A quantitative analysis of the impact on chromatin accessibility by histone modifications and binding of transcription factors in DNase I hypersensitive sites.
It is known that chromatin features such as histone modifications and the binding of transcription factors exert a significant impact on the "openness" of chromatin. In this study, we present a quantitative analysis of the genome-wide relationship between chromatin features and chromatin accessibility in DNase I hypersensitive sites. We found that these features show distinct preference to localize in open chromatin. In order to elucidate the exact impact, we derived quantitative models to directly predict the "openness" of chromatin using histone modification features and transcription factor binding features, respectively. We show that these two types of features are highly predictive for chromatin accessibility in a statistical viewpoint. Moreover, our results indicate that these features are highly redundant and only a small number of features are needed to achieve a very high predictive power. Our study provides new insights into the true biological phenomena and the combinatorial effects of chromatin features to differential DNase I hypersensitivity.
School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China ; Shanghai Center for Bioinformation Technology, 1278 Ke Yuan Road, Shanghai 201203, China.
Peng
P
Cui
Jing
J
Li
Bo
B
Sun
Menghuan
M
Zhang
Baofeng
B
Lian
Yixue
Y
Li
Lu
L
Xie
D000465:Algorithms; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D015894:Genome, Human; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D011485:Protein Binding; D060388:Support Vector Machine; D014157:Transcription Factors / Q000378:metabolism*
D002843:Chromatin; D006657:Histones; D014157:Transcription Factors; D003850:Deoxyribonuclease I