ArticleGenome research2011
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 53 citations in OpenAlex.
- Article
- Yeast Crf1p: An activator in need is an activator indeed.Computational and structural biotechnology journal · 2022Review
- Mediator dynamics during heat shock in budding yeast.Genome research · 2022Article
- Regulation of ribosomal protein genes: An ordered anarchy.Wiley interdisciplinary reviews. RNA · 2021Review
- Mechanisms coordinating ribosomal protein gene transcription in response to stress.Nucleic acids research · 2020Article
- Article
- Intrinsic cooperativity potentiates paralleleLife · 2018Article
- Codon usage of highly expressed genes affects proteome-wide translation efficiency.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The Genetic Makeup and Expression of the Glycolytic and Fermentative Pathways Are Highly Conserved Within theFrontiers in genetics · 2018Article
- Inferring time derivatives including cell growth rates using Gaussian processes.Nature communications · 2016Article
- Patterns of ribosomal protein expression specify normal and malignant human cells.Genome biology · 2016Article
- Prediction of fine-tuned promoter activity from DNA sequence.F1000Research · 2016Article
- Molecular mechanisms of ribosomal protein gene coregulation.Genes & development · 2015Article
- Systematic dissection of the sequence determinants of gene 3' end mediated expression control.PLoS genetics · 2015Article
- Article
- Article
- Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters.Genome research · 2014Article
- Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.Genes & development · 2014Article
- Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.Genome research · 2013Article
- Promoters maintain their relative activity levels under different growth conditions.Molecular systems biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coordinate regulation of ribosomal protein (RP) genes is key for controlling cell growth. In yeast, it is unclear how this regulation achieves the required equimolar amounts of the different RP components, given that some RP genes exist in duplicate copies, while others have only one copy. Here, we tested whether the solution to this challenge is partly encoded within the DNA sequence of the RP promoters, by fusing 110 different RP promoters to a fluorescent gene reporter, allowing us to robustly detect differences in their promoter activities that are as small as ~10%. We found that single-copy RP promoters have significantly higher activities, suggesting that proper RP stoichiometry is indeed partly encoded within the RP promoters. Notably, we also partially uncovered how this regulation is encoded by finding that RP promoters with higher activity have more nucleosome-disfavoring sequences and characteristic spatial organizations of these sequences and of binding sites for key RP regulators. Mutations in these elements result in a significant decrease of RP promoter activity. Thus, our results suggest that intrinsic (DNA-dependent) nucleosome organization may be a key mechanism by which genomes encode biologically meaningful promoter activities. Our approach can readily be applied to uncover how transcriptional programs of other promoters are encoded.
Indexed as
Identifiers
What OpenQuestion holds
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.