Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels

Recent analysis (Dey et al, 2015), demonstrates that the HIV-1 Long Terminal Repeat (HIV LTR) promoter exhibits a range of possible transcriptional burst sizes and frequencies for any mean-expression level. However, these results have also been interpreted as demonstrating that cell-to-cell expression variability (noise) and mean are uncorrelated, a significant deviation from previous results. Here, we re-examine the available mRNA and protein abundance data for the HIV LTR and find that noise in mRNA and protein expression scales inversely with the mean along analytically predicted transcriptional burst-size manifolds. We then experimentally perturb transcriptional activity to test a prediction of the multiple burst-size model: that increasing burst frequency will cause mRNA noise to decrease along given burst-size lines as mRNA levels increase. The data show that mRNA and protein noise decrease as mean expression increases, supporting the canonical inverse correlation between noise and mean.Conflict of InterestThe authors declare that they have no conflict of interest.

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Transcriptional bursting shape autosomal dynamic random monoallelic expression in pre-gastrulation embryos

10.1101/2020.09.18.303776 ◽

2020 ◽

Cited By ~ 1

Author(s):

C H Naik ◽

D Chandel ◽

S Mandal ◽

S Gayen

Keyword(s):

Monoallelic Expression ◽

Wide Spread ◽

Mammalian Development ◽

Burst Frequency ◽

Genome Wide ◽

Allele Specific ◽

Transcriptional Bursting ◽

Burst Kinetics ◽

Cell Expression ◽

Early Mammalian Development

AbstractRecent years, allele-specific single cell RNA-seq (scRNA-seq) analysis have demonstrated wide-spread dynamic random monoallelic expression of autosomal genes (aRME). However, the origin of dynamic aRME remains poorly understood. It is believed that dynamic aRME is originated from discrete transcriptional burst of two alleles. Here, for the first time, we have profiled genome-wide pattern of dynamic aRME and allele-specific burst kinetics in mouse pre-gastrulation embryos. We found wide-spread dynamic aRME across the different lineages of pre-gastrulation embryos and which is linked to the allelic burst kinetics. Specially, we found that expression level and burst frequency are the key determinants of dynamic aRME. Altogether, our study provides significant insight about the origin of prevalent dynamic aRME and cell to cell expression heterogeneity during the early mammalian development.

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Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008772 ◽

2021 ◽

Vol 17 (3) ◽

pp. e1008772

Author(s):

Anton J. M. Larsson ◽

Christoph Ziegenhain ◽

Michael Hagemann-Jensen ◽

Björn Reinius ◽

Tina Jacob ◽

...

Keyword(s):

Allelic Imbalance ◽

Burst Size ◽

Single Cells ◽

Expression Patterns ◽

Allelic Expression ◽

Monoallelic Expression ◽

Burst Frequency ◽

Biallelic Expression ◽

High Consistency ◽

Transcriptional Bursting

Transcriptional bursts render substantial biological noise in cellular transcriptomes. Here, we investigated the theoretical extent of allelic expression resulting from transcriptional bursting and how it compared to the amount biallelic, monoallelic and allele-biased expression observed in single-cell RNA-sequencing (scRNA-seq) data. We found that transcriptional bursting can explain the allelic expression patterns observed in single cells, including the frequent observations of autosomal monoallelic gene expression. Importantly, we identified that the burst frequency largely determined the fraction of cells with monoallelic expression, whereas the burst size had little effect on monoallelic observations. The high consistency between the bursting model predictions and scRNA-seq observations made it possible to assess the heterogeneity of a group of cells as their deviation in allelic observations from the expected. Finally, both burst frequency and size contributed to allelic imbalance observations and reinforced that studies of allelic imbalance can be confounded from the inherent noise in transcriptional bursting. Altogether, we demonstrate that allele-level transcriptional bursting renders widespread, although predictable, amounts of monoallelic and biallelic expression in single cells and cell populations.

