{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Zhou Y"],"funding":["Ministry of Science and Technology of China","Science and Technology Commission of Shanghai Municipality","National Natural Science Foundation of China"],"pagination":["1383-1394"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8494205"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["35(19-20)"],"pubmed_abstract":["Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5' capped antisense eRNA <i>PEARL</i> (<i>Pcdh</i> eRNA associated with R-loop formation) that is transcribed from the protocadherin (<i>Pcdh</i>) <i>α HS5-1</i> enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that <i>PEARL</i> regulates <i>Pcdhα</i> gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the <i>HS5-1</i> enhancer region to promote long-distance chromatin interactions between distal enhancers "],"journal":["Genes & development"],"pubmed_title":["Systematic functional characterization of antisense eRNA of protocadherin <i>α</i> composite enhancer."],"pmcid":["PMC8494205"],"funding_grant_id":["91940303","2017YFA0504203","31630039","2018YFC1004504","21DZ2210200","19JC1412500"],"pubmed_authors":["Wu Q","Xu S","Zhang M","Zhou Y"],"additional_accession":[]},"is_claimable":false,"name":"Systematic functional characterization of antisense eRNA of protocadherin <i>α</i> composite enhancer.","description":"Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5' capped antisense eRNA <i>PEARL</i> (<i>Pcdh</i> eRNA associated with R-loop formation) that is transcribed from the protocadherin (<i>Pcdh</i>) <i>α HS5-1</i> enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that <i>PEARL</i> regulates <i>Pcdhα</i> gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the <i>HS5-1</i> enhancer region to promote long-distance chromatin interactions between distal enhancers ","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Oct","modification":"2025-04-22T09:16:43.865Z","creation":"2025-04-05T22:57:43.694Z"},"accession":"S-EPMC8494205","cross_references":{"pubmed":["34531317"],"doi":["10.1101/gad.348621.121"]}}