亚博首页手机登录网址-最新版

研究方向:

 研究室致力于研究器官(含心脏)发育起源与再生的细胞与分子机制。我们的研究集中在如下两个方向:1. 胚胎期中胚层来源器官(含心脏)干细胞特化与分化的表观遗传调控机制,以及先心病产生的细胞起源机理。我们利用/发展单细胞转录组与表观遗传学技术等手段,探索组织干细胞特化与命运决定的关键增强子组与其调控的转录因子网络。2. 实时成像结合数学模型绘制器官(心脏)发育起源/异常心脏再生的细胞学图谱。我们利用光片显微镜与图像图形处理技术,结合细胞谱系示踪,追踪心脏干细胞的增殖、分化、迁移和分配,绘制细胞图谱。本实验室综合运用发育生物学、表观遗传学、生物信息学、光片显微镜技术和数学建模等多学科交叉工具与方法,解决上述科学问题

研究室成员

研究室主任(PI):何爱彬 研究员 Ph.D Email: ahe@pku.edu.cn

科研助理:刘飞

研究生:罗颖洁、李鑫、岳晏竹、余先红、李晨、张幼东、王千昊、刘雅茜、边云堃、刘敏、刘笑歌

客座学生:张萍

实习本科生学生:高姝(天津大学)、闫帅方(北京师范大学)

研究室地址:亚博首页手机登录网址综合科研楼220-221室,北京,100871.

实验室电话:010-6274-4560

实验室网址:aibinlab.org

代表性科研论文:

1. Xiong H, Luo Y, Wang Q, Yu X and He, A. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions. Nature Methods. 2021.

2. 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.

3. 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. 

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

合作论文:

1.  Xiong H, Luo Y, Wang Q, Yu X and He A. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions. Nat Methods. 2021.

2.  Xiong H and He A. Single-Cell Transcriptomic Analysis of Cardiac Progenitor Differentiation. Curr Cardiol Rep. 2020;22:38.

3.  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, in toto live imaging of cardiomyocyte behaviour during mouse ventricle chamber formation at single-cell resolution. Nat Cell Biol. 2020;22:332-340.

4.  Hu X, Deng Q, Ma L, Li Q, Chen Y, Liao Y, Zhou F, Zhang C, Shao L, Feng J, He T, Ning W, Kong Y, Huo Y, He A, Liu B, Zhang J, Adams R, He Y, Tang F, Bian X and Luo J. Meningeal lymphatic vessels regulate brain tumor drainage and immunity. Cell Res. 2020;30:229-243.

5.  Chang L, Li M, Shao S, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C and Sun Y. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell. 2020.

6.  Li R, Xia X, Wang X, Sun X, Dai Z, Huo D, Zheng H, Xiong H, He A and Wu X. Generation and validation of versatile inducible CRISPRi embryonic stem cell and mouse model. PLoS Biol. 2020;18:e3000749.

7.  Ai S, Xiong H, Li CC, Luo Y, Shi Q, Liu Y, Yu X, Li C and He A. Profiling chromatin states using single-cell itChIP-seq. Nat Cell Biol. 2019;21:1164-1172.

8.  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.

9.  Yang R, Cheng S, Luo N, Gao R, Yu K, Kang B, Wang L, Zhang Q, Fang Q, Zhang L, Li C, He A, Hu X, Peng J, Ren X and Zhang Z. Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biol. 2019;21:2.

10. Du Z, Zheng H, Kawamura YK, Zhang K, Gassler J, Powell S, Xu Q, Lin Z, Xu K, Zhou Q, Ozonov EA, Veron N, Huang B, Li L, Yu G, Liu L, Au Yeung WK, Wang P, Chang L, Wang Q, He A, Sun Y, Na J, Sun Q, Sasaki H, Tachibana K, Peters A and Xie W. Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos. Mol Cell. 2020;77:825-839 e7.

11. 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.

12. 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;125:198-208.

13. 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.

