Education:
1996-2007 Master Degree, Peking University
2001-2006 PhD, University in Basel
Professional Positions:
2006-2007 Postdoc, Medical School of Harvard University/The Howard Hughes Medical Institute(HHMI), USA
2007-2008 Research Assistant, JFRC/HHMI, USA
2009-2010 Assistant Research Fellow, Medical School of Harvard University/The Howard Hughes Medical Institute(HHMI), USA
2010-2014 Associate Professor, School of Medical Sciences, Tsinghua University, Beijing, China
2015-2021 Vice Professor, School of Medical Sciences, Tsinghua University, Beijing, China
2021-2024 Professor, School of Medical Sciences, Tsinghua University, Beijing, China
2024-now Professor, School of Basic Medical Sciences, Tsinghua University, Beijing, China
Research Areas:
Gene regulation and gene function research. We are engaged in the development and application of Drosophila genetic tools. We have developed genome editing technology, transcription activation system, transcription inhibition system, and a new generation of transgenic interference technology in Drosophila. We have used these technologies to deeply explore the epigenetic regulatory mechanisms of Drosophila development and stem cell homeostasis. This laboratory mainly uses molecular biotechnology, combined with cell biology, biochemistry, multi-omics, and other technologies, to study the important functions and various interaction events of related genes in the process of developmental metabolism, stem cell homeostasis maintenance, etc., explore the role of gene interaction events in various life events, and actively carry out the discovery and development of potential molecular targets based on gene function.
Honors and Awards:
Selected Publications:
1. Y Han, B Xu, Y Li, X Lu, J Sun, Q Liu, JQ Ni# , Cutting-edge gene regulatory systems in Drosophila, Hereditas, invited review
2. J Sun, X Wang, R Xu, D Mao, D Shen, X Wang, Y Qiu, Y Han, P Peng, X Kang, R Zhu, Y Jia, X Lu, Y Li, J Yu, Y Wang, L Liu, Z Chang, J Ji, Z Wang, QLiu, S Li#, F Sun#, JQ Ni#，HP1c regulates development and gut homeostasis by suppressing Notch signaling through Su(H)，EMBO Report，Accepted
3. D Mao, Y Jia, P Peng, D Shen, X Ren, R Zhu, Y Qiu, Y Han, J Yu, Q Che, Y Li, X Lu, L Liu, Z Wang, Q Liu, Jin Sun# and JQ Ni#, Enhanced Efficiency of flySAM by Optimization of sgRNA Parameters in Drosophila, GENES GENOM GENET, 2020, doi.org/10.1534
4. Z Li, K Xu, S Zhao, Y Guo, H Chen, JQ Ni, Q Liu, ZWang#, SPATA4 improves aging-induced metabolic dysfunction through promotion of preadipocyte differentiation and adipose tissue expansion, Aging cell, 2020 Dec 13;e13282.
5. L Sun, L Cui, Z Liu, Q Wang, Z Xue, M Wu, T Sun, D Mao, JQ Ni, JC Pastor-Pareja, X Liang#, Katanin p60-like 1 sculpts the cytoskeleton in mechanosensory cilia, J Cell Biol, December 02 2020, 220 (1): e202004184.
