ArticleNucleic acids research2016
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- Sequential and additive expression of miR-9 precursors control timing of neurogenesis.Development (Cambridge, England) · 2022Article
- Oncogenic AURKA-enhanced NCell research · 2021Article
- Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Frontiers in genetics · 2021Article
- miR-223: An Effective Regulator of Immune Cell Differentiation and Inflammation.International journal of biological sciences · 2021Review
- Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing.NAR genomics and bioinformatics · 2020Article
- Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.Nature communications · 2020Article
- Reciprocal regulation of miR-206 and IL-6/STAT3 pathway mediates IL6-induced gefitinib resistance in EGFR-mutant lung cancer cells.Journal of cellular and molecular medicine · 2019Article
- Role of flow-sensitive microRNAs and long noncoding RNAs in vascular dysfunction and atherosclerosis.Vascular pharmacology · 2019Review
- Expanding the repertoire of miRNAs and miRNA-offset RNAs expressed in multiple myeloma by small RNA deep sequencing.Blood cancer journal · 2019Article
- The MicroRNA, miR-18a, Regulates NeuroD and Photoreceptor Differentiation in the Retina of Zebrafish.Developmental neurobiology · 2019Article
- Factors Regulating microRNA Expression and Function in Multiple Myeloma.Non-coding RNA · 2019Review
- Metformin Protects against Oxidative Stress Injury Induced by Ischemia/Reperfusion via Regulation of the lncRNA-H19/miR-148a-3p/Rock2 Axis.Oxidative medicine and cellular longevity · 2019Article
- Inventory of European Sea Bass (Frontiers in genetics · 2019Article
- A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human.Nucleic acids research · 2018Article
- The Stress-Responding miR-132-3p Shows Evolutionarily Conserved Pathway Interactions.Cellular and molecular neurobiology · 2018Article
- Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture.Nucleic acids research · 2017Article
- An integrated expression atlas of miRNAs and their promoters in human and mouse.Nature biotechnology · 2017Article
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11 authors.
Funding
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.
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