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Gonadotropin regulation of glutamate cysteine ligase catalytic and modifier subunit expression in rat ovary is subunit and follicle stage specific

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00531.2004 ◽

2005 ◽

Vol 289 (3) ◽

pp. E391-E402 ◽

Cited By ~ 14

Author(s):

Miyun Tsai-Turton ◽

Ulrike Luderer

Keyword(s):

Enzymatic Activity ◽

Time Course ◽

Female Rats ◽

Mrna Levels ◽

Dependent Manner ◽

Adult Rats ◽

Theca Cells ◽

Protein Levels ◽

Gonadotropin Surge ◽

Cell Expression

We have observed that levels of the antioxidant glutathione (GSH) and protein levels of the catalytic and modifier subunits of the rate-limiting enzyme in GSH synthesis, GCLc and GCLm, increase in immature rat ovaries after treatment with gonadotropin. The goals of the present studies were to delineate the time course and intraovarian localization of changes in GSH and GCL after pregnant mare's serum gonadotropin (PMSG) and after an ovulatory gonadotropin stimulus. Twenty-four hours after PMSG, there was a shift from predominantly granulosa cell expression of gclm mRNA, and to a lesser extent gclc, to predominantly theca cell expression. GCLc immunostaining increased in granulosa and theca cells and in interstitial cells. Next, prepubertal female rats were primed with PMSG, followed 48 h later by 10 IU of hCG. GCLm protein and mRNA levels increased dramatically from 0 to 4 h after hCG and then declined rapidly. There was minimal change in GCLc. The increase in gclm mRNA expression was localized mainly to granulosa and theca cells of preovulatory follicles. To verify that GCL responds similarly to an endogenous preovulatory gonadotropin surge, we quantified ovarian GCL mRNA levels during the periovulatory period in adult rats. gclm mRNA levels increased after the gonadotropin surge on proestrus and then declined rapidly. Finally, we assessed the effects of gonadotropin on ovarian GCL enzymatic activity. GCL enzymatic activity increased significantly at 48 h after PMSG injection and did not increase further after hCG. These results demonstrate that gonadotropins regulate follicular GCL expression in a follicle stage-dependent manner and in a GCL subunit-dependent manner.

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MicroRNAs (miR)-221 and miR-222, both overexpressed in human thyroid papillary carcinomas, regulate p27Kip1 protein levels and cell cycle

Endocrine Related Cancer ◽

10.1677/erc-07-0129 ◽

2007 ◽

Vol 14 (3) ◽

pp. 791-798 ◽

Cited By ~ 265

Author(s):

Rosa Visone ◽

Lucia Russo ◽

Pierlorenzo Pallante ◽

Ivana De Martino ◽

Angelo Ferraro ◽

...

Keyword(s):

Cell Cycle ◽

Protein A ◽

Thyroid Tissue ◽

Inverse Correlation ◽

Bioinformatic Analysis ◽

Human Thyroid ◽

Mrna Levels ◽

Protein Levels ◽

Thyroid Papillary

We have recently reported that MicroRNAs (miR)-221 and miR-222 were up-regulated in human thyroid papillary carcinomas in comparison with the normal thyroid tissue. Bioinformatic analysis proposed the p27Kip1 protein, a key regulator of cell cycle, as a candidate target for the miR-221/222 cluster. Here, we report that the enforced expression of miR-221 and miR-222 was able to reduce p27Kip1 protein levels in thyroid carcinoma and HeLa cells in the absence of significant changes in specific p27Kip1 mRNA levels. This effect is direct as miR-221 and miR-222 negatively regulate the expression of the 3′-untranslated region-based reporter construct from the p27Kip1 gene, and is dependent on two target sites in this region. Consistent with these results, an enforced expression of the miR-221 and miR-222 induced the thyroid papillary carcinoma cell line (TPC-1) to progress to the S phase of the cell cycle. It is likely that the negative regulation of p27Kip1 by miR-221 and miR-222 might also have a role in vivo since we report an inverse correlation between miR-221 and miR-222 up-regulation and down-regulation of the p27Kip1 protein levels in human thyroid papillary carcinomas. Therefore, the data reported here demonstrate that miR-221 and miR-222 are endogenous regulators of p27Kip1 protein expression, and thereby, the cell cycle.

