表观遗传调控与干预重点实验室

1964           毕业于中国科技大学生物物理系

1978 - 1980   吉林大学理论化学进修班学习

1985 - 1987   获洪堡奖学金在德国纽伦堡大学从事量子生物学研究

1994 - 2003   作为访问学者或访问教授先后在香港中文大学、美国加州洛杉矶大学、美国哈佛大学、日本大阪大学蛋白质研究所、台湾理论科学中心等从事合作研究

1989 - 至今   中国科学院生物物理研究所 研究员

2007.11       当选中国科学院院士

2014.07       当选欧亚科学院院士

现为国际人类基因组组织（HUGO）会员；国际数据库组织（CODATA）生物大分子专业组委员；国际纯粹及应用物理学会（IUPAP）生物信息学专业委员会委员；国际学术期刊《Journal of Theoretical Biology》编委。

陈润生院士是我国最早从事理论生物学、生物信息学以及非编码RNA研究的科研人员之一。三十多年来在生物信息学领域进行了系统的研究，曾参加我国第一个完整基因组泉生热袍菌B4基因组序列的组装和基因标识，曾参加人类基因组1%和水稻基因组工作草图的研究。构建了收录非编码RNA及其基因的数据库NONCODE，以及收录非编码RNA与其它生物大分子相互作用的数据库NPInter，这两个数据库也已成为了国际在非编码RNA领域非常有影响力的数据库。共发表SCI学术论文300余篇，自1996年以来在国际学术会议上共作大会报告及分组会报告二十余次。由于其在基因组信息学领域的早期工作，1996年9月29日至10月3日在日本筑波召开的第十五届国际科学技术数据委员会（CODATA）大会上应邀作“Kotani Memorial Lecture”，同时获得“小谷正雄”奖（“Kotani Prize”，生物领域）。2008年获何梁何利基金科学与技术进步奖；2012年获谈家桢生命科学成就奖；2013年获得国家科学技术进步奖二等奖（第一完成人）。

陈润生课题组主要研究方向及相关延申拓展：

（1）利用生物信息学手段并结合实验室多年积累的RNA组学技术，深入开展在肿瘤发生发展以及干细胞重编程过程中非编码RNA的系统发现和功能机制研究；

（2）RNA疫苗与RNA药物；

（3）RNA研究新技术、新方法；

（4）非编码RNA的非经典翻译与功能调控；

（5）着丝粒及组成型异染色质建成过程中非编码RNA的功能与调控机制研究；

（6）小鼠早期胚胎发育过程中非编码RNA的时空表达图谱与功能调控机制研究。

[60] Chen S, Wang H, Zhang D, Chen R, Luo J. Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data. Bioinformatics 2024; 40(6).

[59] Liu L, Liu Z, Liu Q, Wu W, Lin P, . . . Luo J, Rich JN, Xie Q, Jiang T, Chen R. LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2'-O-methylation. Nat Commun 2023; 14(1): 7526.

[58] Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, . . . Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24(6): 430-447.

[57] Yue H, Li A, Tang Y, Chen R. TapHi-C for profiling genome-wide chromosome conformation capture. Trends Plant Sci 2023; 28(10): 1192-3.

[56] Yang Z, Zeng X, Zhao Y, Chen R. AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 2023; 8(1): 115.

[55] Zheng Y, Luo H, Teng X, . . . Zhao Y, Chen R, He S. NPInter v5.0: ncRNA interaction database in a new era. Nucleic Acids Res 2023; 51(D1): D232-D9.

[54] Zhang L, Badai J, Wang G, Ru X, . . . Feng H, Chen R, Zhao Y, Chen Y. Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis. Frontiers in immunology 2023; 14: 1123652.

[53] Zhang C, Wang D, Hao Y, Wu S, Luo J, . . . Fu XD, Yang X, Chen R, Teng Y. LncRNA CCTT-mediated RNA-DNA and RNA-protein interactions facilitate the recruitment of CENP-C to centromeric DNA during kinetochore assembly. Mol Cell 2022; 82(21): 4018-32 e9.

[52] Zhang Y, Qiao X, Liu L, . . . He S, Chen R, Chen C. Long noncoding RNA MAGI2-AS3 regulates the H2O2 level and cell senescence via HSPA8. Redox Biol 2022; 54: 102383.

[51] Yang B, Zhang Y, Sun L, . . . Chen R, Luo J, Wang T, Jiang J, Qin Y. Modulated ultrasmall γ-Fe2O3 nanocrystal assembles for switchable magnetic resonance imaging and photothermal-ferroptotic-chemical synergistic cancer therapy. Advanced Functional Materials 2022.

[50] Wang J, Shi Y, Zhou H, Zhang P, . . . Zhao Y, Zeng X, He S, Chen R. piRBase: integrating piRNA annotation in all aspects. Nucleic Acids Res 2022; 50(D1): D265-D72.

