Research Interests
- ReMap: Large-scale characterization of regulatory regions.
- RNA Pol II: Enhancer transcription in cancer contexts.
- Intergenic transcription: Exploring the relationship between intergenic transcription signals and cancer subtypes.
- Exonic Enhancers: Hidden regulatory elements in plain sight.
Globally
My research focuses on analysing regulatory regions (both coding and non-coding) in the human genome using high-throughput sequencing data, such as ChIP-seq, RNA-seq, DNase-seq, and ATAC-seq.
I aim to understand how the so-called "non-coding genome" — and now the coding genome — plays a central role in gene regulation. Previously labeled as "junk DNA," these regions are now recognised as key players in the complex regulation of our genome. My primary research goal is to uncover how these yet-unannotated regulatory elements influence the expression and dynamics of our genomes.
To address this, we developed ReMap, a resource that catalogs regulatory elements by integrating thousands of publicly available transcription factor ChIP-seq experiments. This effort revealed a highly complex landscape of regulatory elements (enhancers and cis-regulatory modules) in the human genome.
Additionally, we identified intergenic regulatory regions with a strong affinity for RNA Polymerase II (RNAPII) and associated intergenic transcription signals by analysing RNA-seq data in the context of cancer. This allowed us to uncover a connection between intergenic transcription signals and specific cancer subtypes.
Finally, our latest project explores whether coding exons function as novel regulatory elements, capable of influencing the expression of their own genes or nearby ones. How frequently do coding sequences act as enhancers in complex genomes? Addressing this question represents a significant step toward understanding the dual roles of coding regions in gene regulation.
ReMap: https://remap.univ-amu.fr/