TY - JOUR
T1 - Genome-wide nucleosome specificity and directionality of chromatin remodelers
AU - Yen, Kuangyu
AU - Vinayachandran, Vinesh
AU - Batta, Kiran
AU - Koerber, R. Thomas
AU - Pugh, B. Franklin
N1 - Funding Information:
We thank Charles V. Meade, David Goffman, Anna Chan, Kasthuri Kannan, and Yunfei Li for assistance in nucleosome preparation, DNA sequencing, and data analysis. This work was funded by National Institutes of Health Grant 5R01HG4160 and The Pennsylvania Department of Health using Tobacco Settlement Funds.
PY - 2012/6/22
Y1 - 2012/6/22
N2 - How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known. We determined the genome-wide binding of remodeler complexes SWI/SNF, RSC, ISW1a, ISW1b, ISW2, and INO80 to individual nucleosomes in Saccharomyces, and determined their functional contributions to nucleosome positioning through deletion analysis. We applied ultra-high-resolution ChIP-exo mapping to Isw2 to determine its subnucleosomal orientation and organization on a genomic scale. Remodelers interacted with selected nucleosome positions relative to the start and end of genes and produced net directionality in moving nucleosomes either away or toward nucleosome-free regions at the 5′ 3′ ends of genes. Isw2 possessed a subnucleosomal organization in accord with biochemical and crystallographic- based models that place its linker binding region within promoters and abutted against Reb1-bound locations. Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays.
AB - How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known. We determined the genome-wide binding of remodeler complexes SWI/SNF, RSC, ISW1a, ISW1b, ISW2, and INO80 to individual nucleosomes in Saccharomyces, and determined their functional contributions to nucleosome positioning through deletion analysis. We applied ultra-high-resolution ChIP-exo mapping to Isw2 to determine its subnucleosomal orientation and organization on a genomic scale. Remodelers interacted with selected nucleosome positions relative to the start and end of genes and produced net directionality in moving nucleosomes either away or toward nucleosome-free regions at the 5′ 3′ ends of genes. Isw2 possessed a subnucleosomal organization in accord with biochemical and crystallographic- based models that place its linker binding region within promoters and abutted against Reb1-bound locations. Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays.
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U2 - 10.1016/j.cell.2012.04.036
DO - 10.1016/j.cell.2012.04.036
M3 - Article
C2 - 22726434
AN - SCOPUS:84862643713
SN - 0092-8674
VL - 149
SP - 1461
EP - 1473
JO - Cell
JF - Cell
IS - 7
ER -