Novel approaches for epigenomic profiling of repetitive elements

Dr Miguel Branco. Blizard Institute, Queen Mary, University of London
Dr Tobias Ost, Cambridge Epigenetix Limited

Project Description

Transposable elements (TEs) are mobile genetic elements that are highly abundant in virtually all eukaryotic genomes. Host defense strategies against TE expansion involve epigenetic mechanisms, such as DNA methylation, that ensure their silencing[1]. This can in turn have an impact on local chromatin environment and host gene expression. Indeed, DNA methylation at TEs can drive phenotypic changes that are transgenerationally inherited[2]. Despite the potential of TEs for dramatically affecting phenotype, surprisingly little is known about their epigenetics at the single-copy level, which in turn deeply impairs a deeper and wider understanding of their impact on the host. This shortcoming stems solely from the repetitive nature of TEs, which makes it notoriously difficult to assign short reads from high-throughput sequencing to unique locations in the genome[3].

We are looking for a talented graduate student to develop new sequencing strategies that allow for profiling of DNA modifications (methylation, hydroxymethylation) at repetitive loci, especially at evolutionarily young TE copies. These techniques will then be used to profile unique copies of young TEs in mouse and human embryonic stem cells, in order to evaluate the epigenetic variability of TEs and test how this correlates with the local chromatin environment and gene expression.


This is an exciting opportunity for graduates from disciplines related to genetics, epigenetics and molecular biology. Knowledge and experience in high-throughput sequencing technologies would be an advantage, as would bioinformatics skills.

Applicants must hold, or be expected to achieve, a first or high upper second-class undergraduate honours degree or equivalent (for example BA, BSc, MSci) or a Masters degree in a relevant subject. Interested applicants are encouraged to contact Miguel Branco ( in advance of the deadline, 20th January 2017 at 5pm.

To apply you will need to send the following documents in a single email to: All documents must be submitted in unprotected PDF format.

  • Completed Application Form (Sections A and B) including details of two Academic References
  • The disability and ethnic origin monitoring form
  • Official Final Transcripts from Completed Programmes of Study
  • Official Interim Transcripts from On-going Programmes of Study
  • English Language Qualification (if required)
  • Academic CV
  • Copy of Passport

Please click the relevant links below to download a zipped folder of application documents in your preferred format.
Application Pack (Word).zip
Application Pack (PDF).zip


  1. Rowe, H. M. & Trono, D. Dynamic control of endogenous retroviruses during development. Virology 411, 273–287 (2011).
  2. Daxinger, L. & Whitelaw, E. Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 13, 153–162 (2012).
  3. Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13, 36–46 (2012).