1B-111, 1/F, Block 1, To Yuen Building
+852 3442-9078
+852 3442-0549
jian.yan@cityu.edu.hk
CityU Scholars
Molecular Mechanism of Osteosarcoma Tumorigenesis and Pulmonary Metastasis • lncRNA Function • Transcription Factor in Transcriptional Regulation • Genomic Tool Development

Dr Yan received his BSc in biological sciences at Tsinghua University and PhD (in Medical Science) at Karolinska Institutet (Prof. Jussi Taipale), investigating molecular mechanism of transcriptional regulation in colorectal cancer cells. In 2015-2018, Dr Yan conducted postdoc training with Prof Bing Ren at UC San Diego to study 3D genome organization and gene regulation. In August 2018, Dr. Yan joined the Department of Biomedical Sciences as a tenure-track assistant professor. His research now focuses on unravelling the function of noncoding human genome.
Research InterestsDue to high mutation burden in regulatory elements, affected cells develop aberrant gene transcription compared with surrounding normal cells that could device them with growth advantage. Some noncoding RNA transcripts have been used as clinical diagnostic markers for some diseases whereas the molecular mechanism of their relevance largely elusive. Our research goal is to unveil molecular mechanism of how transcriptional aberration affects cellular function and human health issues, using high throughput, state-of-the-art tools. My current interest focuses on developing genomic tools to:
Dissect of lncRNA function and mechanism in disease
Identify of genetic variations that contribute to disease pathogenesis
Study protein-chromatin binding with extremely low number of cells and apply it to study cell heterogeneity
The Ph.D. program position is available all year round. Should you have any interest, please send an email for inquiry with your updated CV enclosed. Note that a valid English language test score fulfilling the university minimum requirement (CET-6 490, TOEFL iBT 79 or IELTS 6.5) should be obtained before admission.
Publications(# corresponding authors; * co-first author)
2021J. Yan#,*, Y. Qiu*, A. dos Santos*, Y. Yin, Yang E. Li, N. Vinckier, N. Nariai, P. Benaglio, A. Raman, X. Li, S. Fan, J. Chiou, F. Chen, K.A. Frazer, K.J. Gaulton, M. Sander, J. Taipale#, B. Ren#, Systematic analysis of binding of transcription factors to noncoding variants, Nature 591 (2021) 147-151.
T. Wang*, W. Sun*, L. Fan*, C. Hua*, N. Wu, S. Fan, J. Zhang, X. Deng#, J. Yan#, An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence, eLife 10 (2021) e61885.
D.S. Tan*, Y. Chen*, Y. Gao, A. Bednarz, Y. Wei, V. Malik, D. HH Ho, M. Weng, S. Y. Ho, Y. Srivastava, S. Velychko, X. Yang, L. Fan, J. Kim, J. Graumann, G. D Stormo, T. Braun, J. Yan, H. R Sch?ler, R. Jauch#. Directed evolution of an enhanced POU reprogramming factor for cell fate engineering, Molecular Biology and Evolution 38(7) (2021) 2854-2868.
R.J. Geusz*, A. Wang*, J. Chiou*, J.J. Lancman*, N. Wetton, S. Kefalopoulou, J. Wang, Y. Qiu, J. Yan, A. Aylward, B. Ren, P. DS Dong, K. J Gaulton#, M. Sander#, Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development, eLife 10 (2021) e59067.
2020W. Yi*, J. Li*, X. Zhu*, X. Wang*, L. Fan, W. Sun, L. Liao, J. Zhang, X. Li, J. Ye, F. Chen, J. Taipale, K.M. Chan#, L. Zhang#, J. Yan#, CRISPR-assisted detection of RNA-protein interactions in living cells, Nature Methods 17(7) (2020) 685-688.
L. Fan, T*. Wang*, C. Hua*, W. Sun*, X. Li, L. Grunwald, J. Liu, N. Wu, X. Shao, Y. Yin, J. Yan#, X. Deng#, A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae, Nature Communications 11(1) (2020) 4947.
J. Yan#, X. Wang, Detection of Disease-associated Mutations and Biomarkers Using Next-generation Sequencing, Detection Methods Precision Medicine 18, (2021) 119. (book chapter)
Z. Wang*, Y. Li*, B. Hou*, M.I. Pronobis*, M. Wang, Y. Wang, G. Cheng, W. Weng,Y. Wang, Y. Tang, X. Xu, R. Pan, F. Lin, N. Wang, Z. Chen, S. Wang, L. z Ma, Y. Li, D. Huang, L. Jiang, Z. Wang, W. Zeng, Y. Zhang, X. Du, Y. Lin, Z. Li, Q. Xia, J. Geng, H. Dai, Y. Yu, X. Zhao, Z. Yuan, J. Yan, Q. Nie, X. Zhang, K. Wang, F. Chen, Q. Zhang, Y. Zhu, S. Zheng, K. D Poss, S. Tao#, X. Meng#, An array of 60,000 antibodies for proteome-scale antibody generation and target discovery, Science Advances 6 (11) (2020) eaax2271.
