miR-634 is a Pol III-dependent intronic microRNA regulating alternative-polyadenylated isoforms of its host gene PRKCA

• Published in: Biochimica et biophysica acta. General subjects Vol. 1861; no. 5; pp. 1046 - 1056
• Main Authors: Paraboschi, Elvezia Maria, Cardamone, Giulia, Rimoldi, Valeria, Duga, Stefano, Soldà, Giulia, Asselta, Rosanna
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2017
• Subjects: asthma; Cell Line; Cell Line, Tumor; Down-Regulation - genetics; Gene Expression Regulation - genetics; Genes, Reporter - genetics; genetic polymorphism; HEK293 Cells; HeLa Cells; Humans; introns; Introns - genetics; microRNA; MicroRNAs - genetics; miR-634; Multiple sclerosis; neoplasms; Polyadenylation - genetics; PRKCA; Promoter; Promoter Regions, Genetic - genetics; Protein Isoforms - genetics; protein kinase C; Protein Kinase C-alpha - genetics; quantitative analysis; reporter genes; reverse transcriptase polymerase chain reaction; RNA Polymerase III - genetics; RNA Polymerase III - metabolism; schizophrenia; sclerosis; Target gene; tissues; Transcription, Genetic - genetics; Transcriptome - genetics; transfection; Promoter; Multiple sclerosis; PRKCA; miR-634; Target gene
• ISSN: 0304-4165; 1872-8006
• DOI: 10.1016/j.bbagen.2017.02.016

The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies. Here, we characterized miR-634 expression profile and searched for its putative targets using a combination of RT-PCR and gene reporter assays. The quantitative analysis of PRKCA and miR-634 transcripts in a panel of human tissues and cell lines revealed discordant expression profiles, suggesting the presence of an independent miR-634 promoter and/or a possible direct role of miR-634 in modulating PRKCA expression. Functional studies demonstrated the existence of a miRNA-specific promoter, which was shown to be Pol-III-dependent. Furthermore, transfection experiments showed that miR-634 is able to target its host gene by specifically down-regulating the shorter alternative-polyadenylated isoforms. MiR-634 is a Pol III-dependent intronic miRNA, which could target its host gene through a “first-order” negative feedback. MiR-634 is one of the few characterized examples of Pol-III-dependent intronic miRNAs. Its independent transcription from the host gene suggests caution in using expression profiles of host genes as proxies for the expression of the corresponding intronic miRNAs. •MiR-634 is an intragenic miRNA that is transcribed independently from its host gene.•MiR-634 is one of the few characterized examples of Pol-III-dependent miRNAs.•MiR-634 targets, among others, some alternative isoforms of its host gene.•ADRB2, promoting glucose uptake in astrocytes, may be a miR-634 indirect target.