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Enhancer RNA activity and target prediction by integrating epigenetic and expression information

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  • Full or part time
    Dr A Joshi
    Prof D Hume
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

The Enhancers RNAs (eRNAs) are produced from enhancers of highly active genes in a cell type specific manner. FANTOM5 consortium has generated deepCAGE time series datasets measuring the activity of promoters and enhancers from 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli [1]. Using this data, it has been shown that enhancer regions can be predicted using bi-directional expression as a proxy [2]. As not all enhancers show a bi-directional expression, this data provides a unique opportunity to investigate the directionality of the eRNA expression. The transcription at promoters is by default uni-directional [3], whether this extends to eRNAs is still unclear. The aim of this project is to integrate expression data with epigenetic modifications (H3K4me1 & H3K27ac) to first group enhancers in three groups – bi-directional, uni-directional and not expressed using deepCAGE data. The next step is to characterise sequence and/or chromatin features associated with eRNA expression and their directionality. Specific sequence and epigenetic features distinguishing the three groups will be identified by collecting ChIP sequencing data for chromatin modifications at enhancers from the ENCODE resource. Identified features will be combined into a classifier to predict enhancer expression from its surrounding sequence and epigenetic signatures.

Intended Outcomes:

New way of integrating expression and epigenetic data
A web resource of eRNA-target prediction across human cell types
Identification of features associated with eRNA directionality

Applications including a full CV with names and addresses (including email addresses) of two academic referees, should be sent to: Liz Archibald, Postgraduate Research Student Administration, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG. Or emailed to [Email Address Removed]. When applying for the studentship please state clearly the title of the studentship and the supervisors in your covering letter.

Funding Notes

All candidates should have or expect to have a minimum of an appropriate upper 2nd class degree. To qualify for full funding students must be UK or EU citizens who have been resident in the UK for 3 years prior to commencement.


Arner, E., Daub, C.O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drabløs, F., Lennartsson, A., Rönnerblad, M., Hrydziuszko, O., Vitezic, M., et al. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 347, 10101014 (2015).
Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., et al An atlas of active enhancers across human cell types and tissues. Nature 507, 455461 (2014).
Duttke, S.H.C., Lacadie, S.A., Ibrahim, M.M., Glass, C.K., Corcoran, D.L., Benner, C., Heinz, S., Kadonaga, J.T., and Ohler, U. Human Promoters Are Intrinsically Directional. Mol. Cell 57, 674684 (2015).

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