Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells.

Cell Systems
Andre J FaureBen Lehner

Abstract

Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core promoter architecture of a gene, with CpG island promoters and a TATA box associated with low and high noise, respectively. High noise is also associated with "conflicting" chromatin states-the absence of transcription-associated histone modifications or the presence of repressive ones in active genes. Genes regulated by pluripotency factors through super-enhancers show high and correlated expression variability, consistent with fluctuations in the pluripotent state. Together, our results provide an integrated view of how core promoters, chromatin, regulation, and pluripotency fluctuations contribute to the variability of gene expression across individual stem cells.

Citations

Oct 26, 2018·Nature·Tzachi HagaiSarah A Teichmann
Jul 26, 2018·Molecular & Cellular Proteomics : MCP·Piotr GrabowskiJuri Rappsilber
Mar 16, 2019·Physiological Genomics·Tristan V de JongVictor Guryev
Apr 6, 2019·Expert Review of Proteomics·Cristina SayagoJavier Munoz
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Dec 22, 2019·Cells·Daniel OsorioJames J Cai
Aug 9, 2020·Molecular Systems Biology·Olga M SigalovaJudith B Zaugg
Apr 26, 2020·Integrative and Comparative Biology·Vitor Coutinho Carneiro, Frank Lyko
Nov 27, 2020·Scientific Reports·Thanutra ZhangRoy Wollman
Feb 6, 2021·Molecular Systems Biology·Vivekanandan RamalingamJulia Zeitlinger
Nov 1, 2018·Molecular & Cellular Proteomics : MCP·Piotr GrabowskiJuri Rappsilber
Jun 10, 2021·Nucleic Acids Research·Amel Toudji-ZouazAntoine Barrière
Oct 5, 2021·Genomics, Proteomics & Bioinformatics·Tao HuXiaowo Wang

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