Mammalian gene expression variability is explained by underlying cell state

• Published in: Molecular systems biology 2020-02, Vol.16 (2), p.e9146-n/a
• Main Authors: Foreman, Robert, Wollman, Roy
• Format: Article
• Language: English
• Subjects: Bursting; Ca2+ signaling; Calcium ions; Calcium Signaling; Calcium signalling; Cell Cycle; Cell Line; Cell Size; Consortia; Covariance; EMBO09; Female; Fluorescence; Fluorescence in situ hybridization; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation; Genes; Humans; In Situ Hybridization, Fluorescence; Mammalian cells; Mammals; MERFISH; Noise; Ribonucleic acid; RNA; RNA, Messenger - genetics; single cell; Single-Cell Analysis; Systems Biology - methods; Transcription; transcriptional bursting; Variability
• ISSN: 1744-4292; 1744-4292
• DOI: 10.15252/msb.20199146

Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele‐specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca 2+ signaling coupled with the dynamic Ca 2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca 2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal. Synopsis Single‐cell coupled measurements of Ca 2+ signaling dynamics, cell size, cell cycle, and expression of Ca 2+ signaling‐related genes show that most of the gene expression variability is not gene‐specific. The remaining gene‐specific variability approaches Poisson limit for most genes. Cell state information, i.e. cell size, cell cycle stage, and Ca 2+ signaling dynamic response to ligand was measured alongside single‐cell measurements of gene expression for 150 genes related to Ca 2+ signaling using MERFISH. The majority of observed gene expression variance can be explained by 13 features related to cell state. The remaining unexplained variance approaches the Poisson limit for most genes. Graphical Abstract Single‐cell coupled measurements of Ca 2+ signaling dynamics, cell size, cell cycle, and expression of Ca 2+ signaling‐related genes show that most of the gene expression variability is not gene‐specific. The remaining gene‐specific variability approaches Poisson limit for most genes.