ArticleNucleic acids research2017
Identification of active miRNA promoters from nuclear run-on RNA sequencing.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
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- A review on the applications of Transformer-based language models for nucleotide sequence analysis.Computational and structural biotechnology journal · 2025Review
- Targeting oncogenic microRNAs from the miR-371~373 and miR-302/367 clusters in malignant germ cell tumours causes growth inhibition through cell cycle disruption.British journal of cancer · 2023Article
- 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
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types.Arteriosclerosis, thrombosis, and vascular biology · 2021Article
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- A two-stream convolutional neural network for microRNA transcription start site feature integration and identification.Scientific reports · 2021Article
- Definition of a small core transcriptional circuit regulated by AML1-ETO.Molecular cell · 2021Article
- Computational annotation of miRNA transcription start sites.Briefings in bioinformatics · 2021Review
- Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data.Computational and structural biotechnology journal · 2021Article
- Molecular Mechanisms of Nutrient-Mediated Regulation of MicroRNAs in Pancreatic β-cells.Frontiers in endocrinology · 2021Review
- Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing.NAR genomics and bioinformatics · 2020Article
- Identification of PparProceedings of the National Academy of Sciences of the United States of America · 2020Article
- MicroRNAs signatures, bioinformatics analysis of miRNAs, miRNA mimics and antagonists, and miRNA therapeutics in osteosarcoma.Cancer cell international · 2020Review
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Epigenetic and transcriptional profiling of triple negative breast cancer.Scientific data · 2019Article
- Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation.BMC genomics · 2018Article
- Solid phase chemistry to covalently and reversibly capture thiolated RNA.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq). MirSTP takes advantage of characteristic bidirectional transcription signatures at active TSSs in GRO/PRO-seq data, and provides accurate TSS prediction for human intergenic miRNAs at a high resolution. MirSTP performed better than existing generalized and experiment specific methods, in terms of the enrichment of various promoter-associated marks. MirSTP analysis of 27 human cell lines in 183 GRO-seq and 28 PRO-seq experiments identified TSSs for 480 intergenic miRNAs, indicating a wide usage of alternative TSSs. By integrating predicted miRNA TSSs with matched ENCODE transcription factor (TF) ChIP-seq data, we connected miRNAs into the transcriptional circuitry, which provides a valuable source for understanding the complex interplay between TF and miRNA. With mirSTP, we not only predicted TSSs for 72 miRNAs, but also identified 12 primary miRNAs with significant RNA polymerase pausing alterations after JQ1 treatment; each miRNA was further validated through BRD4 binding to its predicted promoter. MirSTP is available at http://bioinfo.vanderbilt.edu/mirSTP/.
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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.