Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation
Da Lin,
Weize Xu,
Ping Hong,
Chengchao Wu,
Zhihui Zhang,
Siheng Zhang,
Lingyu Xing,
Bing Yang,
Wei Zhou,
Qin Xiao,
Jinyue Wang,
Cong Wang,
Yu He,
Xi Chen,
Xiaojian Cao,
Jiangwei Man,
Aikebaier Reheman,
Xiaofeng Wu,
Xingjie Hao,
Zhe Hu,
Chunli Chen,
Zimeng Cao,
Rong Yin,
Zhen F. Fu,
Rong Zhou,
Zhaowei Teng,
Guoliang Li (guoliang.li@mail.hzau.edu.cn) and
Gang Cao (gcao@mail.hzau.edu.cn)
Additional contact information
Da Lin: Huazhong Agricultural University
Weize Xu: Huazhong Agricultural University
Ping Hong: Huazhong Agricultural University
Chengchao Wu: Huazhong Agricultural University
Zhihui Zhang: Huazhong Agricultural University
Siheng Zhang: Huazhong Agricultural University
Lingyu Xing: Huazhong Agricultural University
Bing Yang: Huazhong Agricultural University
Wei Zhou: Huazhong Agricultural University
Qin Xiao: Huazhong Agricultural University
Jinyue Wang: Huazhong Agricultural University
Cong Wang: Huazhong Agricultural University
Yu He: Huazhong Agricultural University
Xi Chen: Huazhong Agricultural University
Xiaojian Cao: Huazhong Agricultural University
Jiangwei Man: Huazhong Agricultural University
Aikebaier Reheman: Huazhong Agricultural University
Xiaofeng Wu: Huazhong Agricultural University
Xingjie Hao: Huazhong University of Science and Technology
Zhe Hu: Huazhong Agricultural University
Chunli Chen: Huazhong Agricultural University
Zimeng Cao: Huazhong Agricultural University
Rong Yin: Zhongnan Hospital of Wuhan University
Zhen F. Fu: University of Georgia
Rong Zhou: Zhongnan Hospital of Wuhan University
Zhaowei Teng: Affiliated Hospital of Kunming University of Science and Technology
Guoliang Li: Huazhong Agricultural University
Gang Cao: Huazhong Agricultural University
Nature Communications, 2022, vol. 13, issue 1, 1-19
Abstract:
Abstract Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose “degree of disorder” to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.
Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33558-5
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DOI: 10.1038/s41467-022-33558-5
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