6. X Li, M Liu, X Ren, N Loncle, Q Wang, R Waduge, S Yu, M Boube, H Bourbon, JQ Ni, JY Ji#, The Mediator CDK8-Cyclin C complex modulates Dpp signaling in Drosophila by stimulating Mad-dependent transcription, PLOS GENETICS, 2020 May 28;16(5):e1008832. doi: 10.1371
7. Y chen, T Sun, Z Bi, JQ ni, JC. pastor-pareja#，B Javid#，Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner, Scientific Reports, May 2020, doi.org/10.1038/s41598-020-65348-8
8. Zirin, J; Hu, Y; Liu, L; Yang D; C Ryan; Y Dong; E, Ben; T Rong; V Eric; V Sara; C Cooper; V Christians; C Aram; Sun, J; Wang, X; Jia, Yu; Zhu, R; Peng, P; Yu, J; Shen, D; Qiu, Y; Ayisi,d; R Henna; F Ethan; E Senait; P Annette; S Kuniaki; K Shu; P Liz; M Stephanie; Ni, JQ; P, Norbert#, Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies, Genetics, 2020 Apr;214(4):755-767.doi: 10.1534
9. Li Z, Xu K, Guo Y, Ping L, Gao Y, Qiu Y, Ni JQ, Liu Q, Wang Z#, A high-fat diet reverses metabolic disorders and premature aging by modulating insulin and IGF1 signaling in SIRT6 knockout mice, Aging Cell, 2020 Mar; 19(3):e13104
10. Sapiro L; Freund E; Restrepo L; Qiao HH; Bhate A; Li Q; Ni JQ; Mosca, T; Li, JB#, Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons, Cell Reports, Volume 31, Issue 7, 19 May 2020, 107654
11. MAO Y, Tu R, Huang Y, Mao D, Yang Z, Lau P, Ni JQ#, Guo Y#, Xie T#,The Exocyst Functions in Niche Cells to Promote Germline Stem Cell Differentiation by Directly Controlling EGFR Membrane Trafficking, Development, 2019, 146: dev174615 doi: 10.1242
12. X Wang, D Shen, H Qiao, J Sun, R Xu, Q Liu, JQ Ni#, Guidance for Drosophila Culture and Management, Bio-101, 2019/06/20
13. Sun T, Song Y, Dai J, Mao D, Ma M, Ni JQ, Liang X, Pastor-Pareja J#, Spectraplakin Shot maintains perinuclear microtubule organization in Drosophila polyploid cells, Developmental Cell, April 18, 2019
14. Wang, F, Qiao, HH, Xu, R, Sun J, Zhu RB, Mao D, Ni, JQ# pNP Transgenic RNAi System Manual in Drosophila. BIO-PROTOCOL. Feb 5 2019. 9(3)
15. Xu RG, Wang X, Shen D, Sun J, Qiao H, Wang F, Liu LP, Ni JQ#, Perspectives of gene regulation in Drosophila, J Genet Genomics. 2019.03.006, DOI:org/10.1016/j.jgg
16. Peng P, Wang X, Shen D, Sun J, Jia Y, Xu RG, Zhu LF and Ni JQ#, CRISPR-Cas9 Mediated Genome Editing in Drosophila, Bio-protocol, Jan 20 2019. 9(2)
17. Y Gao; Y Mao; R.G Xu; R Zhu; M Zhang; J Sun; D Shen; P Peng; T Xie#, JQ Ni#, Defining Gene Networks Controlling the Maintenance and Function of the Differentiation Niche by an in vivo Systematic RNAi Screen, J Genet Genomics. Jan 20 2019. 46(1) 19-13.
18. Jia Y, Shen D, Wang X, Sun J, Peng P, Xu RG, Xu BW, Ni JQ#, flySAM Transgenic CRISPRa System Manual. BIO-PROTOCOL. Jan 20 2019. 9(2)
19. Qiao HH, Wang F, Xu RG, Sun J, Zhu R, Mao D, Ren X, Wang X, Jia Y, Peng P, Shen D, Liu LP, Chang Z, Wang G, Li S, Ji JY, Liu Q, Ni JQ# An efficient and multiple target transgenic RNAi technique with low toxicity in Drosophila, NATURE COMMUNICATIONS, 2018 Oct 8;9(1):4160. doi: 10.1038/s41467-018-06537-y.
20. Zheng Y, Xue Y, Ren X, Liu M, Li X, Jia Y, Niu Y, Ni J.Q#, Zhang Y#, Ji JY#. The Lysine Demethylase dKDM2 Is Non-essential for Viability, but Regulates Circadian Rhythms in Drosophila. Front Genet. 2018 Sep 4;9:354. doi: 10.3389/fgene.2018.00354.
21. Sapar ML, Ji H, Wang B, Poe AR, Dubey K, Ren X, Ni J.Q, Han C#. Phosphatidylserine Externalization Results from and Causes Neurite Degeneration in Drosophila. Cell Rep. 2018 Aug 28;24(9):2273-2286. doi: 10.1016/j.celrep.2018.07.095.
