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Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

ABSTRACT: Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

PROVIDER: PRJNA626625 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11575367_1.fastq.gz	Fastqsanger.gz
	SRR11575367_2.fastq.gz	Fastqsanger.gz
	SRR11575368_1.fastq.gz	Fastqsanger.gz
	SRR11575368_2.fastq.gz	Fastqsanger.gz
	SRR11698125_1.fastq.gz	Fastqsanger.gz

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Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

Project description:Enhancers generate bidirectional noncoding enhancer RNAs (eRNA) 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) alpha 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 find that PEARL regulates Pcdh alpha 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 enhancer and target promoter. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 leads 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 Pcdh alpha promoter choice in single cells in the brain.

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Antisense lncRNA transcription mediates DNA demethylation to drive stochastic Protocadherin α promoter choice

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