Introduction
Transcription-replication collisions have a profound impact on genome and epigenome stability, which in turn plays a prominent role in cancer and aging. A sophisticated network of pathways in replication fork protection and restart, RNA polymerase release and reactivation, damage repair and checkpoint, which is coordinated by novel aspect of RNA mediated chromatin regulation, responds to resolve the conflict. With an accurate dissection of the molecular mechanisms that prevent transcription-induced replication stress, we will provide a framework to improve our understanding of the molecular basis of cancer and aging. This knowledge, together with newly developed genomic tools, will be translated into applications in precision medicine.
1.Analyze mechanisms resolving transcription-replication collisions to maintain genome and epigenome stability for precision medicine;
2.Apply RNA-mediated chromatin regulation in stem cells and aging;
3.Assemble multidimensional functional genomics pipelines with novel single molecule direct sequencing technologies.
Group leader
Dr. REN Jie, Principal Investigator at Beijing Institute of Genomics, CAS. In 2010, she received her Ph.D. degree from State University of New York at Stony Brook, followed by postdoctoral research at Cold Spring Harbor Laboratory. In 2018, she joined Beijing Institute of Genomics, CAS. Her research interests focus on the regulatory roles of RNA on chromatin, to elucidate the mechanisms that prevent and resolve transcription-replication collisions at various genetic contexts to protect genome and epigenome stability, to study these mechanisms for better understanding of the molecular basis of cancer and aging, and to develop novel single molecule direct sequencing technologies. She has published a number of research articles in Cell, Nature, Molecular Cell, Cell Stem Cell, Cell Research, etc.
Selected Publications
# First Authors, *Corresponding Authors, &Senior Authors
1. Hao J, Liu QL, Liu M, Yang X, Wang L, Zhang M, Su S, Zhang Y, Xiao W, Chen Y, Yang YG*, Ren J*. DDX21 mediates co-transcriptional RNA m6A modification to promote transcription termination and genome stability. Molecular Cell. 2024 May; 84(9):1711-1726.
2. Wu R, Sun F, Zhang W*, Ren J*, Liu GH*. Targeting aging and age-related diseases with vaccines. Nature Aging. 2024 Apr; 4(4):464-482.
3. Ma S#, Chi X#, Cai Y#, Ji Z#, Wang S*, Ren J*, Liu GH*. Decoding Aging Hallmarks at the Single-Cell Level. Annu Rev. Biomed. Data Sci.. 2023 Aug; 6:129-152.
4. Jing Y#, Jiang X#, Ji Q, Wu Z, Wang W, Liu Z, Guillen-Garcia P, Eseban CR, Ready P, Horvath S, Li J, Geng L, Hu Q, Wang S, Belmonte JCI, Ren J*, Zhang W*, Qu J*, Liu GH*. Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation. Cell Stem Cell. 2023 Nov; 30(11):1452-1471.e10.
5. Ren J#, Song M#, Zhang W#, Cai JP, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Chen XC, Ci W, Ding BS, Ding Q, Gao F, Gao S, Han JD, He QY, Huang K, Ju Z, Kong QP, Li J, Li J, Li J, Li X, Liu B, Liu F, Liu JP, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren R, Song W, Zhou S, Sun L, Sun YE, Sun Y, Tian M, Tian XL, Tian Y, Wang J, Wang S, Wang S, Wang W, Wang X, Wang X, Wang YJ, Wang Y, Wong C, Xiang AP, Xiao Y, Xiao ZX, Xie Z, Xiong W, Xu D, Yang Z, Ye J, Yu W, Yue R, Zhang C, Zhang H, Zhang L, Zhang X, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhao T, Zhao Y, Zhou Z, Zhu D, Zou W, Pei G, Liu GH*. The Aging Biomarker Consortium represents a new era for aging research in China. Nature medicine. 2023 Sep; 29(9):2162-2165.
6. Liu X#, Liu Z#, Wu Z#, Ren J#, Fan Y, Sun L, Cao G, Niu Y, Zhang B, Ji Q, Jiang X, Wang C, Wang Q, Ji Z, Li L, Esteban CR, Yan K, Li W, Cai Y, Wang S, Zheng A, Zhang YE., Tan S, Cai Y, Song M, Lu F, Tang F, Ji W, Zhou Q, Belmonte JCI, Zhang W*, Qu J*, Liu GH*. Resurrection of endogenous retroviruses during aging reinforces senescence. Cell, 2023 Jan; 186(2):287-304.
