Single cell genomics and evolution
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2009-2013 - PhD in Genetics. University of Barcelona (UB). Spain.
2013-2015 - Research associate. Institute for Evolutionary Biology (CSIC-UPF). Spain
2015-2018 - EMBO/WIS Postdoctoral Fellow. Weizmann Institute of Science (WIS). Israel
2019 - Group Leader at the Centre for Genomic Regulation (CRG). Spain
A fundamental question in biology is how the diverse cell types observed in a multicellular organism are encoded by a single genome sequence, and which genome regulatory mechanisms orchestrate the deployment and maintenance of cell type-specific transcriptional programs. However, the diversity and evolutionary dynamics of cell type programs remains almost unexplored beyond selected tissues in a few species. Similarly, little is known about the emergence of complex genome regulatory mechanisms that support cell type-specific programs and cellular memory, for example genome spatial compartmentalization and repressive chromatin modifications.
In recent years, the development of advanced functional genomics technologies has revolutionized the study of cell type and genome regulation, even at single-cell resolution. This opens the way to the comparative analysis of genome regulation in species that represent diverse levels of biological complexity: ranging from unicellular temporal differentiation and simple multicellular behaviours (e.g. in some protistan eukaryotes), through loosely integrated and limitedly diversified ensembles of cell types (e.g. in early-branching animals), to organisms with elaborate tissue and bodyplan organization (e.g in bilaterian animals).
(Illustrations adapted from Sebé-Pedrós et al., Cell 2016, Sebé-Pedrós et al. Cell 2018, Arendt et al. NatRevGen 2016, Bonev & Cavalli, NatRevGen 2016, and Booth & King Nature 2016)
In our group, we combine high-throughput epigenomics and single-cell genomics technologies with advanced computational methods in order to dissect cell type programs and genome regulatory architectures in phylogenetically diverse systems. The comparative analysis of these data allows us (i) to trace the evolution of cell types and genome regulatory mechanisms; (ii) to identify shared principles in genome function; and (iii) to reconstruct regulatory innovations linked to major transitions such as the origin of eukaryotic cells or the emergence of multicellular organisms.