Previously we have studied 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. The epigenetic states of chromatin are regulated by a variety of histone modification enzymes and other chromatin binding factors. Our previous work showed that histone variant H2A.Z critically contributes to transcriptional regulation. To understand how H2A.Z influences transcription, we developed a novel technique, bPPI-seq, to identify genome-wide H2A.Z-interacting proteins in vivo. We show that bPPI-seq is a sensitive and robust technique to identify protein-protein interactions in vivo. Our data indicate that H2A.Z-interacting proteins and H2A-interacting proteins participated in distinct biological processes. The H2A.Z-interacting proteins involved in transcriptional regulation process while most of these terms are not significantly enriched in H2A-interacting proteins. We found that the transcription factor Osr1 interacts with H2A.Z both in vitro and in vivo. Also, it mediates H2A.Z incorporation to a large number of target sites and regulates gene expression. Our data indicate that bPPI-seq can be widely applied to identify genome-wide interacting proteins under physiological conditions. To develop more technologies that can be used to analyze the mammalian epigenomes, we developed 3e Hi-C for analyzing the three dimensional organization in the nucleus (Ren et al., Mol Cell 2017). To characterize genome-wide enhancer-promoter interactions at high resolution, we developed a novel technique, Transposition-mediated Analysis of Chromatin Looping (Trac-looping) (Nature Methods, in press). To analyze the epigenome at a single-cell level, in addition to the previous single-cell DNase-seq assay (Nature 2015), we have developed a single-cell MNase-seq for analysis of genome-wide nucleosome positions (Nature in press).

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U.S. National Heart Lung and Blood Inst
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Baranello, Laura; Kouzine, Fedor; Wojtowicz, Damian et al. (2018) Mapping DNA Breaks by Next-Generation Sequencing. Methods Mol Biol 1672:155-166
Yohe, Marielle E; Gryder, Berkley E; Shern, Jack F et al. (2018) MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma. Sci Transl Med 10:
Hodges, H Courtney; Stanton, Benjamin Z; Cermakova, Katerina et al. (2018) Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nat Struct Mol Biol 25:61-72
Resto, Melissa; Kim, Bong-Hyun; Fernandez, Alfonso G et al. (2017) O-GlcNAcase is an RNA polymerase II elongation factor coupled to pausing factors SPT5 and TIF1?. J Biol Chem 292:16524-16525
Gryder, Berkley E; Yohe, Marielle E; Chou, Hsien-Chao et al. (2017) PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability. Cancer Discov 7:884-899
Miller, Erik L; Hargreaves, Diana C; Kadoch, Cigall et al. (2017) TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol 24:344-352
Nakayama, Robert T; Pulice, John L; Valencia, Alfredo M et al. (2017) SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet 49:1613-1623
Stanton, Benjamin Z; Hodges, Courtney; Calarco, Joseph P et al. (2017) Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nat Genet 49:282-288
Cooper, James; Ding, Yi; Song, Jiuzhou et al. (2017) Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing. Nat Protoc 12:2342-2354
Stanton, Benjamin Z; Hodges, Courtney; Crabtree, Gerald R et al. (2017) A General Non-Radioactive ATPase Assay for Chromatin Remodeling Complexes. Curr Protoc Chem Biol 9:1-10

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