Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer.

Yuxiao Zhou, Siyuan Xu, Mo Zhang, Qiang Wu

Genes & development 2021 Oct 01

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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. © 2021 Zhou et al.; Published by Cold Spring Harbor Laboratory Press.

Citation

Yuxiao Zhou, Siyuan Xu, Mo Zhang, Qiang Wu. Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer. Genes & development. 2021 Oct 01;35(19-20):1383-1394