Just out of sight: determining gene regulatory loci to improve coloboma diagnoses

Location: The Roslin Institute, University of Edinburgh or Newcastle University (Degree registration with University of Edinburgh)

Supervisors: Joe Rainger, The Roslin Institute, University of Edinburgh.

Rachel Queen and Majlinda Lako; Institute of Genetic Medicine at Newcastle University.

Project details: AIM. This work aims to discover regulatory regions of the genome that control optic fissure closure (OFC) genes in developing chicken eyes to identify candidate non-coding loci for molecular diagnoses in human unsolved coloboma patients. OBJECTIVES: (1) Identify regulatory non-coding regions of the chicken genome that display dynamic chromatin accessibility during optic fissure closure using single-cell ATACseq, and match these to specific cell types in the optic fissure. (2) Map optic fissure closure regulatory regions to the human genome and perform variant analysis in patient DNA sequences to identify plausible causative coloboma loci.

Skills and technique training received during PhD: This is predominantly a bioinformatics focused PhD and the successful applicant will receive a wide range of skills and training in various areas of sequence and differential accessibility analyses for single-cell RNAseq and ATACseq, alongside patient DNA sequence database interrogation and variant identification methods. In addition, the successful applicant will learn skills and gain expertise in chicken embryology, eye anatomy, vertebrate developmental biology and the causes of developmental birth defects, in addition to fluorescence and confocal microscopy techniques.

For informal enquiries about the project please contact Dr Joe Rainger ([email protected]). 

A statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [email protected].

When applying for the studentship please state clearly the project title and the supervisor in your covering letter.