Functional Implications of REST Context Across Species and Diverse Cell Types

Abstract

The RE1 silencing transcription factor (REST) recruits chromatin modifying enzymes to repressor element 1 DNA motifs. The REST complex represses genes by removing active and adding repressive histone modifications. Initially identified to repress neuronal genes in non-neuronal cells, REST is also expressed in neurons and has complex roles in neurogenesis. REST expression and localization is anomalous in diseases ranging from cancer to neurological disorders. In normal conditions, REST targets genes in some cells and not others. Within a cell type, REST can recruit different cofactors to its binding sites. Genome-wide analyses of REST occupancy across human cells and between species have not been comprehensively performed and the interplay between context, cofactor colocalization, and functional outcomes at these sites has been understudied.;In this thesis I address the hypotheses that there are large intercellular and interspecies differences in the REST regulatory network and that within these networks, context plays a critical role in genome-wide REST binding, recruitment and regulation.;To test these hypotheses, I performed integrated analyses of ChIP-seq experiments of multiple transcription factors and histone modifications. I found that REST cistromes were distinct across non-neuronal cell types and that neurons exhibited unique binding and features not observed in non-neuronal cells. Further analysis identified multiple contexts that had potential roles in differential cofactor colocalization.;Evaluating human and mouse REST cistromes in embryonic stem cells, I found that there has been human REST regulatory network expansion. I found that REST-associated cistromes at sites occupied in both species were highly similar, suggesting that the regulatory outcomes of REST binding at these sites corresponded. Many of the genes with expanded REST occupancy in humans were enriched for neural functions, including learning or memory and neurological disease-associated genes.;These results indicate that intercellular and interspecies differences in the REST regulatory network are vast and suggest that many different contexts play pivotal roles in REST occupancy and cofactor recruitment.;Taken together, the findings of this thesis enhance the knowledge of REST-mediated regulation and provide new potential avenues for interfering with the REST regulatory network in a more target, cell type and species-specific manner.