22. Xu R, Wang X, Wang F，Sun J, Mao D, Qiao H, Jia Y, Zhu R, Peng P, Liu LP, Ni JQ# Techniques and resource in Drosophila，ACTA LABORATORIUM ANIMAL SCIENTIA SINICA (in Chinese), August 2018, Vol. 26, No. 4
23. Ke H, Feng Z, Liu M, Sun T, Dai J, Ma M, Liu LP, Ni JQ, Pastor-Pareja JC#. Collagen secretion screening in Drosophila supports a common secretory machinery and multiple Rab requirements. J Genet Genomics. 2018 Jun 1. doi: 10.1016/j.jgg.2018.05.002.
24. Wang X, Sun J, Wang F, Qiao H, Mao D, Ni JQ# The generation of novel transgenic lines and applications, Medical science (in Chinese)，DOI:10.3772/j.issn.1673-6516.2018.07.022
25. Jia Y，Xu R，Sun J, Ni JQ# The specific and efficient CRISPR/dCas9 targeting activator—flySAM system, Hereditas, 2018, 5, 40(5): 425―427
26. Y Jia, R.G Xu, X Ren, B Ewen-Campen, R Rajakumar, J Zirin, D Yang-Zhou, R Zhu, F Wang, DMao, P Peng, H.H Qiao, X Wang, L.P Liu, B Xu, J.Y Ji, Q Liu, J Sun#, N Perrimon#, Ni J.Q#, Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM, Proc Natl Acad Sci USA. 2018 May 1;115(18):4719-4724. doi: 10.1073/pnas.1800677115.
27. Ewen-Campen, B., Yang-Zhou, D., Fernandes, V.R., Gonzalez, D.P., Liu, L.P., Tao, R., Ren, X., Sun, J., Hu, Y., Zirin, J., Mohr, S.E., Ni J.Q#, and Perrimon, N#. Optimized strategy for in vivo Cas9-activation in Drosophila. Proc Natl Acad Sci USA. 2017 Aug 29;114(35):9409-9414. doi: 10.1073/pnas.1707635114.
28. Ren X, Holsteens K, Li H, Sun J, Zhang Y, Liu LP, Liu Q, Ni J.Q#. Genome editing in Drosophila melanogaster: from basic genome engineering to the multipurpose CRISPR-Cas9 system. Sci China Life Sci. 2017 May;60(5):476-489. doi: 10.1007/s11427-017-9029-9.
29. Yang, Z., Sun, J., Hu, Y., Wang, F., Wang, X., Qiao, H.H., Xu, J., Mao, D., Ren, X., Pan, L.X., Xu, R.G., Xu, B.W., Zhang, Y., Li, H., Miao, W., Hu, Y., Chang, Z., Wang, D., Li, H., Chang, Z., Liu, L.P., Liu, Q., Ni, J.Q#. Histone H1 defect in escort cells triggers germline tumor in Drosophila ovary. Developmental biology. 2017 Apr 1;424(1):40-49. doi: 10.1016/j.ydbio.2017.02.012.
30. Ma X, Han Y, Song X, Do T, Yang Z, Ni JQ, Xie T#. DNA damage-induced Lok/CHK2 activation compromises germline stem cell self-renewal and lineage differentiation. Development. 2016 Dec 1;143(23):4312-4323.
31. Xiong XP, Kurthkoti K, Chang KY, Li JL, Ren X, Ni JQ, Rana TM, Zhou R#. miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila. PLoS Pathog, 2016,12(11):e1006034
32. Wang X, Qiao H, Pan L, Ren X, Sun J, Xu R, Liu LP, He Z, NI JQ#, The generation and maintenance of transgenic flies, LABORATORY ANIMAL SCIENCE，Vol.33 No.3 June 2016
33. Lu T, Wang S, Gao Y, Mao Y, Yang Z, Liu L, Song X, Ni JQ#, Xie T#. COP9-Hedgehog Axis Regulates the Function of the Germline Stem Cell Progeny Differentiation Niche in the Drosophila Ovary, Development. 2015 Dec 15;142(24):4242-52. doi: 10.1242/dev.124768.