[49] Cui X, Zhang R, Yang Y, Wu E, . . . Sun J, Luo J, Zhang S, Chen R, Xi JJ. Identification and characterization of long non-coding RNA Carip in modulating spatial learning and memory. Cell Rep 2022; 38(8): 110398.

[48] Zhao L, Wang J, Li Y, Song T, . . . Chen R, Zhao Y, He S. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res 2021; 49(D1): D165-D171.

[47] Zhang Q, Wu E, Tang Y, Cai T, . . . Luo J, Chen R, Yang F. Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs. Mol Cell Proteomics 2021; 20: 100109.

[46] Xue H, Niu Y, Segraves K, Nie R, Hao Y, Zhang L, . . . Chen R, Yang X. The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). BMC Genomics 2021; 22(1): 243.

[45] Wu E, Guo X, Teng X, Zhang R, . . . Luo J, Wang J, Chen R. Discovery of Plasma Membrane-Associated RNAs through APEX-seq. Cell Biochem Biophys 2021; 79(4): 905-917.

[44] Li Y, Zhou H, Chen X, Zheng Y, . . . Luo H, Hao Y, Chen R, Zhang P, He S. SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. Genomics Proteomics Bioinformatics 2021; 19(4): 602-610.

[43] Lai C, Liu L, Liu Q, Wang K, Cheng S, . . . Luo J, Wang X, Chen R, Yang P. Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a. Cell Death Differ 2021; 28(10): 2900-2915.

[42] Wang D, Zhou Z, Wu E, Ouyang C, Wei G, . . . Reed SH, Luo J, Chen R. LRIK interacts with the Ku70-Ku80 heterodimer enhancing the efficiency of NHEJ repair. Cell Death Differ 2020; 27(12): 3337-3353.

[41] Fan Z, Chen X, Liu L, Zhu C, Xu J, . . . Cui Y, Zhang X, Chen R. Association of the Polymorphism rs13259960 in SLEAR With Predisposition to Systemic Lupus Erythematosus. Arthritis Rheumatol 2020; 72(6): 985-996.

[40] Hao Y, Wang D, Wu S, Li X, . . . Fu XD, Chen R, He S. Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division. Genome Res 2020; 30(11): 1570-1582.

[39] Wu S, Wu E, Wang D, Niu Y, Yue H, Zhang D, Luo J, Chen R. LncRNA HRCEG, regulated by HDAC1, inhibits cells proliferation and epithelial-mesenchymal-transition in gastric cancer. Cancer Genet 2020; 241: 25-33.

[38] Teng X, Chen X, Xue H, Tang Y, Zhang P, Kang Q, Hao Y, Chen R, Zhao Y, He S. NPInter v4.0: an integrated database of ncRNA interactions. Nucleic Acids Res 2020; 48(D1): D160-D165.

[37] Fan Z, Chen R, Chen X. SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res 2020; 48(D1): D233-D237.

[36] Wang Y, Zhu P, Luo J, Wang J, Liu Z, Wu W, . . . Chen R, Tian Y, Fan Z. LncRNA HAND2-AS1 promotes liver cancer stem cell self-renewal via BMP signaling. EMBO J 2019: e101110.

[35] Chen X, Hao Y, Cui Y, Fan Z, Chen R. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes. Methods Mol Biol 2019; 1870: 189-198.

[34] Wang J, Zhang P, Lu Y, Li Y, Zheng Y, Kan Y, Chen R, He S. piRBase: a comprehensive database of piRNA sequences. Nucleic Acids Res 2019; 47(D1): D175-D180.

[33] Ye B, Liu B, Yang L, Zhu X, Zhang D, Wu W, . . . Chen R, Tian Y, Fan Z. LncKdm2b controls self-renewal of embryonic stem cells via activating expression of transcription factor Zbtb3. EMBO J 2018; 37(8).

[32] Wang Y, Zhu P, Wang J, Zhu X, Luo J, Meng S, . . . Chen R, Tian Y, Fan Z. Long noncoding RNA LncHand2 promotes liver repopulation via c-Met signaling. J Hepatol 2018; 69(4): 861-872.

[31] Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, . . . Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res 2018; 46(D1): D308-D314.

[30] Hao Y, Zhang L, Niu Y, Cai T, Luo J, He S, . . . Chen R. SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Brief Bioinform 2018; 19(4): 636-643.

[29] Cui Y, Chen X, Niu Y, Wang D, Luo H, Fan Z, . . . Chen R. Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data. Brief Bioinform 2018; 19(6): 1302-1309.

[28] Yan X, Zhang D, Wu W, Wu S, Qian J, Hao Y, . . . Chen R, Fan Z. Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a. Cancer Res 2017; 77(23): 6704-6716.

