Browsing by Author "Li, Guipeng"
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Item 3CPET: Finding Co-Factor Complexes from ChIA-Pet Data Using a Hierarchical Dirichlet Process(BioMed Central Ltd, 2015-12-22) Djekidel, Mohamed Nadhir; Liang, Zhengyu; Wang, Qi; Hu, Zhirui; Li, Guipeng; Chen, Yang; Zhang, Michael Q.; 0000 0001 1707 1372 (Zhang, MQ); Zhang, Michael Q.Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies. 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interactions. 3CPET results show biologically significant and accurate predictions when validated against experimental and simulation data.Item Alterations of Specific Chromatin Conformation Affect ATRA-Induced Leukemia Cell Differentiation(Nature Publishing Group) Li, Yanjian; He, Yi; Liang, Zhengyu; Wang, Yang; Chen, Fengling; Djekidel, Mohamed Nadhir; Li, Guipeng; Zhang, Xu; Xiang, Shuqin; Wang, Zejun; Gao, Juntao; Zhang, Michael Q.; Chen, Yang; 0000 0001 1707 1372 (Zhang, MQ); Zhang, Michael Q.Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-induced HL-60 cell differentiation model. The results showed that the boundaries of topological associated domains (TADs) were stable during differentiation; however, the chromatin conformations within several specific TADs were obviously changed. By combining H3K4me3, H3K27ac, and Hi-C signals, we annotated the differential gene- regulatory chromatin interactions upon ATRA induction. The gains and losses of the gene-regulatory chromatin interactions are significantly correlated with gene expression and chromatin accessibility. Finally, we found that the loss of GATA2 expression and DNA binding are crucial for the differentiation process, and changes in the chromatin structure around the GATA2 regulate its expression upon ATRA induction. This study provided both statistical insights and experimental details regarding the relationship between chromatin conformation changes and transcription regulation during leukemia cell differentiation, and the results suggested that the chromatin conformation is a new type of potential drug target for cancer therapy.