Genome-wide analysis of chromatin modifications

National Heart, Lung, And Blood Institute

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Abstract

Previously we have studies the contribution of histone modifications, DNA methylation and their regulatory enzymes to transcriptional regulation in a variety of cellular systems. Recent studies have suggested cellular heterogeneity in gene expression even in the same cell population. The question is whether there is a similar heterogeneity in chromatin states in the apparently same cells. To address this question, we have developed the single-cell DNase-seq technique that can be used to detect chromatin states in single-cells or small number of primary cells. By applying this technique to NIH3T3 and mouse ES cells, we show the the heterogeneity of chromatin accessibility underlies the heterogeneity of gene expression across different cells. We also demonstrated its application in identifying potential functional mutations in human cancers. We have recently collaborated with Dr. Yi Zhang's lab on application of this technique to investigate dynamic changes of chromatin during mouse preimplantation development. We show that the DHS landscape is progressively established with a drastic increase at the 8-cell stage. Paternal chromatin accessibility is quickly reprogrammed after fertilization to the level similar to maternal chromatin, while imprinted genes exhibit allelic accessibility bias. We further demonstrate the function of key transcription factors Nfya and Oct4 during this process. In collaboration with Dr. Davide Levens' lab, we investigated the regulation of DNA topology by topoisomerase I, which is regulated by the C-terminus of RNA polymerase II. We show that TOP1 stimulation by Pol II is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release.