MSc in Biosciences from ENS Lyon, France. PhD in epigenetics and cancer from the Cancer research centre of Lyon, France. Since then, working on RNA-seq and ChIP-seq data at the Roslin Institute, Edinburgh, UK.
Brief description of research project
Alternate TSS, alternate splicing, and non-coding RNAs are three key mechanisms providing cell type specific context to a gene, but little is known about how these events are regulated. Epigenetic marks, such as DNA methylation, DNA hydroxymethylation, histone variants, histone tail and histone core post-translational modifications, are mapped with increasing precision across diverse human tissue and cell types due to the rapid development of high-throughput sequencing. Relationships between gene expression and presence or absence of epigenetic modifications at gene promoters, enhancers or insulator regions have been studied extensively. It is known that introns and exons also bear epigenetic marks correlated with gene expression. Several studies have demonstrated roles for DNA methylation in processes such as constitutive splicing, alternative splicing, repression of hidden alternative start sites and repression of natural antisense transcripts. Histone marks H3K36me3 and H3K9me3 have been linked to splicing though their functional relevance is still unclear. Though the literature elaborates epigenetic regulation of transcript diversity in one or few cell types, there is no systematic study across many cell types so far. This project therefore aims to integrate epigenetic and expression data across multiple cell types to unravel the concomitant epigenetic features of transcript diversity in humans.
Much has been accomplished in the first 12 months of this fellowship, both scientifically and in regards of my professional training. The project progresses steadily, with a few adaptations from the initial proposal. Four main points have been developed:
- The development of a web-application integrating high throughput sequencing (HTS) experiments from multiple sources, recently published in Bioinformatics (Devailly et al., 2016).
- The co-supervision of an undergraduate student on the development of an analytical package for single cell RNA-seq, and of a PhD student on meta-analysis of microarray data from liver samples.
- Analysis of Roapmap Epigenomics whole genome bisulfite sequencing (WGBS) data.
- Training and outreach activities performed during this 12 months.