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TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes

10.1101/2020.11.16.384297 ◽

2020 ◽

Author(s):

Victor L. Bass ◽

Victor C. Wong ◽

M. Elise Bullock ◽

Suzanne Gaudet ◽

Kathryn Miller-Jensen

Keyword(s):

Inflammatory Response ◽

Rna Polymerase Ii ◽

Computational Models ◽

Target Genes ◽

Burst Size ◽

Inverse Correlation ◽

Burst Frequency ◽

Gene Expression Noise ◽

Molecule Inhibitor ◽

Single Transcript

AbstractCell-to-cell heterogeneity is a characteristic feature of the tumor necrosis factor (TNF)-stimulated inflammatory response mediated by the transcription factor NF-κB, motivating an exploration of the underlying sources of this noise. Here we combined single-transcript measurements with computational models to study transcriptional noise at six NF-κB-regulated inflammatory genes. In the basal state, NF-κB-target genes displayed an inverse correlation between mean and noise. TNF stimulation increased transcription while maintaining noise, except for the most repressed genes. By fitting transcript distributions to a two-state model of promoter activity, we found that TNF primarily stimulated transcription by increasing burst size while maintaining burst frequency. Burst size increases were associated with enrichment of initiated-but-paused RNA polymerase II at the promoter, and blocking the release of paused RNAPII with a small molecule inhibitor decreased TNF-stimulated burst size. Finally, we used a mathematical model to show that TNF positive feedback further amplified gene expression noise resulting from burst-size mediated transcription, leading to diverse TNF functional outputs. Our results reveal potential sources of noise underlying intercellular heterogeneity in the TNF-mediated inflammatory response.

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High cooperativity in negative feedback can amplify noisy gene expression

10.1101/125914 ◽

2017 ◽

Author(s):

Pavol Bokes ◽

Yen Ting Lin ◽

Abhyudai Singh

Keyword(s):

Gene Expression ◽

Negative Feedback ◽

Coefficient Of Variation ◽

Burst Size ◽

Burst Frequency ◽

Gene Expression Noise ◽

Protein Levels ◽

Feedback Strength ◽

Cell To Cell Variability ◽

The Impact

AbstractBurst-like synthesis of protein is a significant source of cell-to-cell variability in protein levels. Negative feedback is a common example of a regulatory mechanism by which such stochasticity can be controlled. Here we consider a specific kind of negative feedback, which makes bursts smaller in the excess of protein. Increasing the strength of the feedback may lead to dramatically different outcomes depending on a key parameter, the noise load, which is defined as the squared coefficient of variation the protein exhibits in the absence of feedback. Combining stochastic simulation with asymptotic analysis, we identify a critical value of noise load: for noise loads smaller than critical, the coefficient of variation remains bounded with increasing feedback strength; contrastingly, if the noise load is larger than critical, the coefficient of variation diverges to infinity in the limit of ever greater feedback strengths. Interestingly, high-cooperativity feedbacks have lower critical noise loads, implying that low-cooperativity feedbacks in burst size can be preferable for noisy proteins. Finally, we discuss our findings in the context of previous results on the impact of negative feedback in burst size and burst frequency on gene-expression noise.

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3 ′-5 ′ crosstalk contributes to transcriptional bursting

Genome Biology ◽

10.1186/s13059-020-02227-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Massimo Cavallaro ◽

Mark D. Walsh ◽

Matt Jones ◽

James Teahan ◽

Simone Tiberi ◽

...

Keyword(s):

Stochastic Process ◽

Mammalian Cells ◽

Burst Size ◽

Noise Analysis ◽

Cell Populations ◽

Burst Frequency ◽

Transcriptional Noise ◽

Mrna Species ◽

Genome Wide ◽

Transcriptional Bursting

Abstract Background Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 ′ and 5 ′ ends of a gene that enable reinitiation of transcription upon termination. Results Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment. Conclusions Interactions between the 3 ′ and 5 ′ ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.

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3’-5’ crosstalk contributes to transcriptional bursting

10.1101/514174 ◽

2019 ◽

Author(s):

Massimo Cavallaro ◽

Mark D. Walsh ◽

Matt Jones ◽

James Teahan ◽

Simone Tiberi ◽

...

Keyword(s):

Stochastic Process ◽

Mammalian Cells ◽

Burst Size ◽

Noise Analysis ◽

Cell Populations ◽

Burst Frequency ◽

Transcriptional Noise ◽

Mrna Species ◽

Genome Wide ◽

Transcriptional Bursting

AbstractBackgroundTranscription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3’ and 5’ ends of a gene that enable reinitiation of transcription upon termination.ResultsUsing Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.ConclusionsInteractions between the 3’ and 5’ ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.

