Epigenetics of early human development: From molecular mechanisms to regenerative medicine

The 46th chromosome in XX female mammals, the second X, has to be switched off. That way females equalize gene dosage of X-linked genes with XY males. The process of X-inactivation is a fascinating mechanism of whole chromosome silencing which initiates during early embryonic development and is maintained for life in somatic tissues thereafter. Female embryos do not survive without inactivating the X, while the importance of robust regulation of X-inactivation is evident by hundreds of X-linked diseases, including cancer, ageing and female-specific vulnerabilities to diseases when the process goes awry. Importantly, maintenance of X-inactivation is necessary for the epigenetic stability of human pluripotent stem cells, which often reactivate the inactive X in culture and thus their applicability to cell-based regenerative therapies becomes compromised.

The non-coding RNA, XIST, is expressed on the X chromosome and is the critical factor required to establish X-inactivation. We previously identified that XIST triggers the silencing process through the recruitment of chromatin regulators and the formation of molecular nanomachines termed XIST-SMACs (XIST-Supramolecular Complexes). SMACs have never been studied during human development and we have no knowledge of their molecular organization, which will be critical in order to devise chemical strategies to fight dysregulation of X-inactivation.

Studying X-inactivation in human embryonic stem cell lines (hESCs) or induced pluripotent stem cells (hiPSCs) reprogrammed from somatic cells is essential to understand fundamental gene-regulatory events of early human development. Naïve and primed hPSCs correspond to pre- and post-implantation, a time of human development we know very little about and when X-inactivation occurs. In this project, we will conduct for the first time super-resolution microscopy investigations of the epigenetic changes occurring on the inactivating X using chemical reprogramming of hPSCs as a model system. We will reconstitute RNA-protein supercomplexes and study them through cryo-electron microscopy to elucidate their organization at the molecular level. Finally, we will test highly specific chemical tools to reset the process of X-inactivation and to generate a platform for the generation of epigenetically improved hPSCs to fight X-linked diseases.

These studies will offer an unprecedented view into gene regulation during this critical timepoint in humans, which is when many pregnancies terminate. Ultimately, understanding the molecular mechanisms underpinning formation of XIST-supercomplexes will allow the development of therapeutic applications to tackle dysregulation of XCI in disease or the production of epigenetically stable human pluripotent stem cells.

Environment

The candidate will be embedded in the Department of Cell and Molecular Biology and become a member of the Leicester Institute of Structural and Chemical Biology (LISCB), a research institute of excellence offering access to world class facilities. They will join the LISCB doctoral training programme, which will offer training on both technical and transferable career-development skills. The project will be supervised by our expert team in developmental epigenetics, imaging, structural and chemical biology that will equip the candidate with unique skills on stem cell biology, genome editing, super-resolution microscopy and structural biology methods. As part of this multidisciplinary project the candidate will make use of the multi-million pound state-of-the-art cryo-electron and super-resolution microscopy suites and our human pluripotent stem cell facility.

Pre-requisites

The candidate should be:

• familiarized with molecular and cellular biology and have experience with cell culture
• highly motivated and organized
• fluent in English
• holding (by the start date) a Master's degree (300 ECTS credits)

Application Procedure

Applications must include:

• a motivation letter addressed to Dr Yolanda Markaki
• a complete CV including contact details
• contact details of two referees

All applications must be addressed to Dr Yolanda Markaki - yolanda.markaki@le.ac.uk and be submitted online through the "Apply" button.

Entry requirements

• Those who have a 1st or a 2.1 undergraduate degree in a relevant field are eligible.
• Evidence of quantitative training is required. For example, AS or A level Maths, IB Standard or Higher Maths, or university level maths/statistics course.
• Those who have a 2.2 and an additional Masters degree in a relevant field may be eligible.
• Those who have a 2.2 and at least three years post-graduate experience in a relevant field may be eligible.
• Those with degrees abroad (perhaps as well as postgraduate experience) may be eligible if their qualifications are deemed equivalent to any of the above.
• University English language requirements apply.

To apply

Carefully read the application advice on our website below and submit your PhD application. 

https://le.ac.uk/study/research-degrees/research-subjects/molecular-and-cell-biology