Epigenetics of early human embryonic development

About the Project

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) 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 use CRISPR genome editing tools to manipulate the function of protein-coding genes that are essential in development and X-inactivation and we will study effect in cellular differentiation, SMACs formation and gene silencing through single-molecule FISH and transcriptomics approaches.

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 Division 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

• 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 and be submitted online through the "Apply" button.

please note this is a self-funded PhD opportunity only.

Supervisor contact details:

Dr Yolanda Markaki - yolanda.markaki@leicester.ac.uk
Dr Michael Tellier - mt477@leicester.ac.uk