biostudies-literatureArenas-Mena CNIGMS NIH HHS751https://www.ebi.ac.uk/biostudies/studies/S-EPMC8527612biostudies-literatureUnknown22(1)<h4>Background</h4>The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.<h4>Results</h4>We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimental cis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonicBMC genomicsIdentification and prediction of developmental enhancers in sea urchin embryos.PMC8527612R35 GM130311Arenas-Mena CMiljovska SRice EJErcan SShashikant TDanko CGGurges JWang ZfalseIdentification and prediction of developmental enhancers in sea urchin embryos.<h4>Background</h4>The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.<h4>Results</h4>We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimental cis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonic2021-01-01T00:00:00Z2021 Oct2025-04-19T15:10:18.065Z2025-04-19T15:10:18.065ZS-EPMC85276123466668410.1186/s12864-021-07936-0