Chengqi Lin
Ph.D., Professor (PI)
School of Life Science and Technology, Southeast University
2 Sipailou Road, Nanjing, Jiangsu Province, 210096, China
Tel/Fax: 86-25-83790980
Email: cqlin@seu.edu.cn
Education Background & Academic Experience
1998 - 2003, Southeast University, Clinical Medicine, B.S.
2003 - 2006, Southeast University, Genetics, M.S.
2006 - 2008, National University of Singapore, Research Assistant
2008 - 2013, Stowers Institute for Medical Research, USA, Molecular and Cellular Biology, Ph.D.
2013 - 2016, Institute of Molecular and Cell Biology, A - STAR, Singapore, Young Investigator
2016 - present, School of Life Science and Technology, Southeast University, Professor
Research Interests
Our research centers on the transcriptional and epigenetic mechanisms that govern cell fate determination and embryonic development, with a particular focus on how their dysregulation contributes to human diseases.
We pioneered the discovery of the Super Elongation Complex (SEC) and elucidated its role in releasing RNA polymerase II from promoter-proximal pausing, a critical checkpoint for rapid and coordinated gene activation. We further investigate the regulatory landscape of early embryogenesis, including zygotic genome activation and the function of transposable elements. Our work revealed that LINE-1 elements act as novel enhancers to orchestrate early development, and that mutations in the SEC component ELL3 can lead to embryonic aneuploidy and recurrent miscarriage, directly linking transcriptional control to developmental failure.
At the organismal level, we leverage spatial transcriptomics to decode the molecular logic of organogenesis. By constructing the world’s first single-cell-resolution 3D digital embryo, we identified a Primordium Determination Zone (PDZ) for mesodermal and endodermal organs and systematically mapped the lineage trajectories of early heart development. This foundational framework not only illuminates the fundamental principles governing organogenesis but also provides a theoretical basis for understanding the origins of congenital anomalies and for advancing regenerative medicine.
Publications:
1. Xie P, Shen J, Yang Y, Wang X, Liu W, Cao H, Zheng Y, Wu C, Mao G, Chen L, He J, Zheng W, Yang Z, Zhang X, Jiang X, Yang X, Fang K, Zhang Z, Xue X, Chen X, Wang C, Liu X, Liu L, Yao X, Jing N, Xie W, Liu J, Cao H, Luo Z, Fang X, Lin C. 2025. Digital reconstruction of full embryos during early mouse organogenesis. Cell, 188(17): 4754-4772.
2. He J, Yang Y, Jiang R, Zheng Y, Yang X, Jiang X, Xue X, Yang Z, Jing N, Cao H, Luo Z, Wei K, Xie P, Lin C. 2025. Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors. Genome Biology, 26(1): 158.
3. Guo C, Si S, Fang H, Shuai S, Zhang Y, Du X, Duan B, Wu J, Yao H, Ge Z, Lin C, Luo Z. 2025. LEDGF/p75 promotes transcriptional pausing through preventing SPT5 phosphorylation. Science Advances, 11(3): eadr2131.
4. Zhu S, Xie P, Yang Y, Wang Y, Zhang C, Zhang Y, Si S, Zhang J, He J, Si H, Fang K, Ma B, Jiang X, Huang L, Li J, Min T, Zheng B, Da L, Lin D, Gao K, Li Y, Huang M, Qiao F, Huo H, Feng H, Zhao H, Chen Z, Xu Z, Xie J, Cao H, Liu J, Yao X, Xie W, Sun Y, Wu K, Xiong B, Hu P, Luo Z, Lin C. 2025. Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage. Nature Structural & Molecular Biology, 32(2): 381-392.
5. Mao G, Yang Y, Luo Z, Lin C, Xie P. 2024. SpatialQC: automated quality control for spatial transcriptome data. Bioinformatics, 40(8): btae458.
6. Xie P, Zhu S, Zhang J, Wang X, Jiang X, Xiong F, Chen L, Fang K, Ji Y, Zheng B, Da L, Cao H, Sun Y, Luo Z, Lin C. 2024. 4D live tracing reveals distinct movement trajectories of meiotic chromosomes. Life Medicine, 3(6): lnae038.
