My research focuses upon different topics, in the fields of evolutionary and functional genomics.
Specifically, the following lines of research summarize my most recent research activity:
Evolution 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, ATAC-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 genomic features determining whether a given CRE needs to be evolutionarily conserved across lineages? 4) To what extent transposable elements (TEs) shape the primate regulatory networks?
Enhancer role in cell fate determination: Understanding how cell differentiate from a pluripotent progenitor is a key question in biology and evolution. Specifically, I am interested in how regulatory elements (enhancers and promoters) are reprogrammed by transcription factors and protein complexes to fine-tune cell fate determination and tissue development. I take advantage of cutting-edge genomic techniques as GRO-seq, ATAC-seq, RNA-seq, and ChIP-seq to address these questions, in different biological systems, with a particular interest for the hematopoietic compartment.
Epigenomics and transcriptional regulation: Gene expression and RNA transcription are regulated by transcription factors,and protein complexes that orchestrate the interplay between enhancers, promoters and RNA Polymerase II to ultimately elicit transcription. Many of these mechanisms are evolutionary conserved, others are species specific. One of the most important regulators of transcription is the SWI/SNF complex, which is involved in chromatin remodeling, enhancer configuration, and RNA processing. Importantly, this complex is evolutionarily conserved across Metazoans, and many of its subunits are among the most commonly mutated epigenetic regulators across all cancers. I study how this complex regulates transcription and gene expression, mostly focusing on ARID1A and ARID1B, representing the mutually exclusive DNA binding subunits of the complex.