TY - JOUR
T1 - Subnucleosomal structures and nucleosome asymmetry across a genome
AU - Rhee, Ho Sung
AU - Bataille, Alain R.
AU - Zhang, Liye
AU - Pugh, B. Franklin
N1 - Funding Information:
We thank Yunfei Li, Rohit Reja, and William Lai for bioinformatic support, Matthew Rossi for sharing unpublished ChIP input DNA data, and members of the Pugh laboratory, the Penn State Center for Eukaryotic Gene Regulation, and Philipp Korber for valuable discussions. We are grateful to Bongsoo Park for computational assistance. National Institutes of Health grant HG004160 supported this work. B.F.P. has a financial interest in Peconic, LLC, which utilizes the ChIP-exo technology implemented in this study and could potentially benefit from the outcomes of this research.
Publisher Copyright:
© 2014 Elsevier Inc.
PY - 2014/12/4
Y1 - 2014/12/4
N2 - Genes are packaged into nucleosomal arrays, each nucleosome typically having two copies of histones H2A, H2B, H3, and H4. Histones have distinct posttranslational modifications, variant isoforms, and dynamics. Whether each histone copy within a nucleosome has distinct properties, particularly in relation to the direction of transcription, is unknown. Here we use chromatin immunoprecipitation-exonuclease (ChIP-exo) to resolve the organization of individual histones on a genomic scale. We detect widespread subnucleosomal structures in dynamic chromatin, including what appear to be half-nucleosomes consisting of one copy of each histone. We also detect interactions of H3 tails with linker DNA between nucleosomes, which may be negatively regulated by methylation of H3K36. Histone variant H2A.Z is enriched on the promoter-distal half of the +1 nucleosome, whereas H2BK123 ubiquitylation and H3K9 acetylation are enriched on the promoter-proximal half in a transcription-linked manner. Subnucleosome asymmetries might serve as molecular beacons that guide transcription.
AB - Genes are packaged into nucleosomal arrays, each nucleosome typically having two copies of histones H2A, H2B, H3, and H4. Histones have distinct posttranslational modifications, variant isoforms, and dynamics. Whether each histone copy within a nucleosome has distinct properties, particularly in relation to the direction of transcription, is unknown. Here we use chromatin immunoprecipitation-exonuclease (ChIP-exo) to resolve the organization of individual histones on a genomic scale. We detect widespread subnucleosomal structures in dynamic chromatin, including what appear to be half-nucleosomes consisting of one copy of each histone. We also detect interactions of H3 tails with linker DNA between nucleosomes, which may be negatively regulated by methylation of H3K36. Histone variant H2A.Z is enriched on the promoter-distal half of the +1 nucleosome, whereas H2BK123 ubiquitylation and H3K9 acetylation are enriched on the promoter-proximal half in a transcription-linked manner. Subnucleosome asymmetries might serve as molecular beacons that guide transcription.
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U2 - 10.1016/j.cell.2014.10.054
DO - 10.1016/j.cell.2014.10.054
M3 - Article
C2 - 25480300
AN - SCOPUS:84923596623
SN - 0092-8674
VL - 159
SP - 1377
EP - 1388
JO - Cell
JF - Cell
IS - 6
ER -