Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
| Autor: | Jian Ming Khor, Charles A. Ettensohn, William Douglas, Jennifer Guerrero-Santoro |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
biology
Gene regulatory network Embryonic Development Gene Expression Regulation Developmental biology.organism_classification Blastula Strongylocentrotus purpuratus Cell biology Enhancer Elements Genetic Echinoderm Sea Urchins biology.animal Gene expression Genetics Animals Gene Regulatory Networks Enhancer Gene Sea urchin Genetics (clinical) |
| Zdroj: | Genome Research. 31:1680-1692 |
| ISSN: | 1549-5469 1088-9051 |
| Popis: | We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby 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 was 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 available at Echinobase, the public database of information related to echinoderm genomics. |
| Databáze: | OpenAIRE |
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