ArticleGenome research2015
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
70 citing papers in PubMed, 108 citations in OpenAlex.
- Preclinical Development of a Vectorized Artificial miRNA Gene Therapy for Tauopathies.bioRxiv : the preprint server for biology · 2025Article
- MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution.Genome medicine · 2025Article
- Repeated emergence of giant microRNA hairpins across invertebrates.Cell reports · 2025Article
- Interdependence of Pasha and Drosha for localization and function of the Microprocessor in C. elegans.Nature communications · 2025Article
- A polycistronic locus encodes both a tumor-suppressive microRNA and a long non-coding RNA regulating testis morphology in Drosophila.bioRxiv : the preprint server for biology · 2025Article
- The biogenesis and regulation of animal microRNAs.Nature reviews. Molecular cell biology · 2025Review
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A microRNA is the effector gene of a classic evolutionary hotspot locus.Science (New York, N.Y.) · 2024Article
- MBNL splicing factors regulate the microtranscriptome of skeletal muscles.Nucleic acids research · 2024Article
- MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1.Nucleic acids research · 2024Article
- MicroRNAs targeted mTOR as therapeutic agents to improve radiotherapy outcome.Cancer cell international · 2024Review
- Myeloid-derived miR-6236 potentiates adipocyte insulin signaling and prevents hyperglycemia during obesity.Nature communications · 2024Article
- Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments.Proceedings. Biological sciences · 2024Article
- A micro-RNA is the effector gene of a classic evolutionary hotspot locus.bioRxiv : the preprint server for biology · 2024Article
- A computational modeling of pri-miRNA expression.PloS one · 2024Article
- Two for one: regulatory RNAs that encode small proteins.Trends in biochemical sciences · 2023Review
- Deciphering the Functional Long Non-Coding RNAs Derived from MicroRNA Loci.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications.European journal of medicinal chemistry · 2023Review
- 17β-estradiol promotes extracellular vesicle release and selective miRNA loading in ERα-positive breast cancer.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs.NAR cancer · 2023Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.