Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise

Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this “noisy” transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.

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CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

Genome Biology ◽

10.1186/s13059-018-1461-x ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 14

Author(s):

Michael D. Morgan ◽

John C. Marioni

Keyword(s):

Gene Expression ◽

Cpg Island ◽

Gene Expression Noise ◽

Expression Noise

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Enhancement of gene expression noise due to nonspecific transcription factor binding

10.1101/2019.12.24.887984 ◽

2019 ◽

Cited By ~ 1

Author(s):

Supravat Dey ◽

Mohammad Soltani ◽

Abhyudai Singh

Keyword(s):

Gene Expression ◽

Stochastic Dynamics ◽

Gene Expression Noise ◽

Downstream Target ◽

High Affinity ◽

Expression Noise ◽

Degradation Rates ◽

Poisson Limit ◽

Random Fluctuations

ABSTRACTThe genome contains several high-affinity non-functional binding sites for transcription factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the role of such “decoy sites” in controlling noise (random fluctuations) in the level of a TF that is synthesized in stochastic bursts. Prior studies have assumed that decoy-bound TFs are protected from degradation, and in this case decoys function to buffer noise. Relaxing this assumption to consider arbitrary degradation rates for both bound/unbound TF states, we find rich noise behaviors. For low-affinity decoys, noise in the level of unbound TF always monotonically decreases to the Poisson limit with increasing decoy numbers. In contrast, for high affinity decoys, noise levels first increase with increasing decoy numbers, before decreasing back to the Poisson limit. Interestingly, while protection of bound TFs from degradation slows the time-scale of fluctuations in the unbound TF levels, decay of bounds TFs leads to faster fluctuations and smaller noise propagation to downstream target proteins. In summary, our analysis reveals stochastic dynamics emerging from nonspecific binding of TFs, and highlight the dual role of decoys as attenuators or amplifiers of gene expression noise depending on their binding affinity and stability of the bound TF.

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SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401589 ◽

2020 ◽

Vol 10 (9) ◽

pp. 3435-3443

Author(s):

Jian Liu ◽

Laureline Mosser ◽

Catherine Botanch ◽

Jean-Marie François ◽

Jean-Pascal Capp

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Epigenetic Modification ◽

Epigenetic Silencing ◽

Cell Heterogeneity ◽

Gene Expression Noise ◽

Expression Noise ◽

Cell Expression ◽

Cell To Cell Variability ◽

Epigenetic Processes

Abstract Chromatin structure clearly modulates gene expression noise, but the reverse influence has never been investigated, namely how the cell-to-cell expression heterogeneity of chromatin modifiers may generate variable rates of epigenetic modification. Sir2 is a well-characterized histone deacetylase of the Sirtuin family. It strongly influences chromatin silencing, especially at telomeres, subtelomeres and rDNA. This ability to influence epigenetic landscapes makes it a good model to study the largely unexplored interplay between gene expression noise and other epigenetic processes leading to phenotypic diversification. Here, we addressed this question by investigating whether noise in the expression of SIR2 was associated with cell-to-cell heterogeneity in the frequency of epigenetic silencing at subtelomeres in Saccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we found that heterogeneity in the cellular concentration of Sir2 does not lead to heterogeneity in the epigenetic silencing of subtelomeric URA3 between these subpopulations. We also noticed that SIR2 expression noise can generate cell-to-cell variability in viability, with lower levels being associated with better viability. This work shows that SIR2 expression fluctuations are not sufficient to generate cell-to-cell heterogeneity in the epigenetic silencing of URA3 at subtelomeres in Saccharomyces cerevisiae but can strongly affect cellular viability.

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Plasmids for Independently Tunable, Low-Noise Expression of Two Genes

mSphere ◽

10.1128/msphere.00340-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

João P. N. Silva ◽

Soraia Vidigal Lopes ◽

Diogo J. Grilo ◽

Zach Hensel

Keyword(s):

Gene Expression ◽

Protein Expression ◽

Low Noise ◽

Expression Systems ◽

Extrinsic Noise ◽

Gene Expression Noise ◽

Expression Noise ◽

Foreign Proteins ◽

Noise Limit ◽

Cell Variation

ABSTRACTSome microbiology experiments and biotechnology applications can be improved if it is possible to tune the expression of two different genes at the same time with cell-to-cell variation at or below the level of genes constitutively expressed from the chromosome (the “extrinsic noise limit”). This was recently achieved for a single gene by exploiting negative autoregulation by the tetracycline repressor (TetR) and bicistronic gene expression to reduce gene expression noise. We report new plasmids that use the same principles to achieve simultaneous, low-noise expression for two genes inEscherichia coli. The TetR system was moved to a compatible plasmid backbone, and a system based on thelacrepressor (LacI) was found to also exhibit gene expression noise below the extrinsic noise limit. We characterized gene expression mean and noise across the range of induction levels for these plasmids, applied the LacI system to tune expression for single-molecule mRNA detection under two different growth conditions, and showed that two plasmids can be cotransformed to independently tune expression of two different genes.IMPORTANCEMicrobiologists often express foreign proteins in bacteria in order study them or to use bacteria as a microbial factory. Usually, this requires controlling the number of foreign proteins expressed in each cell, but for many common protein expression systems, it is difficult to “tune” protein expression without large cell-to-cell variation in expression levels (called “noise” in protein expression). This work describes two protein expression systems that can be combined in the same cell, with tunable expression levels and very low protein expression noise. One new system was used to detect single mRNA molecules by fluorescence microscopy, and the two systems were shown to be independent of each other. These protein expression systems may be useful in any experiment or biotechnology application that can be improved with low protein expression noise.

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