U129

[10] Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome [J].

Koerber, R. Thomas ;

Rhee, Ho Sung ;

Jiang, Cizhong ;

Pugh, B. Franklin .

MOLECULAR CELL, 2009, 35 (06) :889-902