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BBSRC DTP MRes/PhD Studentship - Mechanisms of post transcriptional rearrangement in humans

This job is no longer available

Recruiter
Newcastle University
Posted
16 April 2012
Ref
HG042
Location
North East England > Tyne & Wear
Discipline
Biology
Level
PhD/Studentships
Course fee
not specified

Further information

BBSRC DTP MRes/PhD Studentship - Mechanisms of post transcriptional rearrangement in humans

  • Reference Code: HG042

Details:

Name of the supervisors
Dr M Jackson
http://www.ncl.ac.uk/igm/staff/profile/michael.jackson

Dr M Santibanez-Koref
http://www.ncl.ac.uk/igm/staff/profile/mauro.santibanez-koref

Professor D Elliott
http://www.ncl.ac.uk/igm/staff/profile/david.elliott

Sponsor
BBSRC  http://www.bbsrc.ac.uk/

Duration of the award
4 Years (MRes in Medical Genetics followed by a three year PhD)
 
Project description
Recent in silico analyses have established that some transcripts can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, PTES). We and others have recently establishes that these transcrips are common in human, can be conserved in other mammals, and can include both linear and circular molecules (Al Balool et al. 2011 Genome Research 21[11]:1788-99; Salzman et al. 2012 Plos One 7:e30733). Despite this, their distribution, functional significance, and mechanism(s) of generation remain unclear.

This project will use both bioinformatic and experimental approaches to understand these novel transcripts, establish their relationship to normal transcription, and define their biological relevance. It will make use of the wealth of new publicly available human and mouse transcriptome sequence data to characterise PTES on a genome wide scale, to both establish their full distribution, and to identify transcriptional and genomic correlates of the PTES structures identified. It will involve developing appropriate analysis pipelines for next generation sequencing data, as well as models to predict which transcripts are susceptible to PTES.

The results of these in silico analyses will be validated experimentally, and will help to shape subsequent analyses to investigate the mechanism of PTES generation. These will involve the experimental manipulation of full length human genes within large insert genomic clones to identify cis-acting elements affecting PTES generation. In addition, forced expression of specific PTES transcripts will also be used to investigate the impact upon other genes and isoforms using microarray methodology.

Value of the Award and Eligibility
Depending on how you meet the BBSRC's eligibility criteria, you may be entitled to a full or a partial award. A full award covers tuition fees at the UK/EU rate and an annual stipend of £13,590 (2011/12). A partial award covers fees at the UK/EU rate only.

Person Specification
Applicants should have an upper-second-class Honours degree, or international equivalent, in a science or related discipline.  Some programming experience is a pre-requisite, with knowledge of basic molecular biology and bioinformatics desirable.

How to Apply
You must complete the University's postgraduate application form , selecting "Master of Research/Doctor of Philosophy (Medical Sciences) - Medical Genetics"  as the programme of study. Only mandatory fields need to be completed (no personal statement required) but you must attach a copy of your CV and a covering letter, quoting the title of the studentship and reference number HG042.

Closing date for applications
Prompt application is advised as this post is only available until a suitable candidate is appointed.

For further details
Please contact Dr M Jackson, michael.jackson@ncl.ac.uk +44 (0) 191 241 8677.

 

Newcastle University


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