7. Wang K, Liu H, Hu Q, Wang L, Liu J, Zheng Z, Zhang W, Ren J*, Zhu F*, Liu GH*. Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduction and Targeted Therapy, 2022 Nov; 7(1).
8. He M, Chi X, Ren J*. Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe. Methods in Molecular Biology, 2021 Sep; 2196: 97-116.
9. Yang X#, Liu QL#, Xu W#, Zhang YC#, Yang Y, Ju LF, Chen J, Chen YS, Li K, Ren J*, Sun QW*, Yang YG*. m6A promotes R-loop formation to facilitate transcription termination. Cell Research, 2019 Oct; 29(12):1035-1038.
10. Castel S#, Ren J#, Bhattacharjee S, Chang A, Sánchez M, Valbuena A, Antequera F, Martienssen R (# co-first author). Dicer promotes transcription termination at sites of replication stress to maintain genomic stability. Cell, 2014 Oct; 159(3):572-583.
11. Jiang M, Ren J*, Belmonte JCI*, Zhang W*, Liu GH*. Hepatocyte reprogramming in liver regeneration: Biological mechanisms and applications. FEBS. 2023 Dec; 290(24):5674-5688.
12. Wu Z, Ren J*, Liu GH*. Deciphering RNA m6A regulation in aging: Perspectives on current advances and future directions. Aging Cell. 2023 Oct;22(10):e13972.
13. Sun S#, Li J#, Wang S#, Li J#, Ren J#, Bao Z#, Ma X#, Zheng F, Ma S, Sun L, Wang M, Yu Y, Ma M, Wang Q, Chen Z, Ma H, Wang X, Wu Z, Zhang H, Yan K, Yang Y, Zhang Y, Zhang S, Lei J, Teng Z, Liu CM, Bai G, Wang YJ, Li J, Wang X, Zhao G, Jiang T, Belmonte JCI*, Qu J*, Zhang W*, Liu GH*. CHIT1-positive microglia drive motor neuron aging in the primate spinal cord. Nature. 2023 Oct; doi: 10.1038/s41586-023-06783-1.
14. Cai Y#, Xiong M#, Xin Z#, Liu C#, Ren J#, Yang X, Lei J, Li W, Liu F, Chu Q, Yin J, Ye Y, Liu D, Fan Y, Sun S, Zhao Q, Zhao L, Che S, Zheng Y, Yan H, Ma S, Wang S, Belmonte JCI, Qu J*, Zhang W*, Liu GH*. Decoding aging-dependent regenerative decline across tissues at single-cell resolution. Cell Stem Cell. 2023 Oct; S1934-5909(23)00361-2.
15. Zhang H#, Li J#, Yu Y#, Ren J#, Liu Q#, Bao Z, Sun S, Liu X, Ma S, Liu Z, Yan K, Wu Z, Fan Y, Sun X, Zhang Y, Ji Q, Cheng F, Wei PH, Ma X, Zhang S, Xie Z, Niu Y, Wang YJ, Han JD, Jiang T, Zhao G, Ji W, Belmonte JCI, Wang S*, Qu J*, Zhang W*, Liu GH*. Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging. Cell Reports. 2023 Jun 27;42(6):112593.
16. Wu Z#, Lu M#, Liu D#, Shi Y#, Ren J#&, Wang S#, Jing Y, Zhang S, Zhao Q, Li H, Yu Z, Liu Z, Bi S, Wei T, Yang YG, Xiao J, Belmonte JCI, Qu J*, Zhang W*, Ci W*, Liu GH*. m6A epitranscriptomic regulation of tissue homeostasis during primate aging. Nature Aging. 2023 Jun; 3(6):705-721.
