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Host gene capture by transposable elements in eukaryotic genomes


   School of Biological & Chemical Sciences


London United Kingdom Bioinformatics Cell Biology Developmental Biology Evolution Genetics Genomics Molecular Biology Molecular Genetics

About the Project

The following PhD studentship is available in the School of Biological and Chemical Sciences to start in September 2021.

Research Environment

The School of Biological and Chemical Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2014 Research Excellence Framework (REF). We offer a multi-disciplinary research environment and have approximately 160 PhD students working on projects in the biological, chemical and psychological sciences. Our students have access to a variety of research facilities supported by experienced staff, as well as a range of student support services.

Alex de Mendoza’s laboratory is focused on studying the evolution of gene regulation at multiple branches of the tree of life. For more information about previous research from Alex de Mendoza, visit his laboratory website or contact him at

Training and Development

Our PhD students become part of Queen Mary’s Doctoral College which provides training and development opportunities, advice on funding, and financial support for research. Our students also have access to a Researcher Development Programme designed to help recognise and develop key skills and attributes needed to effectively manage research, and to prepare and plan for the next stages of their career.

In this project, you will be trained in state-of-the-art comparative genomics and epigenomics (repeat annotation, Whole Genome Bisulfite sequencing, ChIP-seq, DAP-seq) and molecular biology (cloning, nucleic acid extraction). You will get hands on experimental approaches and develop proficiency in computational and statistical analyses. In addition to focused training, you will be trained in project management and presentation skills and encouraged to develop international collaborations and networking.

Project Details

The information encoded in a genome is the roadmap to make an organism, yet in most eukaryotes the genome is not organised in a tidy manner. Most genomes have been invaded by genetic parasites, also known as transposable elements, that need to be silenced to avoid genome instability. To control transposons, eukaryotes have evolved various regulatory systems, many of which are dependent on chromatin, which refers to the proteins and chemical modifications that wrap around DNA. However, transposable elements have found mechanisms to evade silencing by the host. One of these mechanisms is the acquisition of host genes. These host genes are incorporated into the coding sequence of the transposable element and are then used to the advantage of the transposable element, facilitating its expansion within the host genome. On many occasions the captured genes are involved in chromatin regulation, suggesting that transposable elements are repurposing tools originally selected to silence them. This project will explore how prevalent is this process of gene capture by transposable elements, focusing on distantly related eukaryotic groups. Furthermore, examples of captured genes will be functionally tested to understand the functions they perform in the transposable element life cycle.

  • In this project you will rigorously explore this topic combining state-of-the-art experimental and computational approaches.
  • You will have access to large genomic databases, and in-house live organisms to fuel your investigation.
  • You will gain experience of eukaryotic macroevolution and molecular techniques (nucleic acid manipulation, DNA cloning, epigenomic profiling), bioinformatics (comparative genomics, pipelines to analyse high-throughput sequencing data), and statistics (using R programming language). 
  • You will be encouraged to develop your own ideas and hypotheses.

Application Requirements

Applications are invited from outstanding candidates with, or expecting to receive, a first or upper-second class honours bachelors degree or a masters degree in an area relevant to the project (i.e. molecular biology, genetics, developmental and cell biology, bioinformatics).

In a multidisciplinary project like this, candidates are unlikely to have a background in all disciplines involved. The most important qualification is motivation, enthusiasm and that the project appeals to you. However, previous computational experience would be a plus. We can envisage strong candidates coming through a variety of routes including:

  • Bioinformatics 
  • Molecular biology
  • Cell biology

Applicants from outside of the UK are required to provide evidence of their English language ability. Please see our English language requirements page for details.

The School of Biological and Chemical Sciences is committed to promoting diversity in science; we have been awarded an Athena Swan Silver Award. We positively welcome applications from underrepresented groups.

http://hr.qmul.ac.uk/equality/

https://www.qmul.ac.uk/sbcs/about-us/athenaswan/

To apply, please submit an online application through our website by the stated deadline, including your CV, personal statement, transcripts and certificates for previous degrees and references: Apply Online


Funding Notes

This studentship is open to UK residents eligible for 'home' fee status and is funded by Queen Mary University of London. It will cover tuition fees, and provide an annual tax-free maintenance allowance for 3 years at the Research Council rate (£17,609 in 2021/22).

References

- Capture of a functionally active Methyl-CpG Binding Domain by an arthropod retrotransposon family.
de Mendoza A, Pflueger J, Lister R. Genome Research. 29(8):1277-1286.

- Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R. Nature Communications. 9(1):1341. 2018.

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