ArticleGenome biology2024
Effect of genomic and cellular environments on gene expression noise.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives.PLoS computational biology · 2025Article
- Expression of Fluorescence Reporters and Natural Products in Native GutACS synthetic biology · 2025Article
- Massively parallel characterization of insulator activity across the genome.Nature communications · 2024Article
- Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives.bioRxiv : the preprint server for biology · 2024Article
- Effect of genomic and cellular environments on gene expression noise.Genome biology · 2024Article
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Authors and funding
4 authors.
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Abstract
backgroundIndividual cells from isogenic populations often display large cell-to-cell differences in gene expression. This "noise" in expression derives from several sources, including the genomic and cellular environment in which a gene resides. Large-scale maps of genomic environments have revealed the effects of epigenetic modifications and transcription factor occupancy on mean expression levels, but leveraging such maps to explain expression noise will require new methods to assay how expression noise changes at locations across the genome.
resultsTo address this gap, we present Single-cell Analysis of Reporter Gene Expression Noise and Transcriptome (SARGENT), a method that simultaneously measures the noisiness of reporter genes integrated throughout the genome and the global mRNA profiles of individual reporter-gene-containing cells. Using SARGENT, we perform the first comprehensive genome-wide survey of how genomic locations impact gene expression noise. We find that the mean and noise of expression correlate with different histone modifications. We quantify the intrinsic and extrinsic components of reporter gene noise and, using the associated mRNA profiles, assign the extrinsic component to differences between the CD24+ "stem-like" substate and the more "differentiated" substate. SARGENT also reveals the effects of transgene integrations on endogenous gene expression, which will help guide the search for "safe-harbor" loci.
conclusionsTaken together, we show that SARGENT is a powerful tool to measure both the mean and noise of gene expression at locations across the genome and that the data generatd by SARGENT reveals important insights into the regulation of gene expression noise genome-wide.
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