My research focuses upon different topics, in the fields of evolutionary and functional genomics.
Specifically, the following lines of research summarize my academic activity:
Evolutionary genomics of gene regulation: Recent advances in High Throughput DNA sequencing (NGS) revolutionized the field of genomics, opening tons of new possibilities for understanding the function and the evolution of genomes. In this context, I focus on the evolution of cis-regulatory elements, with a particular interest on enhancers and promoters in humans and other primates. Using techniques like ChIP-seq and RNA-seq, I am interested in cis-regulatory elements (CREs) active and poised in the primate genomes, trying to address some of the following questions: 1) what are the tempo and mode of cis-regulatory evolution in primates? 2) Are CREs evolving uniformly and at a steady rate across the lineage? 3) what are the genomics features determining whether a given CRE needs to be evolutionarily conserved across primates? 4) To what extent transposable elements (TEs) shape the primate regulatory network?
Enhancer configuration during organismal differentiation: Understanding how cell differentiate from a pluripotent progenitor is a key question in biology and evolution. Specifically, I am interested in how cis-regulatory elements (enhancers and promoters) reprogram and reorganize in the different steps of cell and organismal differentiation. I leverage NGS assays like GRO-seq, ATAC-seq and ChIP-seq to address these questions, in different biological systems, with a particular interest for the hematopoietic system.
Genomics of transcriptional regulation: Gene expression and RNA transcription are regulated by transcription factors, master regulators and protein complexes, which orchestrate the interplay between enhancers, promoters and gene bodies. Many of these mechanisms are evolutionary conserved, others are species specific. One of the most important regulators of transcription and gene expression is the SWI/SNF complex, which is involved in chromatin remodeling, enhancer configuration and RNA processing. Interestingly, this complex is evolutionarily conserved across Metazoans, and many of its components are among the most commonly mutated epigenetic regulators across all cancers. I study how this complex regulates gene expression and more specifically I aim to assess the impact that the most common genetic mutations in SWI/SNF have on transcriptional gene regulation.