Open AccessSystematic functional characterization of antisense eRNA of protocadherin α composite enhancer
Author(s) -
Yuxiao Zhou,
Siyuan Xu,
Mo Zhang,
Qiang Wu
Publication year - 2021
Publication title -
genes and development
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.136
H-Index - 438
eISSN - 1549-5477
pISSN - 0890-9369
DOI - 10.1101/gad.348621.121
Subject(s) - enhancer , enhancer rnas , biology , chromatin , crispr , protocadherin , microbiology and biotechnology , promoter , locus control region , dna , regulation of gene expression , gene , gene expression , genetics , cell , cadherin
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 PEARL ( Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin ( Pcdh ) α HS5-1 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 PEARL regulates Pcdhα gene expression by forming local RNA–DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancers and target promoters. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 lead to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdhα promoter choice in single cells in the brain.