ArticleNucleic acids research2011
PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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104 citing papers in PubMed.
- Review
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- Non-coding RNAs in congenital heart disease and placental development: Bridging molecular mechanisms to clinical biomarkers and therapies.Non-coding RNA research · 2026Review
- GPXplore: an intelligent computational framework for precise gene promoter extraction.Frontiers in bioinformatics · 2026Article
- RNAa-Mediated Gene Activation in the Regulation of Stem Cell Fate.Biomolecules · 2025Review
- Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements.Cell reports · 2025Article
- MicroRNA-Mediated Regulation of Vascular Endothelium: From Pro-Inflammation to Atherosclerosis.International journal of molecular sciences · 2025Review
- Regulation of pyroptosis in diabetic nephropathy by long non-coding and circular RNAs.Clinical and experimental medicine · 2025Review
- LIET model: capturing the kinetics of RNA polymerase from loading to termination.Nucleic acids research · 2025Article
- Understanding lncRNAs: key regulators of myogenesis and lipogenesis in farm animals.Frontiers in veterinary science · 2025Review
- Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.Journal of molecular biology · 2025Review
- DNA-directed termination of mammalian RNA polymerase II.Genes & development · 2024Article
- An RNA-centric view of transcription and genome organization.Molecular cell · 2024Review
- DIS3 ribonuclease is essential for spermatogenesis and male fertility in mice.Development (Cambridge, England) · 2024Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions.Scientific reports · 2023Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Loss of ribonuclease DIS3 hampers genome integrity in myeloma by disrupting DNA:RNA hybrid metabolism.The EMBO journal · 2022Article
- Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains.International journal of molecular sciences · 2022Review
44 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
PROMoter uPstream Transcripts (PROMPTs) were identified as a new class of human RNAs, which are heterologous in length and produced only upstream of the promoters of active protein-coding genes. Here, we show that PROMPTs carry 3'-adenosine tails and 5'-cap structures. However, unlike mRNAs, PROMPTs are largely nuclear and rapidly turned over by the RNA exosome. PROMPT-transcribing DNA is occupied by RNA polymerase II (RNAPII) complexes with serine 2 phosphorylated C-terminal domains (CTDs), mimicking that of the associated genic region. Thus, the inefficient elongation capacity of PROMPT transcription cannot solely be assigned to poor CTD phosphorylation. Conditions that reduce gene transcription increase RNAPII occupancy of the upstream PROMPT region, suggesting that they reside in a common transcription compartment. Surprisingly, gene promoters that are actively transcribed by RNAPI or RNAPIII also produce PROMPTs that are targeted by the exosome. RNAPIII PROMPTs bear hallmarks of RNAPII promoter-associated RNAs, explaining the physical presence of RNAPII upstream of many RNAPIII-transcribed genes. We propose that RNAPII activity upstream gene promoters are wide-spread and integral to the act of gene transcription.
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