Event:

Cerebellum expanded in parallel to the neocortex during human evolution and is increasingly recognised to play important roles in the evolution of cognition. I will present studies in which we used single-nucleus measurements of gene expression and chromatin accessibility to trace the development of the cerebellum from early neurogenesis to adulthood in mammals.
First, we generated single-nucleus RNA-sequencing data for 400,000 cells from two eutherian species (human, mouse) and a marsupial (opossum). Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Transcriptome comparisons showed that the cerebellar cell type-defining programs have been preserved for at least 160 million years of mammalian evolution. However, we also identified numerous genes that either gained or lost expression in cerebellar cell types in one of the studied species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level.
Next, to gain insights into the changes in cis-regulatory elements (CREs) driving the identified differences in gene expression between species, we produced single-nucleus ATAC-sequencing data for 350,000 cells from four primates (human, bonobo, rhesus macaque, marmoset), a rodent (mouse), and a marsupial (opossum). Based on these data, we developed a sequence-based deep learning model, demonstrating the conservation of the regulatory code in the cerebellar cell types across mammals. We applied this model to orthologous genomic sequences from 240 mammalian species to reconstruct the evolutionary histories of human CREs. We found that evolutionarily novel CREs contributed to the divergence in gene expression observed between humans and other mammals, and validated some of the predicted CREs using enhancer reporter assays in primary cultures of mouse cerebellar granule cells.
Altogether, our work unveils shared and lineage-specific gene-expression programs governing the development of cerebellar cells and expands our understanding of the molecular basis of mammalian brain evolution.