KRAB zinc finger proteins (KZFPs) are the largest family of transcription factors in the human genome. Human KZFPs are evolutionary conserved at various levels (primate, mammals) and target equally old remnants of transposable elements that have lost their mobilization potential millions of years ago. KZFPs binding these elements function as epigenetic switches, controlling chromatin accessibility of regulatory platforms derived from transposable elements to rewire gene regulatory networks in a cell context-specific fashion.
This project follows on a discovery (Imbeault lab) that found mutations in primate-specific KZFP ZNF808 as a cause of neonatal diabetes in humans. When ZNF808 is lost, upregulation of genes in proximity to its transposable elements targets drive an aberrant reactivation of a liver-associated genetic programme during differentiation toward the pancreatic lineage. This pathological context unveiled the importance of ZNF808 silencing MER11 elements during pancreas differentiation but left unresolved the normal role of these transposons in other areas of development.
This PhD project will investigate the normal activity of MER11 elements. By analysis of single-cell ATAC-seq datasets, we have found that some MER11 elements are normally active in hepatocytes, but many more in foetal trophoblasts, an important component of placenta. To determine the role of these elements and which genes they regulate, we will use “best in class” trophoblast culture systems derived from human stem cells (Fogarty lab). This project is expected to yield insight in primate-specific evolution of gene regulation and its impact on development of placenta at the crossroads of gene regulation, non-coding genome and human disease.
3-month rotation: Design and test CRISPRi vectors against high-priority MER11 elements, followed by validation using qRT-PCR.
Year 1: A target gene of MER11 elements is associated with preeclampsia in GWAS studies – its role in trophoblast biology will be characterized in priority by targeting its downregulation by CRISPRi followed by RNA-seq. You will also learn how to analyze RNA-seq data and enhance the analysis with the help of public datasets.
Year 2/3: The role(s) of candidate MER11 elements and associated gene targets in maintaining trophoblast self-renewal, as well as their role in trophoblast homeostasis, function and differentiation will be elucidated. The strategy will primarily employ CRISPRi vectors targeting candidate MER11 elements, but also overexpression of KZFPs from lentiviral vectors.
Year 3/4: Which transcription factors binding sites found on MER11 elements are important for their activity will be characterized using large scale mutagenesis (with support from the Xianghua Li lab).
