ArticleNature genetics2016
Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.
Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Transcriptional interference revisited.Nature genetics · 2026Review
- Dual promoter-enhancer activities reflect a unified regulatory logic.Nature communications · 2026Article
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation.Nature communications · 2025Article
- Gene regulation by convergent promoters.Nature genetics · 2025Article
- DNA-directed termination of mammalian RNA polymerase II.Genes & development · 2024Article
- Active enhancers: recent research advances and insights into disease.Biology direct · 2024Review
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- Enhancer-MDLF: a novel deep learning framework for identifying cell-specific enhancers.Briefings in bioinformatics · 2024Article
- Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways.Cell reports · 2023Article
- High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription.Nature communications · 2023Article
- iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species.Nucleic acids research · 2022Article
- Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting.NAR genomics and bioinformatics · 2022Article
- Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics.Nature reviews. Molecular cell biology · 2022Review
- Unique features of transcription termination and initiation at closely spaced tandem human genes.Molecular systems biology · 2022Article
- Prediction of histone post-translational modification patterns based on nascent transcription data.Nature genetics · 2022Article
- Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells.Nucleic acids research · 2022Article
- Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
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11 authors.
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Abstract
Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here we found that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but owing to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolution shapes transcriptomes.
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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.