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Centre for Trophoblast Research


Functional role of non-CpG methylation in human placenta

Supervisors: Russell Hamilton and Miguel Constancia

The methylation of cytosine residues within CpG dinucleotides is essential to cell differentiation and normal development. In recent years, whole genome bisulphite sequencing has confirmed significant levels on non-CpG methylation (i.e CpA, CpT and CpC) in specific tissues and cell types, including the placenta, and at particular regions of the genome. However, the functional relevance of non-CpG methylation at most sites remains unknown.

The overall aim of this project is to characterize the distribution, regulation and function of non-CpG methylation in human placenta.  The specific questions to be addressed are: What is the composition of all methylated cytosine loci in the genome of human term placenta? Are there non-CpG methylation differences according to gender? What are the loci with the highest levels of non-CpG methylation? Are these placental-specific? What is the relationship between CpG and non-CpG occurrence and how do they relate to gene expression? What is the intrinsic capacity of non-CpG methylation in transcriptional repression? What are the genomic features of the placental non-CpG methylation in small for gestational age (SGA) babies?

To address these questions the student will perform bioinformatic analysis on existing whole-genome bisulphite sequencing and RNA-Seq data sets, and will generate new tools for the specific-analysis of non-CpG methylation and differential methylation calling. The student will validate non-CpG methylation findings in a replication cohort of term placentas, and use recently described early placenta organoids to assess the degree of non-CpG methylation stability during placental development. He/she will use well-established quantitative reporter assays using in vitro methylated plasmids as well as CRISPR based epigenetic editing in cell lines/organoids to provide functional evidence for a role of non-CpG methylation in the control of gene activity. The studies will also include biochemical assays of Methyl-binding proteins as potential mediators of non-CpG function.