14. Liu L, Cai J, Wang H, Liang X, Zhou Q, Ding C, Zhu Y, Fu T, Guo Q, Xu Z, Xiao L, Liu J, Yin Y, Fang L, Xue B, Wang Y, Meng ZX, He A, Li JL, Liu Y, Chen XW and Gan Z. Coupling of COPII vesicle trafficking to nutrient availability by the IRE1alpha-XBP1s axis. Proc Natl Acad Sci U S A. 2019;116:11776-11785.

15. Ma C, Niu R, Huang T, Shao LW, Peng Y, Ding W, Wang Y, Jia G, He C, Li CY, He A and Liu Y. N6-methyldeoxyadenine is a transgenerational epigenetic signal for mitochondrial stress adaptation. Nat Cell Biol. 2019;21:319-327.

16. An NA, Ding W, Yang XZ, Peng J, He BZ, Shen QS, Lu F, He A, Zhang YE, Tan BC, Chen JY and Li CY. Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. Genome Biol. 2019;20:24.

17. 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.

18. Zhang M, Dong Y, Hu F, Yang D, Zhao Q, Lv C, Wang Y, Xia C, Weng Q, Liu X, Li C, Zhou P, Wang T, Guan Y, Guo R, Liu L, Geng Y, Wu H, Du J, Hu Z, Xu S, Chen J, He A, Liu B, Wang D, Yang YG and Wang J. Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes. Nat Immunol. 2018;19:279-290.

19. Zhou P, Gu F, Zhang L, Akerberg BN, Ma Q, Li K, He A, Lin Z, Stevens SM, Zhou B and Pu WT. Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq. Elife. 2017;6.

20. Zhang S-J, Wang C, Yan S, Fu A, Luan X, Li Y, Sunny Shen Q, Zhong X, Chen J-Y, Wang X, Chin-Ming Tan B, He A and Li C-Y. Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. Mol Biol Evol. 2017;34:2453-2468.

21. Yang Y, Liu B, Xu J, Wang J, Wu J, Shi C, Xu Y, Dong J, Wang C, Lai W, Zhu J, Xiong L, Zhu D, Li X, Yang W, Yamauchi T, Sugawara A, Li Z, Sun F, Li X, Li C, He A, Du Y, Wang T, Zhao C, Li H, Chi X, Zhang H, Liu Y, Li C, Duo S, Yin M, Shen H, Belmonte JCI and Deng H. Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Cell. 2017;169:243-257.e25.

22. Wang F, Song W, Zhao H, Ma Y, Li Y, Zhai D, Pi J, Si Y, Xu J, Dong L, Su R, Zhang M, Zhu Y, Ren X, Miao F, Liu W, Li F, Zhang J, He A, Shan G, Hui J, Wang L and Yu J. The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis. Cell Res. 2017;27:416-439.

23. Han X, Li P, Yang Z, Huang X, Wei G, Sun Y, Kang X, Hu X, Deng Q, Chen L, He A, Huo Y, Li D, Betzig E and Luo J. Zyxin regulates endothelial von Willebrand factor secretion by reorganizing actin filaments around exocytic granules. Nat Commun. 2017;8:14639.

24. 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.

25. 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.

26. Xiao C, Gao L, Hou Y, Xu C, Chang N, Wang F, Hu K, He A, Luo Y, Wang J, Peng J, Tang F, Zhu X and Xiong J-W. Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nat Commun. 2016;7:13787.

27. Lin Z, Guo H, Cao Y, Zohrabian S, Zhou P, Ma Q, VanDusen N, Guo Y, Zhang J, Stevens SM, Liang F, Quan Q, van Gorp PR, Li A, Dos Remedios C, He A, Bezzerides VJ and Pu WT. Acetylation of VGLL4 Regulates Hippo-YAP Signaling and Postnatal Cardiac Growth. Dev Cell. 2016.

