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CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness
BACKGROUND: Population 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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020341/ https://www.ncbi.nlm.nih.gov/pubmed/29945659 http://dx.doi.org/10.1186/s13059-018-1461-x |
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author | Morgan, Michael D. Marioni, John C. |
author_facet | Morgan, Michael D. Marioni, John C. |
author_sort | Morgan, Michael D. |
collection | PubMed |
description | BACKGROUND: Population 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. RESULTS: In 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. CONCLUSIONS: Thus, 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1461-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6020341 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60203412018-07-06 CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness Morgan, Michael D. Marioni, John C. Genome Biol Research BACKGROUND: Population 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. RESULTS: In 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. CONCLUSIONS: Thus, 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1461-x) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-26 /pmc/articles/PMC6020341/ /pubmed/29945659 http://dx.doi.org/10.1186/s13059-018-1461-x Text en © The Author(s) 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Morgan, Michael D. Marioni, John C. CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title | CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title_full | CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title_fullStr | CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title_full_unstemmed | CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title_short | CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness |
title_sort | cpg island composition differences are a source of gene expression noise indicative of promoter responsiveness |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020341/ https://www.ncbi.nlm.nih.gov/pubmed/29945659 http://dx.doi.org/10.1186/s13059-018-1461-x |
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