2019X. Wang#, M.J. Cairns, J. Yan#, Super-enhancers in transcriptional regulation and genome organization, Nucleic Acids Research 47(22) (2019) 11481-11496.
W.W. Greenwald*, J. Chiou*, J. Yan*, Y. Qiu*, N. Dai*, A. Wang, N. Nariai, A. Aylward, J.Y. Han, N. Kadakia, N. Barrufet, M. Okino, F. Drees, N. Vinckier, L. Minichiello, D. Gorkin, J. Avruch, K. Frazer, M. Sander, B. Ren, K.J. Gaulton#, Pancreatic islet chromatin accessibility and conformation defines distal enhancer networks of type 2 diabetes risk, Nature Communications 10 (2019) 2078.
2018 and earlier (representative)J. Yan*, S.A. Chen*, A. Local, T. Liu, Y. Qiu, K.M. Dorighi, S. Preissl, C.M. Rivera, C. Wang, Z. Ye, K. Ge, M. Hu, J. Wysocka, B. Ren#, Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers, Cell Research 28(2) (2018) 204-220.
Y. Yin, E. Morgunova, A. Jolma, E. Kaasinen, B. Sahu, S. Khund-Sayeed, P.K. Das, T. Kivioja, K. Dave, F. Zhong, K.R. Nitta, M. Taipale, A. Popov, P.A. Ginno, S. Domcke, J. Yan, D. Schubeler, C. Vinson, J. Taipale#, Impact of cytosine methylation on DNA binding specificities of human transcription factors, Science 356(6337) (2017).
Q. Huang*, T. Whitington*, P. Gao, J.F. Lindberg, Y. Yang, J. Sun, M.R. V?is?nen, R. Szulkin, M. Annala, J. Yan, L.A. Egevad, K. Zhang, R. Lin, A. Jolma, M. Nykter, A. Manninen, F. Wiklund, M.H. Vaarala, T. Visakorpi, J. Xu, J. Taipale#, G. Wei#. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding, Nature Genetic 46(2) (2014) 126-35.
J. Yan*, M. Enge*, T. Whitington, K. Dave, J. Liu, I. Sur, B. Schmierer, A. Jolma, T. Kivioja, M. Taipale, J. Taipale#, Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites, Cell 154(4) (2013) 801-813.
A. Jolma*, J. Yan*, T. Whitington, J. Toivonen, K.R. Nitta, P. Rastas, E. Morgunova, M. Enge, M. Taipale, G. Wei, K. Palin, J.M. Vaquerizas, R. Vincentelli, N.M. Luscombe, T.R. Hughes, P. Lemaire, E. Ukkonen, T. Kivioja, J. Taipale#, DNA-binding specificities of human transcription factors, Cell 152(1-2) (2013) 327-339.
I.K. Sur, O. Hallikas, A. Vaharautio, J. Yan, M. Turunen, M. Enge, M. Taipale, A. Karhu, L.A. Aaltonen, J. Taipale#, Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors, Science 338(6112) (2012) 1360-3.
N. Makinen, M. Mehine, J. Tolvanen, E. Kaasinen, Y. Li, H.J. Lehtonen, M. Gentile, J. Yan, M. Enge, M. Taipale, M. Aavikko, R. Katainen, E. Virolainen, T. Bohling, T.A. Koski, V. Launonen, J. Sjoberg, J. Taipale, P. Vahteristo, L.A. Aaltonen#, MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas, Science 334(6053) (2011) 252-5.
S. Tuupanen, M. Turunen, R. Lehtonen, O. Hallikas, S. Vanharanta, T. Kivioja, M. Bj?rklund, G. Wei, J. Yan, I. Niittym?ki, J. Mecklin, H. J?rvinen, A. Ristim?ki, M. Di-Bernardo, P. East, L. Carvajal-Carmona, R.S. Houlston, I. Tomlinson, K. Palin, E. Ukkonen, A. Karhu, J. Taipale#, L.A. Aaltonen#. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling, Nature Genetics 41(8) (2009) 885-90.
12 July 2021


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