7. Xie P, Jiang X, He J, Pan Q, Yang X, Zheng Y, Fan W, Wu C, Zheng W, Fang K, Si S, Zhu S, Yang Y, Zhong T, Yang Z, Wei K, Xie W, Jing N, Luo Z, Lin C. 2024. Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics. eLife.
8. Meng S, Liu X, Zhu S, Xie P, Fang H, Pan Q, Fang K, Li F, Zhang J, Che Z, Zhang Q, Mao G, Wang Y, Hu P, Chen K, Sun F, Xie W, Luo Z, Lin C. 2023. Young LINE-1 transposon 5’UTRs marked by elongation factor ELL3 function as enhancers to regulate naïve pluripotency in embryonic stem cells. Nature Cell Biology, 25(9): 1319-1331.
9. Che Z, Liu X, Dai Q, Fang K, Guo C, Yue J, Fang H, Xie P, Luo Z, Lin C. 2023. Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation. Journal of Molecular Cell Biology, 15(8): mjad049.
10. Guo C, Zhang Y, Shuai S, Sigbessia A, Hao S, Xie P, Jiang X, Luo Z, Lin C. 2023. The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release. EMBO Reports, 24(1): e55699.
11. Guo C, Luo Z, Lin C. 2022. Phase Separation Properties in Transcriptional Organization. Biochemistry, 61(22): 2456-2460.
12. Zhao X, Fang K, Liu X, Yao R, Wang M, Li F, Hao S, He J, Wang Y, Fan M, Huang W, Li Y, Gao C, Lin C, Luo Z. 2022. QSER1 preserves the suppressive status of the pro-apoptotic genes to prevent apoptosis. Cell Death & Differentiation, 30(2): 478-490.
13. Wang Y, Ma B, Liu X, Gao G, Che Z, Fan M, Meng S, Zhao X, Sugimura R, Cao H, Zhou Z, Xie J, Lin C, Luo Z. 2022. ZFP281-BRCA2 prevents R-loop accumulation during DNA replication. Nature Communications, 13(1): 3493.
14. Guo C, Luo Z, Lin C. 2021. Phase separation, transcriptional elongation control, and human diseases. Journal of Molecular Cell Biology, 13(4): 314-318.
15. Yue J, Dai Q, Hao S, Zhu S, Liu X, Tang Z, Li M, Fang H, Lin C, Luo Z. 2021. Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells. Journal of Biological Chemistry, 296: 100319.
16. Du H, Chen C, Wang Y, Yang Y, Che Z, Liu X, Meng S, Guo C, Xu M, Fang H, Wang F, Lin C, Luo Z. 2020. RNF219 interacts with CCR4-NOT in regulating stem cell differentiation. Journal of Molecular Cell Biology, 12(11): 894-905.
17. Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K, Jin W. 2020. Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Research, 30(8): 1097-1106.
18. Guo C, Che Z, Yue J, Xie P, Hao S, Xie W, Luo Z, Lin C. 2020. ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation. Science Advances, 6(14): eaay4858.
19. Luo Z, Liu X, Xie H, Wang Y, Lin C. 2019. ZFP281 recruits MYC to active promoters in regulating transcriptional initiation and elongation. Molecular and Cellular Biology, 39(22): MCB.00329-19.
20. Zhang Y, Wang C, Liu X, Yang Q, Ji H, Yang M, Xu M, Zhou Y, Xie W, Luo Z, Lin C. 2018. AFF3-DNA methylation interplay in maintaining the mono-allelic expression pattern of XIST in terminally differentiated cells. Journal of Molecular Cell Biology, 11(9): 761-769.
21. Wu J, Tao N, Tian Y, Xing G, Lv H, Han J, Lin C, Xie W. 2017. Proteolytic maturation of Drosophila Neuroligin 3 by tumor necrosis factor α-converting enzyme in the nervous system. Biochimica et Biophysica Acta (BBA) - General Subjects, 1862(1): 62-70.
22. Dai Q, Shen Y, Wang Y, Wang X, Francisco JC, Luo Z, Lin C. 2017. Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells. Nucleic Acids Research, 45(21): 12301-12310.