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The Effects of Vitamin K1 and Warfarin on Prothrombin Expression in Human Hepatoblastoma (HepG2) Cells

Thrombosis and Haemostasis ◽

10.1055/s-0038-1656315 ◽

1992 ◽

Vol 68 (01) ◽

pp. 040-047 ◽

Cited By ~ 3

Author(s):

C Scott Jamison ◽

Bryan F Burkey ◽

Sandra J Friezner Degen

Keyword(s):

Total Protein ◽

Hepg2 Cells ◽

Enzyme Linked Immunosorbent Assay ◽

Response Analysis ◽

Secreted Protein ◽

Mrna Levels ◽

Vitamin K1 ◽

Maximal Increase ◽

Protein Levels ◽

Warfarin Treatment

SummaryCultures of human hepatoblastoma (HepG2) cells were treated with vitamin K1 or warfarin and prothrombin antigen and mRNA levels were determined. With 3 and 6 h of 10 µg vitamin K1 treatment secreted prothrombin antigen levels, relative to total secreted protein levels, were increased 1.5-fold and 2.1-fold, respectively, over ethanol-treated control levels as determined by an enzyme-linked immunosorbent assay. Dose-response analysis with 3 h of 25 µg/ml vitamin K1 treatment demonstrated a maximal increase of 2.0-fold in secreted prothrombin antigen levels, relative to total secreted protein levels, over ethanol-treated control levels. Pulse-chase analysis with 35S-methionine and immunoprecipitation of 35S-labelled prothrombin demonstrated that, with vitamin K1 treatment (25 µg/ml, 3 h), the rate of prothrombin secretion increased approximately 2-fold and the total amount (intra- and extracellular) of prothrombin synthesized increased approximately 50% over ethanol-treated control levels. Warfarin treatment (1, 5, or 10 µg/ml, 24 h) resulted in decreases in secreted prothrombin antigen levels, relative to total protein levels to approximately 85%, 87% or 81% of ethanol-treated control levels. Analysis of total RNA isolated from these cultures by Northern and solution hybridization techniques demonstrated that prothrombin mRNA was approximately 2.1 kb and that neither vitamin K1 nor warfarin treatment affected the quantity of prothrombin mRNA (ranging from 240–350 prothrombin mRNA molecules per cell). These results demonstrate that vitamin K1 and warfarin, in addition to effects on γ-carboxylation, affect prothrombin synthesis post-transcriptionally, perhaps influencing translation, post-translational processing and/or secretion mechanisms.

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Negative Correlation Between Serum Levels of Homocysteine and Apolipoprotein M

Current Molecular Medicine ◽

10.2174/1566524019666190308115624 ◽

2019 ◽

Vol 19 (2) ◽

pp. 120-126

Author(s):

J. Wei ◽

Y. Yu ◽

Y. Feng ◽

J. Zhang ◽

Q. Jiang ◽

...

Keyword(s):

Negative Correlation ◽

Hepg2 Cells ◽

Serum Levels ◽

Significant Negative Correlation ◽

Mrna Levels ◽

Rt Pcr ◽

Apolipoprotein M ◽

Protein Mass ◽

Protein Levels ◽

Phosphoinositide 3 Kinase

Background: Homocysteine (Hcy) has been suggested as an independent risk factor for atherosclerosis. Apolipoprotein M (apoM) is a constituent of the HDL particles. The goal of this study was to examine the serum levels of homocysteine and apoM and to determine whether homocysteine influences apoM synthesis. Methods: Serum levels of apoM and Hcy in 17 hyperhomocysteinemia (HHcy) patients and 19 controls were measured and their correlations were analyzed. Different concentrations of homocysteine (Hcy) and LY294002, a specific phosphoinositide 3- kinase (PI3K) inhibitor, were used to treat HepG2 cells. The mRNA levels were determined by RT-PCR and the apoM protein mass was measured by western blot. Results: We found that decreased serum apoM levels corresponded with serum HDL levels in HHcy patients, while the serum apoM levels showed a statistically significant negative correlation with the serum Hcy levels. Moreover, apoM mRNA and protein levels were significantly decreased after the administration of Hcy in HepG2 cells, and this effect could be abolished by addition of LY294002. Conclusions: resent study demonstrates that Hcy downregulates the expression of apoM by mechanisms involving the PI3K signal pathway.

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