ArticleGenome biology2018
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 47 citations in OpenAlex.
- Epigenetics, Modifiers, and Molecular Noise: Rethinking Pathophysiology in Dilated and Hypertrophic Cardiomyopathies.International journal of molecular sciences · 2026Review
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- Coordinated single-nucleus responses for quantitative disease resistance involve a calcium-associated switch in transcriptional noise.Genome biology · 2025Article
- GAIN-BRCA: a graph-based AI-net framework for breast cancer subtype classification using multiomics data.Bioinformatics advances · 2025Article
- Optimal solution to the set cover problem with a vicinity constraint for estimating genotype tissue expression profiles.Bioinformatics advances · 2025Article
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- Promoter evolution of mammalian gene duplicates.BMC biology · 2023Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
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- Predicting which genes will respond to transcription factor perturbations.G3 (Bethesda, Md.) · 2022Article
- Interplay between genetic, epigenetic, and gene expression variability: Considering complexity in evolvability.Evolutionary applications · 2021Review
- Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance.American journal of human genetics · 2020Article
- Predictive features of gene expression variation reveal mechanistic link with differential expression.Molecular systems biology · 2020Article
- Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.PLoS genetics · 2020Article
- Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises.Nucleic acids research · 2020Article
- Challenges in measuring and understanding biological noise.Nature reviews. Genetics · 2019Review
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundPopulation phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between genetically identical cells is referred to as gene expression noise, the sources of which are not well understood.
resultsIn this work, by studying gene expression noise between multiple cell lineages and mammalian species, we find consistent evidence of a role for CpG islands as sources of gene expression noise. Variation in noise among CpG island promoters can be partially attributed to differences in island size, in which short islands have noisier gene expression. Building on these findings, we investigate the potential for short CpG islands to act as fast response elements to environmental stimuli. Specifically, we find that these islands are enriched amongst primary response genes in SWI/SNF-independent stimuli, suggesting that expression noise is an indicator of promoter responsiveness.
conclusionsThus, through the integration of single-cell RNA expression profiling, chromatin landscape and temporal gene expression dynamics, we have uncovered a role for short CpG island promoters as fast response elements.
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