ArticleNucleic acids research2017
Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution.Genome medicine · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
- TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.Genome biology · 2025Article
- Viral influencers: deciphering the role of endogenous retroviral LTR12 repeats in cellular gene expression.Journal of virology · 2025Review
- Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro.Arteriosclerosis, thrombosis, and vascular biology · 2024Article
- Article
- Transposable elements as tissue-specific enhancers in cancers of endodermal lineage.Nature communications · 2023Article
- A pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies.Redox biology · 2023Article
- Dynamic release of neuronal extracellular vesicles containing miR-21a-5p is induced by hypoxia.Journal of extracellular vesicles · 2023Article
- Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.Genome research · 2023Article
- miRNA-encapsulated abiotic materials and biovectors for cutaneous and oral wound healing: Biogenesis, mechanisms, and delivery nanocarriers.Bioengineering & translational medicine · 2023Review
- Screening of candidate genes associated with high titer production of oncolytic measles virus based on systems biology approach.Virus genes · 2022Article
- miR-218: A Stress-Responsive Epigenetic Modifier.Non-coding RNA · 2022Review
- Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro.Scientific reports · 2022Article
- Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types.Arteriosclerosis, thrombosis, and vascular biology · 2021Article
- A microRNA expression and regulatory element activity atlas of the mouse immune system.Nature immunology · 2021Article
- Genomic Landscapes of Noncoding RNAs RegulatingMolecular and cellular biology · 2021Article
- NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli.Cardiovascular research · 2021Article
- Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour.Planta · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Changes in mature microRNA (miRNA) levels that occur downstream of signaling cascades play an important role during human development and disease. However, the regulation of primary microRNA (pri-miRNA) genes remains to be dissected in detail. To address this, we followed a data-driven approach and developed a transcript identification, validation and quantification pipeline for characterizing the regulatory domains of pri-miRNAs. Integration of 92 nascent transcriptomes and multilevel data from cells arising from ecto-, endo- and mesoderm lineages reveals cell type-specific expression patterns, allows fine-resolution mapping of transcription start sites (TSS) and identification of candidate regulatory regions. We show that inter- and intragenic pri-miRNA transcripts span vast genomic regions and active TSS locations differ across cell types, exemplified by the mir-29a∼29b-1, mir-100∼let-7a-2∼125b-1 and miR-221∼222 clusters. Considering the presence of multiple TSS as an important regulatory feature at miRNA loci, we developed a strategy to quantify differential TSS usage. We demonstrate that the TSS activities associate with cell type-specific super-enhancers, differential stimulus responsiveness and higher-order chromatin structure. These results pave the way for building detailed regulatory maps of miRNA loci.
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