[27] Wang Z, Hao Y, Zhang C, Wang Z, Liu X, Li G, . . . Chen R, Jiang T. The Landscape of Viral Expression Reveals Clinically Relevant Viruses with Potential Capability of Promoting Malignancy in Lower-Grade Glioma. Clin Cancer Res 2017; 23(9): 2177-2185.

[26] Sun Y, Wei G, Luo H, Wu W, Skogerbo G, Luo J, Chen R. The long noncoding RNA SNHG1 promotes tumor growth through regulating transcription of both local and distal genes. Oncogene 2017; 36(49): 6774-6783.

[25] Liu B, Ye B, Yang L, Zhu X, Huang G, Zhu P, . . . Chen R, Tian Y, Fan Z. Long noncoding RNA lncKdm2b is required for ILC3 maintenance by initiation of Zfp292 expression. Nat Immunol 2017; 18(5): 499-508.

[24] Chen X, Hao Y, Cui Y, Fan Z, He S, Luo J and Chen R. LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics 2017; 33: 112-118.

[23] Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, . . . Chen R. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res 2016; 44: D203-208.

[22] Liu L, Yue H, Liu Q, Yuan J, Li J, Wei G, . . . Chen R. LncRNA MT1JP functions as a tumor suppressor by interacting with TIAR to modulate the p53 pathway. Oncotarget 2016; 7: 15787-15800.

[21] Cui Y, Chen X, Luo H, Fan Z, Luo J, He S, . . . Chen R. BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. Bioinformatics 2016; 32: 1740-1742.

[20] Xiao T, Liu L, Li H, Sun Y, Luo H, Li T, . . . Chen R. Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPalpha. Stem Cell Reports 2015; 5: 856-865.

[19] Wang Y, He L, Du Y, Zhu P, Huang G, Luo J, . . . Chen R, Fan Z. The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling. Cell Stem Cell 2015; 16: 413-425.

[18] Yuan J, Wu W, Xie C, Zhao G, Zhao Y and Chen R. NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res 2014; 42: D104-108.

[17] Li J, Chen Z, Tian L, Zhou C, He MY, Gao Y, . . . Chen R, He J. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut 2014; 63: 1700-1710.

[16] Lu X, Wang L, Chen S, He L, Yang X, Shi Y, . . . Chen R, . . . Coronary ADG-WR. Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease. Nature Genetics 2012; 44: 890-4.

[15] Wang Y, Chen J, Wei G, He H, Zhu X, Xiao T, . . . Chen R. The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression. Nucleic Acids Res 2011; 39: 5203-5214.

[14] Zhao Y, He S, Liu C, Ru S, Zha H, Yang Z, . . . Chen R. MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends in Genetics 2008; 24: 323-327.

[13] He S, Su H, Liu C, Skogerbo G, He H, He D, . . . Chen R. MicroRNA-encoding long non-coding RNAs. BMC Genomics 2008; 9: 236

[12] Aftab MN, He H, Skogerbo G and Chen R. Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins. BMC Genomics 2008; 9: 278.

[11] He H, Wang J, Liu T, Liu XS, Li T, Wang Y, . . . Chen R. Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 2007; 17: 1471-1477.

[10] Zhang Z, Liu C, Skogerbo G, Zhu X, Lu H, Chen L, . . . Chen R. Dynamic changes in subgraph preference profiles of crucial transcription factors. Plos Computational Biology 2006; 2: 383-391.

[9] Zhang Y, Li S, Skogerbo G, Zhang Z, Zhu X, Zhang Z, . . . Chen R. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics 2006; 7:

[8] Muzny D, Scherer S, Kaul R, Wang J, Yu J, Sudbrak R, . . . Chen R, . . .Gibbs R. The DNA sequence, annotation and analysis of human chromosome 3. Nature 2006; 440: 1194-1198.

[7] He H, Cai L, Skogerbo G, Deng W, Liu T, Zhu X, . . . Chen R. Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Res 2006; 34: 2976-2983.

[6] Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, . . . Chen R. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res 2006; 16: 20-29.

[5] Liu C, Bai B, Skogerbo G, Cai L, Deng W, Zhang Y, . . . Chen R. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 2005; 33: D112-D115.

[4] Yu J, Hu S, Wang J, Wong G, Li S, Liu B, . . . Chen R, . . . Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 2002; 296: 79-92.

[3] Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, . . . Chen R. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 2003; 31: 2443-2450.

[2] Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, . . . Chen R, . . . Yang H. A complete sequence of the T tengcongensis genome. Genome Res 2002; 12: 689-700.

[1] Li W, Fang W, Ling L, Wang J, Xuan Z and Chen R. Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis. Journal of Biological Physics 2002; 28: 439-447.

（资料来源：陈润生院士，2024-07-30）