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Development of a Reverse ChIP-Sequencing (RChIPS) technology to discover novel proteins regulating gene expression


Faculty of Health and Life Science

Dr U McClurg , Dr Suzanne Madgwick , Prof C E Eyers Friday, January 22, 2021 Competition Funded PhD Project (Students Worldwide)
Liverpool United Kingdom Biochemistry Bioinformatics Cell Biology Developmental Biology Genetics Molecular Biology

About the Project

Background: The ability to turn gene expression on and off is the founding principle the processes directing health and disease executed by large multi-protein machineries serving as repressors or activators. Identifying DNA interacting protein landscape has been critical for scientific progress and has facilitated wide reaching technological, agricultural and medical advances. This has largely been made possible thanks to the development of chromatin immunoprecipitation sequencing (ChIP-seq) methodology which revolutionised the field allowing scientists to identify all DNA bound to a protein of interest. However, ChIP-seq approach is protein centric and we currently lack technology to unbiasedly identify proteins bound to a DNA sequence of interest.

Objectives and Experimental Approaches: In this project you will develop a specific, standardised approach for the discovery of DNA binding proteins utilising the recent advances in Mass Spectrometry that provide high sensitivity. More importantly, our approach will be unbiased and, will not require prior knowledge of any regulatory binding sites for comparative analysis so that our technique may be used with any promoter or enhancer of interest. Furthermore, by employing different cell models we will be able to identify the interplay between repressing and promoting protein interactants on DNA sequences.

In this project you will apply the novel technology to answer a fundamental biological question; what regulates expression of meiotic synaptonemal complex genes at meiosis initiation and furthermore what controls their concerted and synchronised silencing across the genome after fertilisation and across somatic tissues. Consequently, this project will not only develop a new technology that will be made available to laboratories world-wide allowing the discovery of DNA protein-interactomes, but will also answer a fundamental biological question with implications for fertility, developmental biology and cancer.

Our interdisciplinary project will involve a unique breadth of training across three laboratories (see links below) with complementary approaches utilising our world-class facilities including cell biology, proteomics (https://www.liverpool.ac.uk/pfg/), genetics (https://www.liverpool.ac.uk/genomic-research/) and imaging techniques (https://cci.liv.ac.uk/); all providing training in quantitative skills. This project is suited to students who need flexible working arrangements. We invite, welcome and champion applications from minority backgrounds. A broad range of inter-disciplinary approaches will encourage innovative thinking and develop diverse technical expertise. Furthermore, this multi-disciplinary training will give the student a broad range of skills allowing them a wide choice of career options, both within and outside of academia, after the PhD.

 

In addition, the student will join our Molecular Physiology and Cell Signalling Department (https://www.liverpool.ac.uk/translational-medicine/departmentsandgroups/cellular-and-molecular-physiology/about/) as a member of a supportive team of PhD and Post-Doctoral scientists with similar interests, participating regularly in broad ranging group meetings and scientific symposia.

Primary Supervisor -

https://www.liverpool.ac.uk/integrative-biology/staff/urszula-mcclurg/

https://www.cilianetwork.org.uk/people/umcclurg

Secondary supervisors –

https://research.ncl.ac.uk/celldivisionbiology/people/staffprofilesuzannemadgwick.html

https://www.liverpool.ac.uk/integrative-biology/staff/claire-eyers/

Informal enquiries may be made to

HOW TO APPLY

Applications should be made by emailing with a CV and a covering letter, including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project/s and at the selected University. Applications not meeting these criteria will be rejected. We will also require electronic copies of your degree certificates and transcripts.

In addition to the CV and covering letter, please email a completed copy of the Application Details Form (Word document) to , noting the additional details that are required for your application which are listed in this form. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.


Funding Notes

Studentships are funded by the Biotechnology and Biological Sciences Research Council (BBSRC) for 4 years. Funding will cover tuition fees at the UK rate only, a Research Training and Support Grant (RTSG) and stipend. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

References

1. A pseudo-meiotic centrosomal function of TEX12 in cancer. BioRxiv https://doi.org/10.1101/509869.
2. Aneuploidy in oocytes is prevented by sustained CDK1 activity through degron masking in Cyclin B1. Developmental Cell 2019; 48(5)
3. Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation. EMBO Journal 2019; 38(21)
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