Determinants of nucleosome positioning

被引:494
作者
Struhl, Kevin [1 ]
Segal, Eran [2 ,3 ]
机构
[1] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
[2] Weizmann Inst Sci, Dept Comp Sci & Appl Math, IL-76100 Rehovot, Israel
[3] Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel
基金
美国国家卫生研究院; 欧洲研究理事会;
关键词
HISTONE-DNA INTERACTIONS; GENE-EXPRESSION; HIGH-RESOLUTION; IN-VITRO; CHROMATIN; YEAST; TRANSCRIPTION; ORGANIZATION; REVEALS; SEQUENCES;
D O I
10.1038/nsmb.2506
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Nucleosome positioning is critical for gene expression and most DNA-related processes. Here we review the dominant patterns of nucleosome positioning that have been observed and summarize the current understanding of their underlying determinants. The genome-wide pattern of nucleosome positioning is determined by the combination of DNA sequence, ATP-dependent nucleosome remodeling enzymes and transcription factors that include activators, components of the preinitiation complex and elongating RNA polymerase II. These determinants influence each other such that the resulting nucleosome positioning patterns are likely to differ among genes and among cells in a population, with consequent effects on gene expression.
引用
收藏
页码:267 / 273
页数:7
相关论文
共 69 条
[1]   Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans [J].
Adelman, Karen ;
Lis, John T. .
NATURE REVIEWS GENETICS, 2012, 13 (10) :720-731
[2]   A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters [J].
Badis, Gwenael ;
Chan, Esther T. ;
van Bakel, Harm ;
Pena-Castillo, Lourdes ;
Tillo, Desiree ;
Tsui, Kyle ;
Carlson, Clayton D. ;
Gossett, Andrea J. ;
Hasinoff, Michael J. ;
Warren, Christopher L. ;
Gebbia, Marinella ;
Talukder, Shaheynoor ;
Yang, Ally ;
Mnaimneh, Sanie ;
Terterov, Dimitri ;
Coburn, David ;
Yeo, Ai Li ;
Yeo, Zhen Xuan ;
Clarke, Neil D. ;
Lieb, Jason D. ;
Ansari, Aseem Z. ;
Nislow, Corey ;
Hughes, Timothy R. .
MOLECULAR CELL, 2008, 32 (06) :878-887
[3]   A map of nucleosome positions in yeast at base-pair resolution [J].
Brogaard, Kristin ;
Xi, Liqun ;
Wang, Ji-Ping ;
Widom, Jonathan .
NATURE, 2012, 486 (7404) :496-501
[4]   Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output [J].
Celona, Barbara ;
Weiner, Assaf ;
Di Felice, Francesca ;
Mancuso, Francesco M. ;
Cesarini, Elisa ;
Rossi, Riccardo L. ;
Gregory, Lorna ;
Baban, Dilair ;
Rossetti, Grazisa ;
Grianti, Paolo ;
Pagani, Massimiliano ;
Bonaldi, Tiziana ;
Ragoussis, Jiannis ;
Friedman, Nir ;
Camilloni, Giorgio ;
Bianchi, Marco E. ;
Agresti, Alessandra .
PLOS BIOLOGY, 2011, 9 (06)
[5]   Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium [J].
Chang, Gue Su ;
Noegel, Angelika A. ;
Mavrich, Travis N. ;
Mueller, Rolf ;
Tomsho, Lynn ;
Ward, Elissa ;
Felder, Marius ;
Jiang, Cizhong ;
Eichinger, Ludwig ;
Gloeckner, Gernot ;
Schuster, Stephan C. ;
Pugh, B. Franklin .
GENOME RESEARCH, 2012, 22 (06) :1098-1106
[6]   DISTINGUISHING BETWEEN MECHANISMS OF EUKARYOTIC TRANSCRIPTIONAL ACTIVATION WITH BACTERIOPHAGE-T7 RNA-POLYMERASE [J].
CHEN, W ;
TABOR, S ;
STRUHL, K .
CELL, 1987, 50 (07) :1047-1055
[7]   Distinct frequency-distributions of homopolymeric DNA tracts in different genomes [J].
Dechering, KJ ;
Cuelenaere, K ;
Konings, RNH ;
Leunissen, JAM .
NUCLEIC ACIDS RESEARCH, 1998, 26 (17) :4056-4062
[8]   RECONSTITUTION OF SHORT-SPACED CHROMATIN FROM THE HISTONE OCTAMER AND EITHER HMG-14,17 OR HISTONE-H1 [J].
DREW, HR .
JOURNAL OF MOLECULAR BIOLOGY, 1993, 230 (03) :824-836
[9]   DNA BENDING AND ITS RELATION TO NUCLEOSOME POSITIONING [J].
DREW, HR ;
TRAVERS, AA .
JOURNAL OF MOLECULAR BIOLOGY, 1985, 186 (04) :773-790
[10]   Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation [J].
Fan, Xiaochun ;
Moqtaderi, Zarmik ;
Jin, Yi ;
Zhang, Yong ;
Liu, X. Shirley ;
Struhl, Kevin .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (42) :17945-17950