17. Aging Biomarker Consortium, Bao H, Cao J, Che M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chheter JK, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wu R, Xia K, Xiao F, Xu L, Xu Y, Yan H, Yang L, Yang R, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhu Q, Zhu Z, Cao F*, Cao Z*, Chan P*, Chen C*, Chen HZ*, Chen G*, Ci W*, Ding BS*, Ding Q*, Gao F*, Han JDJ*, Huang K*, Ju Z*, Kong Q*, Li J*, Li J*, Li X*, Liu B*, Liu L*, Liu Q*, Liu Q*, Liu X*, Liu Y*, Luo X*, Ma S*, Ma X*, Mao Z*, Nie J*, Qu J*, Ren J*, Ren R*, Song M*, Zhou S*, Sun Y*, Tian M*, Wang SS*, Wang S*, Wang X*, Wang X*, Wang YJ*, Wang Y*, Wong CCL*, Xiang AP*, Xiao Y*, Xie Z*, Xu D*, Yue R*, Zhang C*, Zhang H*, Zhang L*, Zhang W*, Zhang Y*, Zhang YW*, Zhang Z*, Zhao T*, Zhao Y*, Zhu D*, Zou W*, Pei G*, Liu GH*. Biomarkers of aging. Science China – Life Sciences. 2023 May; 66(5):893-1066.
18. Wu Z, Ren J*, Liu GH*. Glutathione restoration: a sword to combat skeletal muscle stem cell aging. Life Metabolism. 2023 Mar. DOI:10.1093/lifemeta/load012.
19. Sun S#, Ma S#, Cai Y#, Wang S#, Ren J#, Yang Y#, Ping J, Wang X, Zhang Y, Yan H, Li W, Esteban CR, Yu Y, Liu F, Belmonte JCI, Zhang W, Qu J, Liu GH. A single-cell transcriptomic atlas of exercise-induced anti-inflammatory and geroprotective effects across the body. Innovation, 2023 Jan; 4(1):100380.
20. Yan H#, Wang R#, Ma S#, Huang D#, Wang S#, Ren J#, Lu C, Chen X, Lu X, Zheng Z, Zhang W, Qu Jing, Zhou Y, Liu GH. Lineage Landscape: a comprehensive database that records lineage commitment across species. Nucleic Acids Research, 2023 Jan; 51(D1): D1061–D1066.
21. Cai Y, Song W, Li J, Jing Y, Liang C, Zhang L, Zhang X, Zhang W, Liu B, An Y, Li J, Tang B, Pei S, Wu X, Liu Y, Zhuang CL, Ying Y, Dou X, Chen Y, Xiao FH, Li D, Yang R, Zhao Y, Wang Y, Wang L, Li Y, Ma S*, Wang S*, Song X*, Ren J*, Zhang L*, Wang J*, Zhang W*, Xie Z*, Qu J*, Wang J*, Xiao Y*, Tian Y*, Wang G*, Hu P*, Ye J*, Sun Y*, Mao Z*, Kong QP*, Liu Q*, Zou W*, Tian XL*, Xiao ZX*, Liu Y*, Liu JP*, Song M*, Han JD*, Liu GH*. The landscape of aging. Science China-Life Sciences, 2022 Dec; 65(12):2354-2454.
22. Zhang S#, Wu ZM#, Shi Y#, Wang S#, Ren J#, Yu ZH, Huang DY, Yan KW, He YF, Liu XQ, Ji QZ, Liu BB, Liu ZP, Qu J, Liu GH, Ci WM, Wang XQ, Zhang WQ. FTO stabilizes MIS12 and counteracts senescence. Protein Cell, 2022 Dec; 13(12): 954-960.
23. Liu ZP#, Ji QZ#, Ren J#&, Yan P#, Wu Z#, Wang S#&, Sun L, Wang Z, Li J, Sun G, Liang C, Sun R, Jiang X, Wang Q, Hu J, Bi S, Wei G, Cao G, Zhao G, Wang H, Zhou Q, Belmonte JCI, Qu J, Zhang WQ, Liu GH. Large-Scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging. Developmental Cell, 2022 Jun; 57(11): 1347-1368.e12.
24. Ma S#, Wang S#&, Ye Y#, Ren J#&, Chen R#, Li W&, Li J, Zhao L, Zhao Q, Sun G, Jing Y, Zuo Y, Yang Y, Xiong M, Wang Q, Lei J, Sun S, Long X, Song M&, Yu S&, Chan P&, Wang JW&, Zhou Q&, Belmonte JCI&, Qu J*, Zhang WQ*, Liu GH*. Heterochronic parabiosis induces systemic rejuvenation and stem cell revitalization across aged tissues. Cell Stem Cell, 2022 Jun; 29(6):990-1005.e10.
