ArticleNature structural & molecular biology2013
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.
Article in Nature structural & molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers, 1 of them a synthesis that pooled it.
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Who cites it
181 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Adulthood depletion of Integrator extends lifespan and healthspan via defective pre-mRNA processing.bioRxiv : the preprint server for biology · 2026Article
- Dual promoter-enhancer activities reflect a unified regulatory logic.Nature communications · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- RNAa-Mediated Gene Activation in the Regulation of Stem Cell Fate.Biomolecules · 2025Review
- Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci.Genes & development · 2025Article
- Condensation of ZFP207 and U1 snRNP promotes spliceosome assembly.Nature structural & molecular biology · 2025Article
- 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
- Restrictor slows early transcription elongation to render RNA polymerase II susceptible to termination at non-coding RNA loci.bioRxiv : the preprint server for biology · 2025Article
- Multiple Forms and Functions of Premature Termination by RNA Polymerase II.Journal of molecular biology · 2025Review
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- DIS3 ribonuclease is essential for spermatogenesis and male fertility in mice.Development (Cambridge, England) · 2024Article
121 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Active human promoters produce promoter-upstream transcripts (PROMPTs). Why these RNAs are coupled to decay, whereas their neighboring promoter-downstream mRNAs are not, is unknown. Here high-throughput sequencing demonstrates that PROMPTs generally initiate in the antisense direction closely upstream of the transcription start sites (TSSs) of their associated genes. PROMPT TSSs share features with mRNA-producing TSSs, including stalled RNA polymerase II (RNAPII) and the production of small TSS-associated RNAs. Notably, motif analyses around PROMPT 3' ends reveal polyadenylation (pA)-like signals. Mutagenesis studies demonstrate that PROMPT pA signals are functional but linked to RNA degradation. Moreover, pA signals are under-represented in promoter-downstream versus promoter-upstream regions, thus allowing for more efficient RNAPII progress in the sense direction from gene promoters. We conclude that asymmetric sequence distribution around human gene promoters serves to provide a directional RNA output from an otherwise bidirectional transcription process.
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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.