杨红波

基本信息

姓名：

杨红波

职称：

研究员

导师类型：

博士生导师

专业：

遗传学

研究方向：

3D表观基因组学

邮箱地址：

hongboyang@fudan.edu.cn

个人简介

杨红波，复旦大学生殖与发育研究院研究员，1999-2009北京大学生命科学院本科-博士，2010-2015美国圣地亚哥大学医学院心血管系博后，2015-2021历任美国宾州州立大学Hershey医学院生化与分子生物学系和芝加哥西北大学Feinberg医学院生化与分子遗传学系助理教授与研究系列助理教授，主要以人类样本和食蟹猴，小鼠，斑马鱼等模式动物研究人类疾病中的3D表观基因组学调控机制。最主要原创贡献包括研究建立了第一个斑马鱼表观遗传组和3D基因组信息图谱 （2020 Nature）；解析儿童白血病单碱基变异的3D基因组调控功能； （2022 Nature Genetics）；参与“DNA元件百科全书(Encyclopedia of DNA Elements, ENCODE)”计划小鼠早期发育阶段表观遗传功能组图谱与“4D 核体（4DN）计划”和癌症遗传组信息图谱（2020 Nature， 2020 Nature Communications）；开发单分子光学图谱检测技术鉴定全基因组水平的人类DNA复制起始点 （2021 Molecular Cell）以及维他命K和DHA在脑血管内皮细胞的维持和血脑屏障中的作用（2013 Development, 2015 Nature Genetics）。曾获得NIH RO1，American Heart Association和W.W. SMITH 等多项资助。已参与发表34篇高质量研究论文包括Nature （6篇），Cell，Nature Genetics （3篇），Nature Cell Biology， Molecular Cell 等期刊，总引用3600，H指数24。目前研究集中在人类胚胎的早期发育与胚胎/配子源性疾病的表观组学与3D基因组学。

主要科研项目

1. “听力障碍的高效预防、预警策略”，国自然重大项目子课题四主持，82271669， 项目负责人

2. PKM2介导的组蛋白修饰和染色质三维结构变异对多囊卵 巢综合症发生的影响及机制研究， 国自然面上项目，82271669 ， 项目负责人

代表性论文（^#第一作者，*通讯作者）

1. Yang H#, Luan Y#, Liu T#, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F. A map of cis-regulatory elements and 3D genome structures in the zebrafish genome Nature, 2020 Dec;588(7837):337-343 DOI:10.1038/s41586-020-2962-9.28. 

2. Hongbo Yang#, Hui Zhang#, Yu Luan#, Tingting Liu, Kathryn G Roberts, Mao-xiang Qian, Bo Zhang, Wenjian Yang, Virginia Perez-Andreu, Jie Xu, Sriranga Iyyanki, Da Kuang, Heng Xu, Shalini C Reshmi, Julie Gastier-Foster, Colton Smith, Ching-Hon Pui, William E Evans, Stephen P Hunger, Mary V Relling, Charles G Mullighan, Mignon L Loh, Feng Yue & Jun J Yang；Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation Nature Genetics 2022 54, pages170–179

3. Guemez-Gamboa A^#,, Nguyen LN^#,, Yang H^#,, Zaki MS, Kara M, Ben-Omran T, Akizu N, Rosti RO, Rosti B, Scott E, Schroth J, Copeland B, Vaux KK, Cazenave-Gassiot A, Quek DQ, Wong BH, Tan BC, Wenk MR, Gunel M, Gabriel S, Chi NC, Silver DL^*, Gleeson JG^*. Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Nature Genetics. 2015 Jul;47(7):809-13. doi: 10.1038/ng.3311. [Epub ahead of print] *authors contributed equally 

4. Hyung Joo Lee^#, Yiran Hou^#, Ju Heon Maeng^#, Yujie Chen, Heather A Lawson, Hongbo Yang^*, Feng Yue^* & Ting Wang^*. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish，Genome Research 2022 Jul;32(7):1424-1436

5. Weitao Wang^#, Kyle Klein^#, Karel Proesmans^#, Hongbo Yang^#, Claire Marchal, Xiaopeng Zhu, Tyler Borman, Alex Hastie, Zhiping Weng, John Bechhoefer, Chun-Long Chen, David M. Gilbert and Nicholas Rhind. Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Timing. Molecular Cell, 2021, VOLUME 81, ISSUE 14, P2975-2988. 

