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Deciphering the function of noncoding transcription at regulatory elements

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  • Full or part time
    Dr P Madapura
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

A PhD studentship is available in the lab of Pradeepa Madapura on “Deciphering the function of noncoding transcription at regulatory elements”
Project details: Interplay among histone modifying complexes and proteins that recognize these modifications, along with chromatin remodelers are likely to play key role in enhancer function. However, there are no thorough investigations on the importance of histone modifications and protein complexes associated with enhancers and their effect on target genes in vivo. Research in our laboratory is aimed at deciphering the functions of candidate enhancer-associated proteins and histone modifications. We routinely use nuclease deficient CRISPR-Cas9 (dCas9) to fuse protein of interest and which can be directed to specific loci. We aim to use this methodology to assess the direct consequences of each of these proteins on enhancer function. To study the effect of these proteins at the targeted enhancer loci, we will assay for eRNA production by RT-qPCR, histone modifications will be assessed by ChIP-qPCR. Florescent in situ hybridization (FISH) method will be used to study the chromatin structure at enhancers and along with special proximity to their putative target genes. This unique use of genome engineering to study enhancers is essential in order to dissect out the direct effect of each of these components in enhancer mechanisms.
New genomics section is the result of an initiative to strengthen the area of genomics in the School by hiring young and successful experts on different areas of genome biology. On top of the state-of-the art facilities available in the School, the section also has access to new labs, a cluster of servers, a MiSeq machine, as well as other major molecular biology equipment. The candidate will benefit from this rich and fresh intellectual environment and the novel infrastructures.
Desirable:The applicants should show keen interest in Chromatin, Gene regulation, and willingness to learn NGS data analysis. The candidate should have a good understanding of the research field and demonstrate the ability to think independently and work in group.

Funding Notes

Additional questions and queries about the studentship can be addressed to [Email Address Removed])


Pradeepa M M, Grimes G R, Kumar Y, Olley G, Taylor G, Schneider R and Bickmore W A. (2015) Histone H3 globular domain acetylations identify new class of enhancers. Nature Genetics 2016 (in press).
Taylor G, Eskeland R. Balkan B H, Pradeepa M M and Bickmore W A. (2013) H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res. doi: 10.1101/gr.155028.113.

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