ArticleGenome biology and evolution2011
Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- Molecular models of bidirectional promoter regulation.Current opinion in structural biology · 2024Review
- DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes.Molecular cell · 2023Article
- Higher-order modular regulation of the human proteome.Molecular systems biology · 2023Article
- Article
- Early fate of exogenous promoters in E. coli.Nucleic acids research · 2020Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast.RNA (New York, N.Y.) · 2018Article
- The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level.Genetics · 2018Article
- It's easier to get along with the quiet neighbours.Molecular systems biology · 2017Article
- Pervasive coexpression of spatially proximal genes is buffered at the protein level.Molecular systems biology · 2017Article
- Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.Nature communications · 2017Article
- A Slowed Cell Cycle Stabilizes the Budding Yeast Genome.Genetics · 2017Article
- Sequence-Modified Antibiotic Resistance Genes Provide Sustained Plasmid-Mediated Transgene Expression in Mammals.Molecular therapy : the journal of the American Society of Gene Therapy · 2017Article
- Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation.Development (Cambridge, England) · 2016Article
- The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity.Biophysical reviews · 2016Review
- GFOD1 and peejar are promising markers for clear-cell renal cell carcinoma disease progression.Oncotarget · 2016Article
- Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.Nucleic acids research · 2016Article
- Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector.Scientific reports · 2015Article
- Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences.Journal of biosciences · 2015Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How is noise in gene expression modulated? Do mechanisms of noise control impact genome organization? In yeast, the expression of one gene can affect that of a very close neighbor. As the effect is highly regionalized, we hypothesize that genes in different orientations will have differing degrees of coupled expression and, in turn, different noise levels. Divergently organized gene pairs, in particular those with bidirectional promoters, have close promoters, maximizing the likelihood that expression of one gene affects the neighbor. With more distant promoters, the same is less likely to hold for gene pairs in nondivergent orientation. Stochastic models suggest that coupled chromatin dynamics will typically result in low abundance-corrected noise (ACN). Transcription of noncoding RNA (ncRNA) from a bidirectional promoter, we thus hypothesize to be a noise-reduction, expression-priming, mechanism. The hypothesis correctly predicts that protein-coding genes with a bidirectional promoter, including those with a ncRNA partner, have lower ACN than other genes and divergent gene pairs uniquely have correlated ACN. Moreover, as predicted, ACN increases with the distance between promoters. The model also correctly predicts ncRNA transcripts to be often divergently transcribed from genes that a priori would be under selection for low noise (essential genes, protein complex genes) and that the latter genes should commonly reside in divergent orientation. Likewise, that genes with bidirectional promoters are rare subtelomerically, cluster together, and are enriched in essential gene clusters is expected and observed. We conclude that gene orientation and transcription of ncRNAs are candidate modulators of noise.
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.