Additional evidence of HS5-1 enhancer eRNA PEARL for protocadherin alpha gene regulation.

The regulation of target genes by distal enhancers usually determines the fate and function of cells. Active enhancers in specific regions of chromatin may transcribe bidirectionally to produce long non-coding enhancer RNA (eRNA) to regulate gene expression. We recently found that an antisense enhancer eRNA PEARL (Pcdh eRNA associated with R-loop formation) regulates gene expression of members of the Pcdhα cluster via R-loop formation. To further explore the biological function of eRNA, we performed additional genetic and molecular experiments such as CRISPR (clustered regularly interspaced short palindromic repeats) DNA-fragment editing, RT-PCR, and qPCR. First, we performed expression analyses of the HS5-1 eRNA PEARL and found that it was expressed in a tissue-specific manner. In addition, upon CRISPR DNA-fragment deletion or inversion of the CTCF sites in the HS5-1 enhancer region, the expression of eRNA PEARL was reduced to 2%-10% and the expression of Pcdhα gene cluster was also reduced to 13%-68% of the original levels. Finally, deletion of the bidirectional transcription start site (TSS) of HS5-1 eRNA or inversion of TSS of the eRNA PEARL resulted in approximately 60% or 40% decrease of levels of Pcdhα gene expression. In summary, these data suggested a functional role of the HS5-1 eRNA in gene regulation of the Pcdhα cluster, providing a new direction for future researches on the regulatory mechanisms of clustered Pcdh gene expression in the brain.