TY - JOUR
T1 - Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states
AU - Zhou, Jian
AU - Troyanskaya, Olga G.
N1 - Funding Information:
We thank Victoria Yao and Aaron K. Wong for critically reading the manuscript and helpful suggestions. This work was primarily supported by US National Institutes of Health (NIH) grants R01 GM071966 and R01 HG005998 to O.G.T. This work was supported in part by the US National Science Foundation (NSF) CAREER award (DBI-0546275), US NIH award T32 HG003284 and US NIH grant P50 GM071508. O.G.T. is a senior fellow of the Genetic Networks programme of the Canadian Institute for Advanced Research (CIFAR).
Publisher Copyright:
© 2016, Nature Publishing Group. All rights reserved.
PY - 2016/2/4
Y1 - 2016/2/4
N2 - Interpreting the functional state of chromatin from the combinatorial binding patterns of chromatin factors, that is, the chromatin codes, is crucial for decoding the epigenetic state of the cell. Here we present a systematic map of Drosophila chromatin states derived from data-driven probabilistic modelling of dependencies between chromatin factors. Our model not only recapitulates enhancer-like chromatin states as indicated by widely used enhancer marks but also divides these states into three functionally distinct groups, of which only one specific group possesses active enhancer activity. Moreover, we discover a strong association between one specific enhancer state and RNA Polymerase II pausing, linking transcription regulatory potential and chromatin organization. We also observe that with the exception of long-intron genes, chromatin state transition positions in transcriptionally active genes align with an absolute distance to their corresponding transcription start site, regardless of gene length. Using our method, we provide a resource that helps elucidate the functional and spatial organization of the chromatin code landscape.
AB - Interpreting the functional state of chromatin from the combinatorial binding patterns of chromatin factors, that is, the chromatin codes, is crucial for decoding the epigenetic state of the cell. Here we present a systematic map of Drosophila chromatin states derived from data-driven probabilistic modelling of dependencies between chromatin factors. Our model not only recapitulates enhancer-like chromatin states as indicated by widely used enhancer marks but also divides these states into three functionally distinct groups, of which only one specific group possesses active enhancer activity. Moreover, we discover a strong association between one specific enhancer state and RNA Polymerase II pausing, linking transcription regulatory potential and chromatin organization. We also observe that with the exception of long-intron genes, chromatin state transition positions in transcriptionally active genes align with an absolute distance to their corresponding transcription start site, regardless of gene length. Using our method, we provide a resource that helps elucidate the functional and spatial organization of the chromatin code landscape.
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U2 - 10.1038/ncomms10528
DO - 10.1038/ncomms10528
M3 - Article
C2 - 26841971
AN - SCOPUS:84957565411
SN - 2041-1723
VL - 7
JO - Nature communications
JF - Nature communications
M1 - 10528
ER -