ArticleGenome biology2013
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Characterization, functional exploration, and evolutionary analysis of mirtronic microRNAs reveal their origin in the invasive vector mosquito, Aedes albopictus.Insect science · 2026Article
- The Life of MicroRNAs: Biogenesis, Function and Decay in Cancer.Biomolecules · 2025Review
- Partners in Silencing: Decoding the Mammalian Argonaute Interactome.Non-coding RNA · 2025Review
- Coding Genes Helped the Origination and Diversification of Intragenic MicroRNAs.Molecular biology and evolution · 2025Article
- Mapping the microRNA landscape in the older adult brain and its genetic contribution to neuropsychiatric conditions.Nature aging · 2025Article
- Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains.Frontiers in genetics · 2025Article
- Genetic regulation of microRNAs in the older adult brain and their contribution to neuropsychiatric conditions.bioRxiv : the preprint server for biology · 2024Article
- Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5'-flanking regions of tRNA genes.Journal of biochemistry · 2024Article
- MicroRNA-138: an emerging regulator of skeletal development, homeostasis, and disease.American journal of physiology. Cell physiology · 2023Review
- Mutations Causing X-Linked Amelogenesis Imperfecta Alter miRNA Formation from Amelogenin Exon4.Journal of dental research · 2023Article
- A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases.International journal of molecular sciences · 2023Article
- Functional mapping of microRNA promoters with dCas9 fused to transcriptional regulators.Frontiers in genetics · 2023Article
- The microRNA Lifecycle in Health and Cancer.Cancers · 2022Review
- miR-140-5p and miR-140-3p: Key Actors in Aging-Related Diseases?International journal of molecular sciences · 2022Review
- An miRNA derived from amelogenin exon4 regulates expression of transcription factor Runx2 by directly targeting upstream activators Nfia and Prkch.The Journal of biological chemistry · 2022Article
- GATA3 Inhibits Viral Infection by Promoting MicroRNA-155 Expression.Journal of virology · 2022Article
- The balance between the intronic miR-342 and its host gene Evl determines hematopoietic cell fate decision.Leukemia · 2021Article
- Splice and Dice: Intronic microRNAs, Splicing and Cancer.Biomedicines · 2021Review
- Multifaceted Regulation of MicroRNA Biogenesis: Essential Roles and Functional Integration in Neuronal and Glial Development.International journal of molecular sciences · 2021Review
3 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, we describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. We validate our results with existing annotation, PolII occupancy data and read coverage from RNA-seq data. Compared to previous methods PROmiRNA increases the detection rate of intronic promoters by 30%, allowing us to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation. PROmiRNA can be downloaded from http://promirna.molgen.mpg.de.
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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.