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ERNA: A graphic user interface-based tool for RNA sequencing data analysis [microRNA-Seq]

ABSTRACT: we performed RNA sequencing analysis using 7 human plasma samples and evaluated efficiency and accuracy of eRNA on miRNA-seq data analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53451 | GEO | 2014/06/01

SECONDARY ACCESSION(S): PRJNA232039

REPOSITORIES: GEO

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eRNA: A graphic user interface-based tool for RNA sequencing data analysis [microRNA-Seq]

Project description:we performed RNA sequencing analysis using 7 human plasma samples and evaluated efficiency and accuracy of eRNA on miRNA-seq data analysis. We sequenced microRNAs from the 7 human tissue samples with replicates (A1/A8, B2/B9, C3/C10, D4/D11, E5/E12, F6/F13, G7/G14) using NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB). After that, we identified miRNAs in these plasma samples against known human matured miRNAs.

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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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