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Chen Lab: Chromatin Biology
School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
United Kingdom

genetic screen, transcription, gene function, cell fate specification, and transgenerational epigenetic inheritance


C. elegans, and mammalian cell line-based assays


C. elegans phenotypical assays, ChIP-seq, RNA-seq, DRIP-seq and other genomic approaches.

Collaborations outside COST

The role of R-loops in hematopoietic stem cell develop and leukaemia, with Dr. Edwin Chen, Leeds

Short description of ongoing research projects

Our main research interest is to understand the mechanistic action of epigenetic control in common human diseases. We aim to identify and characterise the conserved regulatory circuits underlie human diseases such as cancer, and age-related diseases. Therefore, we use the powerful genetic model organism C. elegans to study conserved regulatory events at the chromatin level. These round worms (nematodes) share 70% of proteins encoded in the human genome. Most proteins involved in transcription and chromatin function are highly conserved. The comprehensive genetic tools (e.g. the genome-wide RNAi library), short life cycle (only 3 days), and the ease of molecular experiments (e.g. CRISPR genome editing) make C. elegans a great experimental system to address big biological questions to aid the understanding of the underlying mechanisms for human diseases. We currently are investigating the interplay between chromatin modifiers in the cell fate specification using functional genomic and proteomic approaches, and how this interplay impacts on the formation of pathological DNA structure leading to incorrect cell fate and human cancer (Collaboration with Dr. Edwin Chen) 

  1. Ho JWK, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RAJ, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE. Comparative analysis of metazoan chromatin organization Nature 512 449-452, 2014. DOI:10.1038/nature13415
  2. Chen RAJ, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J Extreme HOT regions are CpG-dense promoters in C. elegans and humans Genome Research 24 1138-1146, 2014. DOI:10.1101/gr.161992.113
  3. Chen RAJ, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LDW, Jeffers TE, Ahringer J. The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures Genome Research 23 1339-1347, 2013. DOI:10.1101/gr.153668.112
  4. Graham SC, Bahar MW, Cooray S, Chen RAJ, Whalen DM, Abrescia NGA, Alderton D, Owens RJ, Stuart DI, Smith GL, Grimes JM Vaccinia virus proteins A52 and B14 share a Bcl-2-like fold but have evolved to inhibit Nf-κB rather than apoptosis PLoS Pathogens 4 -, 2008. DOI:10.1371/journal.ppat.1000128
  5. Chen RAJ, Ryzhakov G, Cooray S, Randow F, Smith GL Inhibition of IκB kinase by vaccinia virus virulence factor B14 PLoS Pathogens 4 -, 2008. DOI:10.1371/journal.ppat.0040022
Other activities of potential interest to others

British Genetic Society

Cost UE