{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Arenas-Mena C"],"funding":["NIGMS NIH HHS"],"pagination":["751"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8527612"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["22(1)"],"pubmed_abstract":["<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 embryonic"],"journal":["BMC genomics"],"pubmed_title":["Identification and prediction of developmental enhancers in sea urchin embryos."],"pmcid":["PMC8527612"],"funding_grant_id":["R35 GM130311"],"pubmed_authors":["Arenas-Mena C","Miljovska S","Rice EJ","Ercan S","Shashikant T","Danko CG","Gurges J","Wang Z"],"additional_accession":[]},"is_claimable":false,"name":"Identification and prediction of developmental enhancers in sea urchin embryos.","description":"<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 embryonic","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Oct","modification":"2025-04-19T15:10:18.065Z","creation":"2025-04-19T15:10:18.065Z"},"accession":"S-EPMC8527612","cross_references":{"pubmed":["34666684"],"doi":["10.1186/s12864-021-07936-0"]}}