The role of sleep on chromatin and transcriptional regulation across vertebrate evolution.

A key aspect of survival is an organism’ ability to adapt their behavior based on experience. At the cellular level, a well-established view of how experience can stably change behavior is that new mRNA and protein synthesis occurs, and that this new state becomes stably encoded in the chromatin, the complex of DNA and proteins that determines transcriptional state. Sleep is an extremely conserved drive found across the animal kingdom that may facilitate these processes. We hypothesize that one of the evolutionary conserved functions of sleep is to influence gene expression and chromatin regulation. There are multiple lines of evidence that support the idea that sleep is important for transcriptional regulation and chromatin stability, but to date no one has directly compared transcriptional responses to sleep loss across vertebrate species or between brain and other tissues within the same species. This is important because to determine conserved mechanisms it is necessary to compare across evolutionary time. Another key limitation of all omics studies of sleep is the lack of resolution at the single-cell level. This is important because, as show in our preliminary studies, different cell types respond differently to sleep loss. In addition, the lack of resolution at the single cell-level can make mapping correspondence between changes in gene expression and changes in chromatin inaccurate. The application of single-cell transcriptomic and epigenomic analysis is a promising avenue to understand transcriptional regulation. However, single-cell approaches have not yet been applied to understand how sleep influences transcription and chromatin regulation. In this Maximizing Investigators Research Award (MIRA) we will utilize state of the art single-cell genomic technology to define, for the first time, common sleep-dependent transcriptional and epigenetic programs across different cell-types between two distantly related vertebrate species: Mouse and Zebrafish. This proposal leverages expertise in comparative genomics and evolution, computational biology and the application of transcriptomic and epigenomic technology to study brain and behavior, training I have acquired throughout my PhD and post-doctoral fellowship. The goal is to establish a program of research focused on understanding how sleep across different species can alter transcription and chromatin accessibility in different cell-types. In the short-term this proposal will produce a comprehensive cell atlas of sleep-dependent regulation of gene expression and chromatin states, as well as publicly available software for single-cell data analysis. In the long-term these studies will serve as the basis for functional studies to define evolutionary conserved mechanisms by which sleep can modulate gene expression and chromatin architecture.