title: Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
abstract: 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.
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark chirag.nepal@bric.ku.dk.
authors.forename: Chirag
authors.initials: C
authors.lastname: Nepal
authors.affiliation: Zebrafish Neurogenetics Team, Paris-Saclay Institute of Neuroscience, CNRS UMR9197 - Université Paris Sud, 91198 Gif-sur-Yvette, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Coolen
authors.affiliation: School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, UK.
authors.forename: Yavor
authors.initials: Y
authors.lastname: Hadzhiev
authors.affiliation: Zebrafish Neurogenetics Team, Paris-Saclay Institute of Neuroscience, CNRS UMR9197 - Université Paris Sud, 91198 Gif-sur-Yvette, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Cussigh
authors.affiliation: Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Mydel
authors.affiliation: Department of Clinical Medicine, University of Bergen, Norway.
authors.forename: Vidar M
authors.initials: VM
authors.lastname: Steen
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.affiliation: Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
authors.forename: Jesper B
authors.initials: JB
authors.lastname: Andersen
authors.affiliation: Zebrafish Neurogenetics Team, Paris-Saclay Institute of Neuroscience, CNRS UMR9197 - Université Paris Sud, 91198 Gif-sur-Yvette, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Bally-Cuif
authors.affiliation: School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, UK f.mueller@bham.ac.uk.
authors.forename: Ferenc
authors.initials: F
authors.lastname: Müller
authors.affiliation: Institute of Clinical Sciences MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway b.lenhard@imperial.ac.uk.
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000032:analysis; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D015027:Zebrafish / Q000196:embryology / Q000235:genetics
chemical_list: D002843:Chromatin; D006657:Histones; D035683:MicroRNAs; D012322:RNA Precursors; D058727:RNA, Small Untranslated; D012319:RNA Polymerase II; D043244:Ribonuclease III