23. Francisco JC, Dai Q, Luo Z, Wang Y, Chong RH, Tan YJ, Xie W, Lee GH, Lin C. 2017. Transcriptional elongation control of the HBV cccDNA transcription by Super Elongation Complex (SEC) and BRD4. Molecular and Cellular Biology, 37(18): MCB.00040-17.
24. Wang Y, Shen Y, Dai Q, Yang Q, Zhang Y, Wang X, Xie W, Luo Z, Lin C. 2017. A permissive chromatin state regulated by ZFP281-AFF3 in controlling the imprinted Meg3 polycistron. Nucleic Acids Research, 45(3): 1177-1185.
25. Luo Z, Lin C. 2016. Enhancer, epigenetics and human diseases. Current Opinion in Genetics & Development, 36: 27-33.
26. Luo Z, Lin C, Shilatifard A. 2016. Regulation of imprinted gene expression by allele-specific enhancer activity. Genes & Development, 30(1): 92-101.
27. De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. 2015. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Research, 25(8): 1229-1243.
28. Luo Z, Gao X, Lin C, Smith ER, Marshall SA, Swanson SK, Florens L, Washburn MP, Shilatifard A. 2015. Zic2 is an enhancer-binding factor required for embryonic stem cell specification. Molecular Cell, 57(4): 685-694.
29. Hu D, Smith ER, Garruss AS, Mohaghegh N, Varberg JM, Lin C, Jackson J, Gao X, Saraf A, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. 2013. The little elongation complex functions at initiation and elongation phases of snRNA gene transcription. Molecular Cell, 51(4): 493-505.
30. Lin C, Garrus AS, Luo Z, Guo F, Shilatifard A. 2013. The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell, 152(1-2): 144-156.
31. Luo Z, Lin C, Shilatifard A. 2012. The super elongation complex (SEC) family in transcriptional control. Nature Reviews Molecular Cell Biology, 13(9): 543-547.
32. Luo Z, Lin C, Guest E, Garrett AS, Mohaghegh N, Swanson S, Marshall S, Florens L, Washburn MP, Shilatifard A. 2012. The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output. Molecular and Cellular Biology, 32(13): 2608-2617.
33. Smith ER, Lin C, Garrett AS, Thornton J, Mohaghegh N, Hu D, Jackson J, Saraf A, Swanson SK, Seidel C, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. 2011. The little elongation complex regulates small nuclear RNA transcription. Molecular Cell, 44(6): 954-965.
34. Lin C, Garrett AS, De Kumar B, Smith ER, Gogol M, Seidel C, Krumlauf R, Shilatifard A. 2011. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes & Development, 25(14): 1486-1498.
35. Takahashi H, Parmely TJ, Sato S, Tomomori-Sato C, Banks CA, Kong SE, Szutorisz H, Swanson SK, Martin-Brown S, Washburn MP, Florens L, Seidel CW, Lin C, Smith ER, Shilatifard A, Conaway RC, Conaway JW. 2011. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell, 146(1): 92-104.
36. Smith E, Lin C, Shilatifard A. 2011. The super elongation complex (SEC) and MLL in development and disease. Genes & Development, 25(7): 661-672.
37. Mohan M, Lin C, Guest E, Shilatifard A. 2010. Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis. Nature Reviews Cancer, 10(10): 721-728.
38. Mohan M, Herz HM, Takahashi YH, Lin C, Lai KC, Zhang Y, Washburn MP, Florens L, Shilatifard A. 2010. Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes & Development, 24(6): 574-589.
39. Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, Washburn MP, Conaway JW, Conaway RC, Shilatifard A. 2010. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Molecular Cell, 37(3): 429-437.
40. Wang P, Lin C, Smith ER, Guo H, Sanderson BW, Wu M, Gogol M, Alexander T, Seidel C, Wiedemann LM, Ge K, Krumlauf R, Shilatifard A. 2009. Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Molecular and Cellular Biology, 29(22): 6074-6085.
41. Lin C, Yuan YA. 2008. Structural insights into histone H3 lysine 56 acetylation by Rtt109. Structure, 16(10): 1503-1510.
42. Chen HY, Yang J, Lin C, Yuan YA. 2008. Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Reports, 9(8): 754-760.