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Weidemann DE, Holehouse J, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. SCIENCE ADVANCES 2023; 9:eadh5138. [PMID: 37556551 PMCID: PMC10411910 DOI: 10.1126/sciadv.adh5138] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Gene expression inherently gives rise to stochastic variation ("noise") in the production of gene products. Minimizing noise is crucial for ensuring reliable cellular functions. However, noise cannot be suppressed below a certain intrinsic limit. For constitutively expressed genes, this limit is typically assumed to be Poissonian noise, wherein the variance in mRNA numbers is equal to their mean. Here, we demonstrate that several cell division genes in fission yeast exhibit mRNA variances significantly below this limit. The reduced variance can be explained by a gene expression model incorporating multiple transcription and mRNA degradation steps. Notably, in this sub-Poissonian regime, distinct from Poissonian or super-Poissonian regimes, cytoplasmic noise is effectively suppressed through a higher mRNA export rate. Our findings redefine the lower limit of eukaryotic gene expression noise and uncover molecular requirements for achieving ultralow noise, which is expected to be important for vital cellular functions.
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Affiliation(s)
- Douglas E. Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - James Holehouse
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87510, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Weidemann DE, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531283. [PMID: 36945401 PMCID: PMC10028819 DOI: 10.1101/2023.03.06.531283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Stochastic variation in gene products ("noise") is an inescapable by-product of gene expression. Noise must be minimized to allow for the reliable execution of cellular functions. However, noise cannot be suppressed beyond an intrinsic lower limit. For constitutively expressed genes, this limit is believed to be Poissonian, meaning that the variance in mRNA numbers cannot be lower than their mean. Here, we show that several cell division genes in fission yeast have mRNA variances significantly below this limit, which cannot be explained by the classical gene expression model for low-noise genes. Our analysis reveals that multiple steps in both transcription and mRNA degradation are essential to explain this sub-Poissonian variance. The sub-Poissonian regime differs qualitatively from previously characterized noise regimes, a hallmark being that cytoplasmic noise is reduced when the mRNA export rate increases. Our study re-defines the lower limit of eukaryotic gene expression noise and identifies molecular requirements for ultra-low noise which are expected to support essential cell functions.
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Affiliation(s)
- Douglas E Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Majewska K, Wróblewska-Ankiewicz P, Rudzka M, Hyjek-Składanowska M, Gołębiewski M, Smoliński DJ, Kołowerzo-Lubnau A. Different Patterns of mRNA Nuclear Retention during Meiotic Prophase in Larch Microsporocytes. Int J Mol Sci 2021; 22:8501. [PMID: 34445207 PMCID: PMC8395157 DOI: 10.3390/ijms22168501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/18/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies show a crucial role of post-transcriptional processes in the regulation of gene expression. Our research has shown that mRNA retention in the nucleus plays a significant role in such regulation. We studied larch microsporocytes during meiotic prophase, characterized by pulsatile transcriptional activity. After each pulse, the transcriptional activity is silenced, but the transcripts synthesized at this time are not exported immediately to the cytoplasm but are retained in the cell nucleus and especially in Cajal bodies, where non-fully-spliced transcripts with retained introns are accumulated. Analysis of the transcriptome of these cells and detailed analysis of the nuclear retention and transport dynamics of several mRNAs revealed two main patterns of nuclear accumulation and transport. The majority of studied transcripts followed the first one, consisting of a more extended retention period and slow release to the cytoplasm. We have shown this in detail for the pre-mRNA and mRNA encoding RNA pol II subunit 10. In this pre-mRNA, a second (retained) intron is posttranscriptionally spliced at a precisely defined time. Fully mature mRNA is then released into the cytoplasm, where the RNA pol II complexes are produced. These proteins are necessary for transcription in the next pulse to occur.mRNAs encoding translation factors and SERRATE followed the second pattern, in which the retention period was shorter and transcripts were rapidly transferred to the cytoplasm. The presence of such a mechanism in various cell types from a diverse range of organisms suggests that it is an evolutionarily conserved mechanism of gene regulation.
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Affiliation(s)
- Karolina Majewska
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
| | - Patrycja Wróblewska-Ankiewicz
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
| | - Magda Rudzka
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
| | - Malwina Hyjek-Składanowska
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
| | - Marcin Gołębiewski
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
| | - Agnieszka Kołowerzo-Lubnau
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (K.M.); (P.W.-A.); (M.R.); (M.H.-S.)
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland;
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Mixture distributions in a stochastic gene expression model with delayed feedback: a WKB approximation approach. J Math Biol 2020; 81:343-367. [PMID: 32583030 PMCID: PMC7363733 DOI: 10.1007/s00285-020-01512-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/11/2020] [Indexed: 12/21/2022]
Abstract
Noise in gene expression can be substantively affected by the presence of production delay. Here we consider a mathematical model with bursty production of protein, a one-step production delay (the passage of which activates the protein), and feedback in the frequency of bursts. We specifically focus on examining the steady-state behaviour of the model in the slow-activation (i.e. large-delay) regime. Using a formal asymptotic approach, we derive an autonomous ordinary differential equation for the inactive protein that applies in the slow-activation regime. If the differential equation is monostable, the steady-state distribution of the inactive (active) protein is approximated by a single Gaussian (Poisson) mode located at the globally stable fixed point of the differential equation. If the differential equation is bistable (due to cooperative positive feedback), the steady-state distribution of the inactive (active) protein is approximated by a mixture of Gaussian (Poisson) modes located at the stable fixed points; the weights of the modes are determined from a WKB approximation to the stationary distribution. The asymptotic results are compared to numerical solutions of the chemical master equation.
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Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. Cell Syst 2018; 7:398-411.e6. [DOI: 10.1016/j.cels.2018.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/28/2018] [Accepted: 09/05/2018] [Indexed: 12/28/2022]
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