28. Prendiville TW, Guo H, Lin Z, Zhou P, Stevens SM, He A, VanDusen N, Chen J, Zhong L, Wang D-Z, Gao G and Pu WT. Novel Roles of GATA4/6 in the Postnatal Heart Identified through Temporally Controlled, Cardiomyocyte-Specific Gene Inactivation by Adeno-Associated Virus Delivery of Cre Recombinase. PLoS One. 2015;10:e0128105.

29. Chen J-Y, Shen QS, Zhou W-Z, Peng J, He BZ, Li Y, Liu C-J, Luan X, Ding W, Li S, Chen C, Tan BC-M, Zhang YE, He A and Li C-Y. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet. 2015;11:e1005391.

30. Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang D-Z, Li K, Wang J, Wanders RJA, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK and Pu WT. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat Med. 2014;20:616-23.

31. Wang F, Zhu Y, Guo L, Dong L, Liu H, Yin H, Zhang Z, Li Y, Liu C, Ma Y, Song W, He A, Wang Q, Wang L, Zhang J, Li J and Yu J. A regulatory circuit comprising GATA1/2 switch and microRNA-27a/24 promotes erythropoiesis. Nucleic Acids Res. 2014;42:442-57.

32. Prendiville TW, Ma Q, Lin Z, Zhou P, He A and Pu WT. Ultrasound-guided Transthoracic Intramyocardial Injection in Mice. J Vis Exp. 2014.

33. He A, Gu F, Hu Y, Ma Q, Yi Ye L, Akiyama JA, Visel A, Pennacchio LA and Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014;5:4907.

34. Aronson BE, Rabello Aronson S, Berkhout RP, Chavoushi SF, He A, Pu WT, Verzi MP and Krasinski SD. GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27. Biochim Biophys Acta. 2014.

35. Zhou P, Zhang Y, Ma Q, Gu F, Day DS, He A, Zhou B, Li J, Stevens SM, Romo D and Pu WT. Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification. Proc Natl Acad Sci U S A. 2013;110:15395-400.

36. Ge F, Yuan S, Su L, Shen Z, He A, Huang T and Gong W. Alteration of innate immunity by donor IL-6 deficiency in a presensitized heart transplant model. PLoS One. 2013;8:e77559.

37. Zhou P, He A and Pu WT. Regulation of GATA4 Transcriptional Activity in Cardiovascular Development and Disease. Curr Top Dev Biol. 2012;100:143-69.

38. Ounzain S, Kobayashi S, Peterson RE, He A, Motterle A, Samani NJ, Menick DR, Pu WT, Liang Q and Chong NW. Cardiac expression of ms1/STARS, a novel gene involved in cardiac development and disease, is regulated by GATA4. Mol Cell Biol. 2012;32:1830-43.

39. 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.

40. He A and Pu WT. Mature Cardiomyocytes Recall Their Progenitor Experience Via Polycomb Repressive Complex 2. Circulation Research. 2012;111:162-164.

41. 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.

42. Seok HY, Tatsuguchi M, Callis TE, He A, Pu WT and Wang DZ. miR-155 inhibits expression of the MEF2A protein to repress skeletal muscle differentiation. J Biol Chem. 2011;286:35339-46.

43. Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT and Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics. 2011;27:715-7.

44. 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.

45. He A and Pu WT. Genome-wide location analysis by pull down of in vivo biotinylated transcription factors. Curr Protoc Mol Biol. 2010;Chapter 21:Unit 21.20.

46. 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.

47. 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.

48. He A, Liu X, Liu L, Chang Y and Fang F. How many signals impinge on GLUT4 activation by insulin? Cell Signal. 2007;19:1-7.

专利:

   1. Abin He, Shanshan Ai, and Chen Li. Micro-ChIP (itChIP) Method. PCT patent number: WO/2019/153852.

   2. Abin He, Shanshan Ai, and Yingjie Luo. A Fusion protein for ChIP-seq kit (CoBATCH). PCT patent number: WO/2019/153851.