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Professor Vardhman Rakyan, PhD

Vardhman

Professor of Epigenetics

Centre: Centre for Genomics and Child Health

Email: v.rakyan@qmul.ac.uk
Telephone: 020 7882 8140

Profile

For my PhD (1999-2002) I investigated epigenetic inheritance under the supervision of Prof. Emma Whitelaw, University of Sydney, Australia. From 2003-2007, I was a CJ Martin Postdoctoral Fellow at the Sanger Institute, Cambridge, UK; where, under the guidance of Dr Stephan Beck, I developed functional genomics tools for genome-wide DNA methylation analyses.

 

Summary

 The overall goals of the lab are to understand the molecular basis of the non-genetically determined component of mammalian phenotypes and diseases. Within this context, we are particularly interested in ‘epialleles' – loci at which the epigenetic state varies as a result of stochastic, genetic and/or environmental influences. We pursue several complementary lines of investigation that integrate molecular genomics, computational biology, mouse models, and human cohorts to understand the role of epialleles in complex phenotypes and diseases, transgenerational epigenetic inheritance, and environmental epigenomics.

Teaching

Problem Based Learning (1st year MeD), FunMed 1 Lecture, SSC

 

Research

Research Interests:

Gene-environment interactions at ribosomal DNA (rDNA) – Epigenetic silencing of rDNA is a conserved stress response in eukaryotes. We study how genetic variation influences the rDNA stress response in humans and mice.
 
Ageing – DNA methylation is currently known to be the most accurate molecular biomarker of age in humans. We study the molecular basis of this phenomenon in humans and a variety of other mammals.
 
Research Group Members

Dr Robert Seaborne, Postdoctoral Research Assistant
Dr Francisco Rodriquez Algarra
Dr Pui Pik Law
Ama Brew

Publications

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK*, Beck S*, Leslie RD*. Nat Commun. 2016 Nov 29;7:13555. 


Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice.
Holland ML, Lowe R, Caton PW, Gemma C, Carbajosa G, Danson AF, Carpenter AA, Loche E, Ozanne SE, Rakyan VK.
Science. 2016 Jul 29;353(6298):495-8. 
 
Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans.
Beyan H, Down TA, Ramagopalan SV, Uvebrant K, Nilsson A, Holland ML, Gemma C, Giovannoni G, Boehm BO, Ebers GC, Lernmark Å, Cilio CM, Leslie RD, Rakyan VK.
Genome Res. 2012 Nov;22(11):2138-45

Epigenome-wide association studies for common human diseases. 
Rakyan VK, Down TA, Balding DJ, Beck S. Nat Rev Genet. 2011 Jul 12;12(8):529-41.

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. 
Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD. Genome Res. 2010 20(4):434-9.

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. 
Down TA*, Rakyan VK* (* joint first and corresponding authors), Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 26(7):779-85.
 

View all Vardhman Rakyan's Research Publications at: http://www.researchpublications.qmul.ac.uk

Supervision

Zakaryya Ahmad, PhD Student

Selin Yildizoglu, PhD Student