Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling

ABSTRACT: We used CAGE-seq (Capped Analysis of Gene Expression with Sequencing) to profile eRNA expression and enhancer activity during embryogenesis of the sea urchin, Strongylocentrotus purpuratus. We identified >18,000 enhancers that were active during late oogenesis and early development and documented a burst of enhancer activation during cleavage and early blastula stages. Most enhancers were located near gene bodies and eRNA expression levels were highest for elements near core promoters. Transcriptional signals from enhancers generally paralleled the expression levels of likely target genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays were associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are publicly available at Echinobase (www.echinobase.org).

ORGANISM(S): Strongylocentrotus purpuratus

PROVIDER: GSE169227 | GEO | 2021/06/30

REPOSITORIES: GEO