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Elucidating the transcriptomic regulation of tissue fusion processes during embryonic development

  • Full or part time
  • Application Deadline
    Saturday, November 30, 2019
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

What are the gene regulatory networks that contract and coordinate the expression of key genes required for normal tissue fusion in embryonic development? What is their role and impact on developmental disorders, such as cleft palate, coloboma, spina bifida and septal heart defects?

This project in the Rainger lab at Roslin Institute will provide a first insight into answering these questions through combining next-generation sequencing technologies and chicken embryology. We have established the embryonic chicken eye as a novel model for investigating tissue-fusion and optical disorders (Ref - PMC6606025), which provides highly-accessible and unprecedented amounts of epithelial tissues undergoing fusion for cell isolation and ‘omic analyses. The starting point of your project will be to use this model to perform ATAC-seq to define fusion-specific genetic regulatory elements (Ref - PMC4374986). You will then incorporate this data with our existing transcriptomic data to directly correlate open chromatin with specific gene expression. Using in vivo approaches and functional assays you will next prove their specificity and requirement during tissue-fusion in the embryonic eye, and other sites of embryonic tissue fusion. You may also choose to develop and perform in silico analyses to reveal regulatory networks, and interrogate human genome sequences to reveal associations of these regulatory elements with human congenital tissue-fusion diseases

Key words: ATACseq, RNAseq, Chicken embryology, developmental biology, functional genetics, bioinformatics, tissue fusion, coloboma, developmental defects.

The Rainger lab and Roslin Institute commit to support the professional and career development and success of researchers, ensuring equality of opportunity regardless of background or any protected characteristic as defined by the Equality Act (2010). Roslin Institute hold an Athena Swann Gold Award.

Start Date - September 2020
Duration - 3.5 years
Location - The Roslin Institute, University of Edinburgh
Stipend - £15,009 (in 2019)
Primary Supervisor and contact for enquiries - Dr Joe Rainger

Funding Notes


All candidates should have or expect to have a minimum of an appropriate upper 2nd class degree or equivalent, and be resident in the UK or an EU member state.

Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be sent to the PGR student team at .


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