25. Han X#, Guo J#, Wang M#, Zhang N#, Ren J#, Yang Y, Chi X, Chen Y, Yao H, Zhao YL, Yang YG，Sun Y, Xu J. Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine Reprogramming During Early Human Development. Genomics Proteomics Bioinformatics, 2022 May; S1672-0229(22)00070-5.
26. Liang CQ#, Ke Q#, Liu ZP#, Ren J#, Zhang WQ#, Hu JL, Wang ZH, Chen H, Xia K, Lai XQ, Wang QR, Yang K, Li W, Wu ZM, Wang C, Yan HT, Jiang XY, Ji ZJ, Ma MY, Long X, Wang S, Wang HT, Sun H, Belmonte JCI, Qu J*, Xiang PA*, Liu GH*. BMAL1 moonlighting as a gatekeeper for LINE1 repression and cellular senescence in primates. Nucleic Acids Research, 2022 Apr; 50(6): 3323-3347.
27. Li H#，Zhu L#, Wang R#, Xie L#, Ren J#, Ma S#, Zhang W#, Liu X, Huang Z, Chen B, Li Z, Feng H, Liu GH*, Wang S*, Qu J*, Su W*. Aging weakens Th17 cell pathogenicity and ameliorates experimental autoimmune uveitis in mice, Protein Cell, 2021 Nov; 13:422-445.
28. Zhang H#, Li J#, Ren J#, Sun S, Ma S, Zhang W, Yu Y, Cai Y, Yan K, Li W, Hu B, Chan P, Zhao GG, Belmonte JCI, Zhou Q, Qu J*, Wang S*, Liu GH*. Single-nucleus transcriptomic landscape of primate hippocampal aging. Protein Cell, 2021 Sep; 12(59): 695-716.
29. Lei J#, Jiang X#, Li W#, Ren J#, Wang D#, Ji Z, Wu Z, Cheng F, Cai Y, Yu ZR, Belmonte JCI, Li C, Liu GH*, Zhang W*, Qu J*, Wang S*. Exosomes from antler stem cells alleviate mesenchymal stem cell senescence and osteoarthritis. Protein Cell, 2021 Aug; 13(3): 220-226.
30. Yan P, Liu Z, Song M, Wu Z, Xu W, Li K, Ji Q, Wang S, Liu X, Yan K, Esteban CR, Ci W&, Belmonte JCI&, Xie W&, Ren J&, Zhang W*, Sun Q*, Qu J*, Liu GH*. Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming. Cell Reports 2020 Jul; 32(1): 107870.
31. Liu MH & Ren J*. Long noncoding RNAs in renal diseases. ExRNA, 2019 Dec; 1: 27.
32. Zhu K, Liu M, Fu Z, Liang H, Lin Z, Luo J, Zheng H, Wan P, Zhou Z, Zhang J, Zen K, Chen J*, Hu F*, Zhang C*, Ren J*, Chen X*. Plant microRNAs in larval food regulate honeybee caste development. PLOS Genetics, 2017 Aug; 13(8): e1006946.
33. Ren J, Castel S, Martienssen R. Dicer in action at replication-transcription collisions. Molecular & Cellular Oncology, 2015 Mar; 2(3): e991224.
34. Ren J, Martienssen R. Silent decision: HP1 protein escort heterochromatic RNAs to their destiny. EMBO Journal, 2012 Aug; 31(15):3237-3238.
35. Ren J, Wang CL & Sternglanz R. Promoter strength influences the S phase requirement for establishment of silencing at the Saccharomyces cerevisiae silent mating type Loci. Genetics, 2010 Oct; 186(2):551-560.
Group Members
Dr. CHI Xu, Assistant Professor
Dr. XU Yingying, Assistant Professor
Dr. ZHANG Liyuan, Assistant Professor
Admissions Information
Potential students with diverse background, including biology, medicine, chemistry, mathematics, etc. are encouraged to apply. A successful graduate student will master experimental and/or bioinformatic skills, be able to discover and resolve questions.
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