RT Journal Article SR Electronic T1 Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans JF bioRxiv FD Cold Spring Harbor Laboratory SP 088732 DO 10.1101/088732 A1 Aaron C. Daugherty A1 Robin Yeo A1 Jason D. Buenrostro A1 William J. Greenleaf A1 Anshul Kundaje A1 Anne Brunet YR 2016 UL http://biorxiv.org/content/early/2016/11/19/088732.abstract 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.