Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

• Published in: Nucleic acids research 2016-04, Vol.44 (7), p.3070-3081
• Main Authors: Nepal, Chirag, Coolen, Marion, Hadzhiev, Yavor, Cussigh, Delphine, Mydel, Piotr, Steen, Vidar M, Carninci, Piero, Andersen, Jesper B, Bally-Cuif, Laure, Müller, Ferenc, Lenhard, Boris
• Format: Article
• Language: English
• Subjects: Animals; Chromatin - metabolism; Cognitive Sciences; Danio rerio; Embryonic Development - genetics; Gene Expression Regulation; Gene regulation, Chromatin and Epigenetics; Histones - metabolism; Life Sciences; MicroRNAs - genetics; MicroRNAs - metabolism; Neurobiology; Neurons and Cognition; Promoter Regions, Genetic; Psychology and behavior; Ribonuclease III - metabolism; RNA Polymerase II - analysis; RNA Precursors - genetics; RNA Precursors - metabolism; RNA Processing, Post-Transcriptional; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; Transcription Initiation Site; Transcription, Genetic; Zebrafish - embryology; Zebrafish - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkv1354

MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes, especially in development and differentiation. Our understanding about the transcriptional regulation of miRNA genes is limited by inadequate annotation of primary miRNA (pri-miRNA) transcripts. Here, we used CAGE-seq and RNA-seq to provide genome-wide identification of the pri-miRNA core promoter repertoire and its dynamic usage during zebrafish embryogenesis. We assigned pri-miRNA promoters to 152 precursor-miRNAs (pre-miRNAs), the majority of which were supported by promoter associated post-translational histone modifications (H3K4me3, H2A.Z) and RNA polymerase II (RNAPII) occupancy. We validated seven miR-9 pri-miRNAs by in situ hybridization and showed similar expression patterns as mature miR-9. In addition, processing of an alternative intronic promoter of miR-9-5 was validated by 5' RACE PCR. Developmental profiling revealed a subset of pri-miRNAs that are maternally inherited. Moreover, we show that promoter-associated H3K4me3, H2A.Z and RNAPII marks are not only present at pri-miRNA promoters but are also specifically enriched at pre-miRNAs, suggesting chromatin level regulation of pre-miRNAs. Furthermore, we demonstrated that CAGE-seq also detects 3'-end processing of pre-miRNAs on Drosha cleavage site that correlates with miRNA-offset RNAs (moRNAs) production and provides a new tool for detecting Drosha processing events and predicting pre-miRNA processing by a genome-wide assay.