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Investigating the Drosophila DF31 protein to gain insight into the mechanisms and chromatin maintenance in animal cells


Project Description

The Drosophila DF31 protein is an abundant ribonucleoprotein that localises to euchromatic regions and is involved in maintaining chromosome structure. Loss of DF31 causes chromatin compaction and altered expression of > 300 genes. The specific mechanistic role of DF31 is currently unknown.

To define how DF31 influences chromatin structure we will use high-throughput functional genomics technologies to study the interactions of DF31 with DNA (ChIP-seq) and RNA (RIP-seq). In addition, chromatin structure will be studied by Hi-C analysis in response to gene knockouts using CRISPR-Cas9 and RNAi. Analysis of the resulting data will involve extensive use of bioinformatics tools.

The work is expected to yield fundamental insights into the mechanisms of chromatin maintenance in animal cells, and may suggest novel routes to manipulate chromosome structure and control cell identity.

SKILLS WE EXPECT A STUDENT TO DEVELOP/ACQUIRE WHILST PURSUING THIS PROJECT
** Recombinant DNA methods
** Analysis protein structure and modification
** Cell culture
** Gene transfer and gene editing
** Analysis of protein:protein and protein:nucleic acid interactions and multi-protein complexes.
** Current techniques for analysis of chromatin structure, modification and function.
** RNA/DNA extraction, quantitative PCR
** Fluorescence microscopy
** Retrieval of large genomics datasets from public repositories
** Data analysis using R and Linux/Unix
** Analysis of genomics data (sequences, gene expression data, molecular interaction data) using R/Bioconductor

All necessary skills will be taught.

PRIOR EDUCATIONAL REQUIREMENTS
BSc/BA, 1st class or 2(i) in biomedical science, bioinformatics, molecular biology or related. Preferably also MRes/MSc/MA in similar field, distinction or merit.

HOW TO APPLY

Potential applicants are strongly encouraged to contact the supervisors to discuss project details (contact information below).
Subsequently applications can be made by following the instructions on the MRC-LID site at http://mrc-lid.lshtm.ac.uk/apply/.

Please click on the following link for more information about the MRC-LID programme: http://mrc-lid.lshtm.ac.uk/

For more information on funding please go to: http://mrc-lid.lshtm.ac.uk/faqs/

Supervisor contact details


Funding Notes

The current studentship is part of the MRC London Intercollegiate Doctoral Training Partnership (MRC-LID) between The London School of Hygiene and Tropical Medicine (LSHTM) and St. George's University of London (SGUL)

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