ArticleNature structural & molecular biology2022
Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential.
Article in Nature structural & molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 48 citations in OpenAlex.
- RNA-independent cis-autoregulatory circuits within bidirectional gene pairs control metabolism.Science advances · 2026Article
- Mechanisms of transcription termination across the coding and noncoding loci of the genome.Nature reviews. Molecular cell biology · 2026Review
- Regulation of RNA transcript elongation in metazoans and its relevance to disease.Nature reviews. Molecular cell biology · 2026Review
- Binding of RbFox proteins at weak 5'splice site of A2 induces its alternative splicing in non-muscle myosin heavy-chain IIA mRNA.The Journal of biological chemistry · 2026Article
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.Science (New York, N.Y.) · 2026Article
- Evaluating the representational power of pre-trained DNA language models for regulatory genomics.Genome biology · 2025Article
- Co-option of an endogenous retrovirus (LTR7-HERVH) in early human embryogenesis: becoming useful and going unnoticed.Mobile DNA · 2025Review
- Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci.Genes & development · 2025Article
- Regulation of RNA polymerase II transcription through re-initiation and bursting.Molecular cell · 2025Review
- Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing.Journal of biological engineering · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 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
- Transcriptional rewiring in cancer driven byFrontiers in pharmacology · 2025Review
- Multiple Forms and Functions of Premature Termination by RNA Polymerase II.Journal of molecular biology · 2025Review
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- DNA-directed termination of mammalian RNA polymerase II.Genes & development · 2024Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing.Molecular cell · 2024Review
- An RNA-centric view of transcription and genome organization.Molecular cell · 2024Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Precise regulation of transcription by RNA polymerase II (RNAPII) is critical for organismal growth and development. However, what determines whether an engaged RNAPII will synthesize a full-length transcript or terminate prematurely is poorly understood. Notably, RNAPII is far more susceptible to termination when transcribing non-coding RNAs than when synthesizing protein-coding mRNAs, but the mechanisms underlying this are unclear. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in non-coding RNAs, rather than specific sequence motifs, drives RNAPII termination. Further, we demonstrate that 5' splice sites autonomously stimulate processive transcription, even in the absence of polyadenylation signals. Our results reveal a potent role for the transcribed sequence in dictating gene output and demonstrate the power of INSERT-seq toward illuminating these contributions.
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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.