PT - JOURNAL ARTICLE AU - Aaron C. Daugherty AU - Robin Yeo AU - Jason D. Buenrostro AU - William J. Greenleaf AU - Anshul Kundaje AU - Anne Brunet TI - Chromatin accessibility dynamics reveal novel functional enhancers in <em>C. elegans</em> AID - 10.1101/088732 DP - 2016 Jan 01 TA - bioRxiv PG - 088732 4099 - http://biorxiv.org/content/early/2016/11/19/088732.short 4100 - http://biorxiv.org/content/early/2016/11/19/088732.full AB - Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogenous and simple systems, such as isolated cell populations or early development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism C. elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. Importantly, our analysis of dynamic changes in chromatin accessibility within whole organisms sensitively identified novel cell-type- and temporal-specific enhancers, which we functionally validate in vivo. Furthermore, by integrating transcription factor binding motifs into a machine learning framework, we identify EOR-1 as a potential early regulator of chromatin accessibility changes. Our study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.