Faculty of Biological Sciences

Dr Ron Chen

PhD, Imperial College London
University Academic Fellowship in Pervasive Transcription
School of Molecular and Cellular Biology

Background: Studied viral immunoevasion at Imperial College London in the Lab of Prof. Geoffrey Smith FRS. Subsequently worked with Prof. Julie Ahringer FMedSci on functional genomics at the Gurdon Institute, University of Cambridge. Appointed University Academic Fellow 2015.

Contact:  Garstang 8.52b, +44(0) 1133439608, email address for  

You can read more about Dr Chen's interests here:
Publications in PDFs:
Lab webpage:

Research Interests

Epigenetic control in regulating cell fate specification and oncogenic processes

We are interested in basic biological questions at the chromatin level, underlying the pathogenesis process for the onset of human 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 our big biological questions to aid the understanding of the underlying mechanisms for human diseases.  

CpG-rich promoters are conserved in C. elegans and humans

Our previous work showed that C. elegans CpG-dense promoters are targeted by CFP-1 and marked by H3K4me3, the active promoter mark, thereby sharing strong similarities with human CpG island promoters (Chen et al., 2013 Genome Research & Chen et al., 2014 Genome Research). Both worm and human CpG-rich coding promoters are highly accessible, marked by H3K4me3, and enriched for widely expressed active genes. The finding was highly surprising as CpG island promoters were only thought to have genomic significance in mammals. Currently, C. elegans is the only invertebrate model organism showing CpG-island-like promoter features. This makes C. elegans an attractive model to study conserved transcription regulation events, especially the function of H3K4me3 modifications and other histone modifications found in most of coding gene promoters enriched for CpGs. 

CpG-rich promoters: a HOT regulatory platform for epigenetic control 

CpG-rich promoters are frequently present across the C. elegans and human genome. These widely active genomic regions have been found to harbour highly occupied target (HOT) regions for transcription factors (Chen et al., 2014 Genome Research). It suggests that CpG island promoters can function as regulatory hubs for chromatin regulators and consequently may modulate transcriptional activities. CFP-1 is an evolutionarily conserved non-methylated CpG binding protein that binds to CpG-rich promoters in humans and C. elegans. This conserved epigenetic regulator is part of the COMPASS complex that contains the major transferase for histone 3 lysine 4 tri-methylation (H3K4me3); SET-2 in C. elegans and Set1 in humans. H3K4me3 is frequently found in active promote regions, thus it has been used as an active promoter mark. The role of H3K4me3 in gene expression is unclear. To address this key question in epigenetic control, we are characterising cfp-1 and set-2 loss-of-function C. elegans mutants for their ability in inducing gene expression, specifying cell fate, and modulating chromatin architectures. In parallel, we are also "translating" our C. elegans findings into mammalian tissue cultured cells. 




Current Projects

(1) The interplay between chromatin modifiers/histone modifications in the cell fate specification

(2) The role of epigenetic control in the formation of oncogenic nucleic acid structures in tumour formation 

(Collaboration with Dr. Edwin Chen) 



Faculty Research and Innovation

Studentship information

Undergraduate project topics:

  • Investigating the role of chromatin regulation in cell fate specification and human cancers formation.

Postgraduate studentship areas:

  • The interplay between epigenetic control and oncogenic nucleic acid structure in tumour formation.
  • The identification of non-canonical chromatin regulators responsible for correct cell fate decision in C. elegans.

See also:

Modules taught

BIOC3900 - Cancer Biology
BIOL1302 - Introductory Skills for Biological Sciences
BIOL3398 - Research Tools and Applications
BIOL3399 - Extended Research Project Preparation
BIOL5294M - MSc Bioscience Research Project Proposal
BIOL5382M - Extended Research Project
BIOL5392M - Bioscience MSc Research Project

Group Leader Dr Ron Chen  (University Academic Fellowship in Pervasive Transcription)

Epigenetic control in regulating cell fate specification and oncogenic processes  


Yannic Chen (Primary supervisor) 90% FTE
Rosamund Clifford (Primary supervisor) 90% FTE
. Lalchungnunga (Primary supervisor) 40% FTE
Bharat Pokhrel (Primary supervisor) 90% FTE
Laura Warwick (Primary supervisor) 34% FTE
Benjamin Hopkins (Co-supervisor) 30% FTE
Dominic Lowen (Co-supervisor) 33% FTE
Dovile Milonaityte (Co-supervisor) 25% FTE

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
View abstract

Weick EM, Sarkies P, Silva N, Chen RA, Moss SMM, Cording AC, Ahringer J, Martinez-Perez E, Miska EA PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans Genes and Development 28 783-796, 2014
View abstract

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
View abstract

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
View abstract

Bahar MW, Graham SC, Chen RAJ, Cooray S, Smith GL, Stuart DI, Grimes JM How vaccinia virus has evolved to subvert the host immune response Journal of Structural Biology 175 127-134, 2011
View abstract

McCoy LE, Fahy AS, Chen RAJ, Smith GL Mutations in modified virus Ankara protein 183 render it a non-functional counterpart of B14, an inhibitor of nuclear factorκB activation Journal of General Virology 91 2216-2220, 2010
View abstract

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
View abstract

Chen RAJ, Ryzhakov G, Cooray S, Randow F, Smith GL Inhibition of IκB kinase by vaccinia virus virulence factor B14 PLoS Pathogens 4 -, 2008
View abstract

Cooray S, Bahar MW, Abrescia NGA, McVey CE, Bartlett NW, Chen RAJ, Stuart DI, Grimes JM, Smith GL Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein Journal of General Virology 88 1656-1666, 2007
View abstract

Chen RAJ, Jacobs N, Smith GL Vaccinia virus strain Western Reserve protein B14 is an intracellular virulence factor Journal of General Virology 87 1451-1458, 2006
View abstract

Jacobs N, Chen RAJ, Gubser C, Najarro P, Smith GL Intradermal immune response after infection with Vaccinia virus Journal of General Virology 87 1157-1161, 2006
View abstract