ArticleGenome research2018
Promoter architecture determines cotranslational regulation of mRNA.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from human non-coding genomes.Human molecular genetics · 2022Review
- Reliance of Host-Encoded Regulators of Retromobility on Ty1 Promoter Activity or Architecture.Frontiers in molecular biosciences · 2022Article
- Genome-wide role of codon usage on transcription and identification of potential regulators.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Effects of codon usage on gene expression are promoter context dependent.Nucleic acids research · 2021Article
- Review
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.Nature communications · 2020Article
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
- Extracting novel hypotheses and findings from RNA-seq data.FEMS yeast research · 2020Review
- Article
- Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.Genetics · 2019Article
- Digital expression explorer 2: a repository of uniformly processed RNA sequencing data.GigaScience · 2019Article
- Poor codon optimality as a signal to degrade transcripts with frameshifts.Transcription · 2018Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.
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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.