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Aibin He


Aibin He


Email: ahe(at)pku(dot)edu(dot)cn

Lab Homepage: http://www.imm.pku.edu.cn/wzsy/kytd/32746.htm


Research Area:

    The He lab has a long-standing interest in principles in controlling cell fate decisions and coordinating cell behaviors for mammalian organ formation, and cardiovascular diseases and regeneration To achieve these goals, we have developed a number of novel technologies, including single-cell ChIP-seq (itChIP and CoBATCH) and in toto live-imaging in recent years. We, for the first time, presented a framework of coupling long-term live imaging with digital lineage reconstructions to track uninterrupted cell lineage histories across their past, present, and future to reveal organ-level morphogenetic mechanisms in mammals. Further efforts are directed to devise new single-cell multimodal omics to elucidate the epigenetic mechanisms of gene regulation during cell fate determination, and integrate time-resolved live-imaging methods with single-cell molecular profiling to decipher the holistic blueprint for organ generation and regeneration. We also aspire to apply these cool technologies to early diagnosis of diseases, including myocardial infarction and various blood diseases. We are an interdisciplinary team, combining expertise from developmental biology, epigenetics, bioinformatics, light-sheet microscopy, quantitative imaging analysis and mathematical modeling.

Selected Publications:

1. Yue Y, Zong W, Li X, Li J, Zhang Y, Wu R, Liu Y, Cui J, Wang Q, Bian Y, Yu X, Liu Y, Tan G, Zhang Y, Zhao G, Zhou B, Chen L, Xiao W#, Cheng H#, and He, A#. Long-term live imaging reconstructs in toto cardiomyocyte behaviors underlying mammalian heart chamber formation. Nature Cell Biology. 2020; 22, 332–340.
2. Ai S, Xiong H, Li CC, Luo Y, Shi Q, Liu Y, Yu X, Li C and He A. Profiling chromatin state by single-cell itChIP-seq. Nature Cell Biology. 2019; 21(9):1164-1172. 
3. Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J and He A. CoBATCH for High-throughput Single-cell Epigenomic Profiling. Mol Cell. 2019; 76(1):206-216.
4. Xiong H, Luo Y, Yue Y, Zhang J, Ai S, Li X, Wang X, Zhang YL, Wei Y, Li H, Hu X, Li C and He A. Single-Cell Transcriptomics Reveals Chemotaxis Mediated Intra-Organ Crosstalk During Cardiogenesis. Circ Res. 2019; 125(4):398-410.
5. Li Y, Ai S, Yu X, Li C, Li X, Yue Y, Wei Y, Li CY# and He A#. Replication-Independent Histone Turnover Underlines the Epigenetic Homeostasis in Adult Heart. Circ Res. 2019; 125(2):198-208.
6. Han X, Zhang J, Liu Y, Fan X, Ai S, Luo Y, Li X, Jin H, Luo S, Zheng H, Yue Y, Chang Z, Yang Z, Tang F, He A# and Shen X#. The lncRNA Hand2os1/Uph locus orchestrates heart development through regulation of precise expression of Hand2. Development. 2019; 146(13).
7. Li Y, Li C, Li S, Peng Q, An NA, He A# and Li CY#. Human exonization through differential nucleosome occupancy. Proc Natl Acad Sci U S A. 2018;115:8817-8822.
8. Ai S, Yu X, Li Y, Peng Y, Li C, Yue Y, Tao G, Li C-Y, Pu WT and He A. Divergent Requirements for EZH1 in Heart Development Versus Regeneration. Circ Res. 2017;121:106-112.
9. Ai S, Peng Y, Li C, Gu F, Yu X, Yue Y, Ma Q, Chen J, Lin Z, Zhou P, Xie H, Prendiville TW, Zheng W, Liu Y, Orkin SH, Wang D-Z, Yu J, Pu WT# and He A#. EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent. Elife. 2017;6. 
10. Chen JY, Shen QS, Zhou WZ, Peng J, He BZ, Li Y, Liu CJ, Luan X, Ding W, Li S, Chen C, Tan BC, Zhang YE, He A#, Li CY#. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet. 2015;11:e1005391. 
11. He A#*, Gu F*, Hu Y, Ma Q, Yi Ye L, Akiyama JA, Visel A, Pennacchio LA, Pu WT#. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014;5:4907. 
12. He A, Shen X, Ma Q, Cao J, von Gise A, Zhou P, Wang G, Marquez VE, Orkin SH and Pu WT. PRC2 directly methylates GATA4 and represses its transcriptional activity. Genes Dev. 2012;26:37-42.
13. He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG and Pu WT. Polycomb Repressive Complex 2 Regulates Normal Development of the Mouse Heart. Circ Res. 2012;110:406-15.
14. He A*, Kong SW*, Ma Q and Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A. 2011;108:5632-7.
15. Ikeda S*, He A*, Kong SW, Lu J, Bejar R, Bodyak N, Lee KH, Ma Q, Kang PM, Golub TR and Pu WT. MicroRNA-1 negatively regulates expression of the hypertrophy-associated calmodulin and Mef2a genes. Mol Cell Biol. 2009;29:2193-204.
16. He A, Zhu L, Gupta N, Chang Y and Fang F. Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. Mol Endocrinol. 2007;21:2785-94.


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