Dr Jian Yan (嚴健博士)

PhD (Karolinska Institutet)

Assistant Professor

Dr Jian Yan

Contact Information

Office: 1B-109, 1/F, Block 1,
To Yuen Building
Phone: +852 3442-9078
Fax: +852 3442-0549
Email: jian.yan@cityu.edu.hk
Web: CityU Scholars

Research Interests

  • 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 MSc (in biotechnology) at University of Helsinki. He continued his PhD study in Prof. Jussi Taipale’s lab at Karolinska Institutet, investigating molecular mechanism of transcriptional regulation in colorectal cancer cells. After obtaining PhD degree, Dr Yan moved to San Diego in 2015 to study 3D genome organization and gene regulation as a postdoc fellow with Prof. Bing Ren at Ludwig Institute for Cancer Research.

After more than a decade of biological research training in Asia, Europe and America, he joined the Department of Biomedical Sciences, City University of Hong Kong as a tenure-track assistant professor in fall of 2018, focusing on (epi)genome function in development of complex human diseases using state-of-the-art genomics tools.

Research Interests

The 3 billion base-pair human genome was firstly sequenced fifteen years ago, of which only 1% was discovered to code for protein. After putting over a decade of tremendous efforts, we still know very little about the function of the entire genomic sequence. Genetic and epigenetic evidences have suggested that a large portion of human genome plays a regulatory role in gene transcription and is related to health problems including cancer.

Cancer in general has been identified as uncontrolled cell growth and a large amount of mutations have been detected in cancer genome. Due to high mutation burden in regulatory elements, cancer cells largely develop aberrant gene transcription compared with surrounding normal cells that device them with growth advantage. Some transcripts (including non-coding RNAs) have been used as clinical diagnostic markers for some cancer types whereas the molecular mechanism of their relevance to the cancer development remains largely elusive. Our research goal is to unveil molecular mechanism of how transcriptional aberration affects cancer development, using high throughput, state-of-the-art tools. We hope that such knowledge could be translated to improving disease diagnosis and therapeutic strategy.

As new tool is critical for making breakthrough in research, my current interest is focused on developing genomic tools to:

  1. Dissect of lncRNA function and mechanism in cancer development
  2. Identify of genetic variations that contribute to cancer pathogenesis
  3. Study protein-chromatin binding with extremely low number of cells and apply it to study cancer heterogeneity
  4. Identify genomic loci causing cancer metastasis

Available Positions

We are seeking highly motivated talented researchers to join the lab as Research Assistants, Graduate Students and Postdoc Fellows all year round. Candidates with training background in either genomics, molecular biology, bioinformatics or mouse model are highly encouraged to apply. Should you be interested, please directly e-mail Dr Yan with your CV and contacts of three references.

Selected Publications (within 5 years)

  • Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Research. 2018 Feb;28(2):204-220.
  • Xiong X, Zhang Y, Yan J, Jain S, Chee S, Ren B, Zhao H. A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. ACS Synthetic Biology. 2017 Jun 16;6(6):1034-1042
  • Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 2017 May 5; 356(6337).
  • Liu N, Ter Huurne M, Nguyen LN, Peng T, Wang SY, Studd JB, Joshi O, Ongen H, Bramsen JB, Yan J, et al. The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression. Nature Communications. 2017 Feb 14;8: 14418.
  • Dave K, Sur I, Yan J, Zhang J, Kaasinen E, Zhong F, Blaas L, Li X, Kharazi S, Gustafsson C, De Paepe A, Månsson R, Taipale J. Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. Elife. 2017 Jun 6;6.
  • Huang Q, Whitington T, Gao P, Lindberg JF, Yang Y, Sun J, Väisänen MR, Szulkin R, Annala M, Yan J, et al. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nature Genetics. 2014 Feb; 46(2): 126-35.
  • Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites. Cell. 2013 Aug 15; 154(4): 801-13.
  • Jolma A*, Yan J*, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, et al. DNA-binding specificities of human transcription factors. Cell. 2013 Jan 17; 152(1-2): 327-39.
  • Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science. 2012 Dec 7; 338(6112): 1360-3.
  • Tuupanen S*, Yan J*, Turunen M, Gylfe AE, Kaasinen E, Li L, Eng C, Culver DA, Kalady MF, Pennison MJ, et al. Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583. Cancer Genetics. 2012 Jan-Feb; 205(1-2): 25-33.