34. Sun J, Wei HM, Xu J, Chang JF, Yang Z, Ren X, Lv WW, Liu LP, Pan LX, Wang X, Qiao HH, Zhu B, Ji JY, Yan D, Xie T, Sun FL#, Ni JQ#. Histone H1-Mediated Epigenetic Regulation Controls Germline Stem Cell Self-Renewal by Modulating H4K16 Acetylation, Nature Communications. 2015 Nov 19;6:8856. doi: 10.1038/ncomms9856.
35. Fu Z, Geng C, Wang H, Yang Z, Weng C, Li H, Deng L, Liu L, Liu N, Ni JQ, Xie T# Twin Promotes the Maintenance and Differentiation of Germline Stem Cell Lineage through Modulating Multiple Pathways, Cell Reports. Epub 2015, Nov 5.
36. Pan L, Xie W, Li KL, Yang Z, Xu J, Zhang W, Liu LP, Ren X, He Z, Wu J, Sun J, Wei HM, Wang D, Xie W, Li W, Ni JQ#, Sun FL#. Heterochromatin remodeling by CDK12 contributes to learning in Drosophila, Proc Natl Acad Sci USA. 2015 Nov 10;112(45):13988-93. doi: 10.1073/pnas.1502943112.
37. Wang S, Gao Y, Song X, Ma X, Zhu X, Mao Y, Yang Z, Ni JQ, Li H, Malanowski KE, Anoja P, Park J, Haug J, Xie T#. Wnt signaling-mediated redox regulation maintains the germ line stem cell differentiation niche, ELife. October 9, 2015
38. Perkins LA, Holderbaum L, Tao R, Hu Y, Sopko R, McCall K, Yang-Zhou D, Flockhart I, Binari R, Shim HS, Miller A, Housden A, Foos M, Randkelv S, Kelley C, Namgyal P, Villalta C, Liu LP, Jiang X, Huan-Huan Q, Wang X, Fujiyama A, Toyoda A, Ayers K, Blum A, Czech B, Neumuller R, Yan D, Cavallaro A, Hibbard K, Hall D, Cooley L, Hannon GJ, Lehmann R, Parks A, Mohr SE, Ueda R, Kondo S, Ni JQ, Perrimon N#. The Transgenic RNAi Project at Harvard Medical School: Resources and Validation, Genetics. 2015 Aug 28. pii: Genetics.115.180208.
39. Xie XJ, Hsu FN, Gao X, Xu W, Ni JQ, Xing Y, Huang L, Hsiao HC, Zheng H, Wang C, Zheng Y, Xiao li AM, Yang F, Bondos SE, Ji JY#. CDK8-Cyclin C Mediates Nutritional Regulation of Developmental Transitions through the Ecdysone Receptor in Drosophila, PLoS Biology. 2015 Jul 29;13(7):e1002207.
40. Zang Y, Wan M, Liu M, Ke H, Ma S, Liu LP, Ni JQ, Pastor-Pareja JC#. Plasma membrane overgrowth causes fibrotic collagen accumulation and immune activation in Drosophila adipocytes, Elife. 2015 Jun 19;4:e07187.
41. Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ#, A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila, J Genet Genomics. 2015 Apr 20;42(4):141-9.
42. Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB#, Ni JQ#, Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Reports. 2014 Nov 6;9(3):1151-62.
43. Ren X, Yang Z, Mao D, Chang Z, Qiao HH, Wang X, Sun J, Hu Q, Cui Y, Liu LP, Ji JY, Xu J, Ni JQ#. Performance of the Cas9 Nickase System in Drosophila melanogaster. G3 (Bethesda). 2014 Aug 15;4(10):1955-62.
44. Pan L, Wang S, Lu T, Weng C, Song X, Park JK, Sun J, Yang ZH, Yu J, Tang H, McKearin DM, Chamovitz DA, Ni JQ, Xie T#. Protein competition switches the function of COP9 from self-renewal to differentiation. Nature. 2014 Oct 9;514(7521):233-6.
45. Zheng Y, Hsu FN, Xu W, Xie XJ, Ren X, Gao X, Ni JQ, Ji JY#. A Genetic Analysis of the Lysine Demethylase KDM2 in Drosophila melanogaster. Mech Dev. 2014 Aug;133:36-53.
