Identification of novel regulators of adipogenesis by genome-wide epigenetic mapping of
promoter-enhancer interactions
Supervisor, Miguel Constância (IMS); Co-Supervisor, Peter Fraser (The Babraham Institute)
Knowledge of adipocyte biology is essential for understanding the pathophysiological basis of
obesity and metabolic diseases such as type 2 diabetes. Adipocytes play a central role in systemic
metabolism, coordinating glucose and lipid homeostasis. The development of fat cells from
preadipocytes, or adipogenesis, is one of the most intensively studied examples of cellular
differentiation (1). Crucially, many of the critical aspects of fat cell formation in vivo can be faithfully
recapitulated in in vitro models (1). Recent advances in high-throughput DNA sequencing have
greatly enhanced our ability to study genome function. In particular, it is now possible to perform
studies of 3D nuclear organization, chromatin remodelling and gene regulation in adipogenesis and
cellular differentiation (2). This provides an unparalleled opportunity to unravel new genes involved
in the control of adipocyte function.
In this PhD project you will apply genome-wide screens for enhancer-promoters interactions to the
study of adipogenesis, with the overall aim of finding novel genetic and epigenetic regulators.
Briefly, you will use a novel technique, which was developed in Peter Fraser’s lab, called promoter
capture Hi-C, to map long-range interactions between all promoters and their regulatory elements,
such as enhancers and silencers, during the pre-adipocyte – adipocyte transition in an in vitro model
of human adipogenesis (i.e. Simpson Golabi Behmel Syndrome primary pre-adipocyte cell line). This
genome wide chromosomal interaction data will be integrated with epigenome maps for enhancerspecific and promoter-specific epigenetic marks by ChIP-Seq (3) and genome-wide gene transcription
by RNA-Seq and CAGE (Cap Analysis Gene Expression). This screen will lead to the identification of all
regulatory trans and cis interactions between gene units, and the novel ones will be confirmed by 3C
(2). You will then establish if these novel interactions are conserved in models of mouse
adipogenesis. You will then proceed towards functional studies (e.g. siRNA knockdowns of gene
expression and CRISPR genome editing to disrupt long-range interactions) of selected genes to show
their critical roles in adipogenesis.
Rotation 1 – Constancia lab: in vitro model of adipogenesis; epigenetic techniques
Rotation 2 - Fraser lab: HiC methodology
References:
1- Cristancho AG and Lazar MA (2011) Forming functional fat: a growing understanding of
adipocyte differentiation. Nat Rev Mol Cell Biol 12:722-734.
2- Dekker J et al. (2013) Exploring the three-dimensional organization of genomes: interpreting
chromatin interaction data. Nat Rev Genet 14:390-403
3- Mikkelsen TS et al. (2010) Comparative epigenomic analysis of murine and human adipogenesis.
Cell 143:156-169.