6. Zhang J^#, Lee D, Dhiman V^#, Jiang P*, Xu J^#, McGillivray P^#, Yang H^#, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. An integrative ENCODE resource for cancer genomics. Nature Communications volume 11, Article number: 3696 (2020) 

7. Yang H^#, Fang L, Zhan R, Hegarty JM, Ren J, Hsiai TK, Gleeson JG, Miller YI, Trejo J, Chi NC., Polo-like kinase 2 regulates angiogenic sprouting and blood vessel development. Dev Biol. 2015 May 22. pii: S0012-1606(15)00280- 8. doi: 10.1016/j.ydbio.2015.05.011. [Epub ahead of print] PMID: 26004360 

8. Hegarty JM^#, Yang H^#, Chi NC. (2013) UBIAD1-mediated vitamin K2 synthesis is required for vascular endothelial cell survival and development. Development. 140(8):1713-9. PMID: 23533172 , 

9. Yang H^#, Xiang J^#, Wang N, Zhao Y, Hyman J, Li S, Jiang J, Chen JK, Yang Z^*, Lin S^*. Converse conformational control of smoothened activity by structurally related small molecules. J Biol Chem. 2009 Jul 31;284(31):20876-84. Epub 2009 Apr 14

其他文章：

1. Jie Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Hiu-yuen Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C Hardison, Sinisa Dovat, Leonidas C Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron D Viny, Ross L Levine, David Claxton, James R Broach, Hong Zheng, Feng Yue. Subtype-specific 3D genome alteration in acute myeloid leukaemia Nature 2022/10/26 

 2. Daniel J Emerson, Peiyao A Zhao, Ashley L Cook, R Jordan Barnett, Kyle N Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltan Simandi, Miriam K Minsk, Katelyn R Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, Sergey V Venev, Johan H Gibcus, Hongbo Yang, Takayo Sasaki, Masato T Kanemaki, Feng Yue, Job Dekker, Chun-Long Chen, David M Gilbert, Jennifer E Phillips-Cremins. Cohesin-mediated loop anchors confine the locations of human replication origins Nature 2022 volume 606, pages812–819

 3. Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B.., An atlas of dynamic chromatin landscapes in mouse fetal development Nature volume 583, pages744–751(2020)

4. Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015 Feb 19;518(7539):350-4. doi: 10.1038/nature14217.

5. Zhang R, Han P, Yang H, Ouyang K, Lee D, Lin YF, Ocorr K, Kang G, Chen J, Stainier DY, Yelon D, Chi NC. In Vivo Cardiac Reprogramming Contributes to Zebrafish Heart Regeneration. Nature 2013, 498(7455):497- 501. PMID: 23783515

6. Xie W, Schultz M, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell 153(5):1134-1148. PMID: 23664764

7. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes, Nature Genetics. volume 50, pages1388–1398 (2018)

8. Fei Sun, Jianhong Ou, Adam R. Shoffner, Yu Luan, Hongbo Yang, Lingyun Song, Alexias Safi, Jingli Cao, Feng Yue, Gregory E. Crawford & Kenneth D. Poss. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nature Cell Biology, 2022 May 5.

9. Page DM, Wittamer V, Bertrand JY, Lewis KL, Pratt DN, Delgado N, Schale SE, McGue C, Jacobsen BH, Doty A, Pao Y, Yang H, Chi NC, Magor BG, Traver D. An evolutionarily conserved program of B cell development and activation in zebrafish. Blood. 2013 Jul 16. [Epub ahead of print]

10. Weiwei Huang^#, Xinyuan Li^#, Hongbo Yang*, Hefeng Huang*. The impact of maternal age on aneuploidy in oocytes: Reproductive consequences, molecular mechanisms, and future directions. Ageing Res Rev . 2024 Jun:97:102292.  doi: 10.1016/j.arr.2024.102292.