46. Ma X, Wang S, Do T, Song X, Inaba M, Nishimoto Y, Liu LP, Gao Y, Mao Y, Li H, McDowell W, Park J, Malanowski K, Peak A, Perera A, Li H, Gaudenz K, Haug J, Yamashita Y, Lin H, Ni JQ, Xie T#. Piwi is required in multiple cell types to control germline stem cell lineage development in the Drosophila ovary. PLoS One. 2014 Mar 21;9(3):e90267.
47. Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J#, Perrimon N#, Ni JQ#. An optimized gene editing technology for Drosophila melanogaster using germline-specific Cas9, Proc Natl Acad Sci USA. 2013 Nov 19;110(47):19012-7.
48. Y Yang, L Hou, Y Li, NI JQ and L Liu#, Neuronal necrosis and spreading death in a Drosophila genetic model, Cell Death and Disease, 2013, (2013) 4, e723.
49. Lv WW, Wei HM, Wang DL, Ni JQ, Sun FL#. Depletion of histone deacetylase 3 antagonizes PI3K-mediated overgrowth through the acetylation of histone H4 at lysine 16. J Cell Sci. 2012 Nov 15;125(Pt 22):5369-78.
50. Bejarano F, Bortolamiol-Becet D, Dai Q, Sun K, Saj A, Chou YT, Raleigh DR, Kim K, Ni JQ, Duan H, Yang JS, Fulga TA, Van Vactor D, Perrimon N, Lai EC#. A genomewide transgenic resource for conditional expression of Drosophila microRNAs. Development. 2012 Aug;139(15):2821-31.
51. Zhao X, Feng D, Wang Q, Abdulla A, Xie XJ, Zhou J, Sun Y, Yang ES, Liu LP, Vaitheesvaran B, Bridges L, Kurland IJ, Strich R, Ni JQ, Wang C, Ericsson J, Pessin JE, Ji JY#, Yang F#. A Conserved Function of CDK8 in Suppressing SREBP-dependent Lipogenesis. Journal of Clinical Investigation. 2012 Jul 2;122(7):2417-27.
52. Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N#. A genome-scale shRNA resource for transgenic RNAi in Drosophila . Nature Methods. 2011 May;8(5):405-7.
53. Perrimon N#, Ni JQ, Perkins L. In vivo RNAi: Today and Tomorrow. Cold Spring Harbor Perspectives in Biology. 2010 Aug 1;2(8):a003640.
54. Ni JQ, Liu LP, Binari R, Hardy R, Shim HS, Cavallaro A, Booker M, Pfeiffer BD, Markstein M, Wang H, Villalta C, Laverty TR, Perkins LA, Perrimon N#. A Drosophila Resource of transgenic RNAi lines for Neurogenetics. Genetics. 2009 Aug;182(4):1089-100.
55. Bai J, Binari R, Ni JQ, Vijayakanthan M, Li HS, Perrimon N#. RNA interference screening in Drosophila primary cells for genes involved in muscle assembly and maintenance. Development. 2008 Apr;135(8):1439-49.
56. Ni JQ, Markstein M, Binari R, Pfeiffer B, Liu LP, Villalta C, Booker M, Perkins L, Perrimon N#. Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster. Nature Methods. 2008 January; 5(1): 49–51.
57. Ni JQ, Liu LP, Hess D, Rietdorf J, Sun FL#. Drosophila ribosomal proteins are associated with chromatin through histone H1 and suppress global transcription. Genes Development. 2006 Jul 15;20(14):1959-73.
58. Cen X, Ni JQ, Tan T, Liu X, Li C, Chen J, Huang Y, Zhu S, Bi Q#. Investigation on recombinant hirudin via oral route. Peptides. 2006 Apr;27(4):836-40. Epub 2006 Feb 13.
59. Liu LP*, Ni JQ*, Shi YD, Oakeley EJ, Sun FL#. Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription. Nature Genetics. 2005 Dec; 37(12):1361-6. (*co-first author)
60. De LF, Ni JQ, Vaillant C, Sun FL#. HP1 modulates the transcription of cell-cycle regulators in Drosophila melanogaster. Nucleic Acids Res. 2005. 33(9): 2852-8.
