1
|
Kenworthy AK. What's past is prologue: FRAP keeps delivering 50 years later. Biophys J 2023; 122:3577-3586. [PMID: 37218127 PMCID: PMC10541474 DOI: 10.1016/j.bpj.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) has emerged as one of the most widely utilized techniques to quantify binding and diffusion kinetics of biomolecules in biophysics. Since its inception in the mid-1970s, FRAP has been used to address an enormous array of questions including the characteristic features of lipid rafts, how cells regulate the viscosity of their cytoplasm, and the dynamics of biomolecules inside condensates formed by liquid-liquid phase separation. In this perspective, I briefly summarize the history of the field and discuss why FRAP has proven to be so incredibly versatile and popular. Next, I provide an overview of the extensive body of knowledge that has emerged on best practices for quantitative FRAP data analysis, followed by some recent examples of biological lessons learned using this powerful approach. Finally, I touch on new directions and opportunities for biophysicists to contribute to the continued development of this still-relevant research tool.
Collapse
Affiliation(s)
- Anne K Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| |
Collapse
|
2
|
Ham L, Brackston RD, Stumpf MPH. Extrinsic Noise and Heavy-Tailed Laws in Gene Expression. PHYSICAL REVIEW LETTERS 2020; 124:108101. [PMID: 32216388 DOI: 10.1103/physrevlett.124.108101] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Noise in gene expression is one of the hallmarks of life at the molecular scale. Here we derive analytical solutions to a set of models describing the molecular mechanisms underlying transcription of DNA into RNA. Our ansatz allows us to incorporate the effects of extrinsic noise-encompassing factors external to the transcription of the individual gene-and discuss the ramifications for heterogeneity in gene product abundance that has been widely observed in single cell data. Crucially, we are able to show that heavy-tailed distributions of RNA copy numbers cannot result from the intrinsic stochasticity in gene expression alone, but must instead reflect extrinsic sources of variability.
Collapse
Affiliation(s)
- Lucy Ham
- School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Parkville VIC 3010, Australia
| | - Rowan D Brackston
- Department Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| | - Michael P H Stumpf
- School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Parkville VIC 3010, Australia
- Department Life Sciences, Imperial College London, SW7 2AZ, United Kingdom
| |
Collapse
|
3
|
Choubey S, Kondev J, Sanchez A. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells. Biophys J 2019; 114:2072-2082. [PMID: 29742401 DOI: 10.1016/j.bpj.2018.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/18/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022] Open
Abstract
Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Quantitative information about transcription initiation dynamics can also be extracted from experiments that use electron micrographs of RNA polymerases caught in the act of transcribing a gene (Miller spreads). Inspired by these data, we analyze a general stochastic model of transcription initiation and elongation and compute the distribution of transcription initiation times. We show that different mechanisms of initiation leave distinct signatures in the distribution of initiation times that can be compared to experiments. We analyze published data from micrographs of RNA polymerases transcribing ribosomal RNA genes in Escherichia coli and compare the observed distributions of interpolymerase distances with the predictions from previously hypothesized mechanisms for the regulation of these genes. Our analysis demonstrates the potential of measuring the distribution of time intervals between initiation events as a probe for dissecting mechanisms of transcription initiation in live cells.
Collapse
Affiliation(s)
- Sandeep Choubey
- Department of Physics, Brandeis University, Waltham, Massachusetts
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, Massachusetts
| | - Alvaro Sanchez
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts; Department of Ecology and Evolutionary Biology, Microbial Sciences Institute, Yale University, New Haven, Connecticut.
| |
Collapse
|
4
|
Choubey S. Nascent RNA kinetics: Transient and steady state behavior of models of transcription. Phys Rev E 2018; 97:022402. [PMID: 29548128 DOI: 10.1103/physreve.97.022402] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Indexed: 11/07/2022]
Abstract
Regulation of transcription is a vital process in cells, but mechanistic details of this regulation still remain elusive. The dominant approach to unravel the dynamics of transcriptional regulation is to first develop mathematical models of transcription and then experimentally test the predictions these models make for the distribution of mRNA and protein molecules at the individual cell level. However, these measurements are affected by a multitude of downstream processes which make it difficult to interpret the measurements. Recent experimental advancements allow for counting the nascent mRNA number of a gene as a function of time at the single-cell level. These measurements closely reflect the dynamics of transcription. In this paper, we consider a general mechanism of transcription with stochastic initiation and deterministic elongation and probe its impact on the temporal behavior of nascent RNA levels. Using techniques from queueing theory, we derive exact analytical expressions for the mean and variance of the nascent RNA distribution as functions of time. We apply these analytical results to obtain the mean and variance of nascent RNA distribution for specific models of transcription. These models of initiation exhibit qualitatively distinct transient behaviors for both the mean and variance which further allows us to discriminate between them. Stochastic simulations confirm these results. Overall the analytical results presented here provide the necessary tools to connect mechanisms of transcription initiation to single-cell measurements of nascent RNA.
Collapse
Affiliation(s)
- Sandeep Choubey
- FAS Center for Systems Biology and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
5
|
Yunger S, Kafri P, Rosenfeld L, Greenberg E, Kinor N, Garini Y, Shav-Tal Y. S-phase transcriptional buffering quantified on two different promoters. Life Sci Alliance 2018; 1:e201800086. [PMID: 30456379 PMCID: PMC6238621 DOI: 10.26508/lsa.201800086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 01/17/2023] Open
Abstract
Transcriptional buffering enforced during DNA replication shows that histone acetylation governs the homeostasis process and can also restrict promoters from reaching maximum transcriptional potential Imaging of transcription by quantitative fluorescence-based techniques allows the examination of gene expression kinetics in single cells. Using a cell system for the in vivo visualization of mammalian mRNA transcriptional kinetics at single-gene resolution during the cell cycle, we previously demonstrated a reduction in transcription levels after replication. This phenomenon has been described as a homeostasis mechanism that buffers mRNA transcription levels with respect to the cell cycle stage and the number of transcribing alleles. Here, we examined how transcriptional buffering enforced during S phase affects two different promoters, the cytomegalovirus promoter versus the cyclin D1 promoter, that drive the same gene body. We found that global modulation of histone modifications could completely revert the transcription down-regulation imposed during replication. Furthermore, measuring these levels of transcriptional activity in fixed and living cells showed that the transcriptional potential of the genes was significantly higher than actual transcription levels, suggesting that promoters might normally be limited from reaching their full transcriptional potential.
Collapse
Affiliation(s)
- Sharon Yunger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Pinhas Kafri
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Liat Rosenfeld
- Department of Physics, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Eliraz Greenberg
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Yuval Garini
- Department of Physics, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| |
Collapse
|
6
|
Xu H, Skinner SO, Sokac AM, Golding I. Stochastic Kinetics of Nascent RNA. PHYSICAL REVIEW LETTERS 2016; 117:128101. [PMID: 27667861 PMCID: PMC5033037 DOI: 10.1103/physrevlett.117.128101] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The stochastic kinetics of transcription is typically inferred from the distribution of RNA numbers in individual cells. However, cellular RNA reflects additional processes downstream of transcription, hampering this analysis. In contrast, nascent (actively transcribed) RNA closely reflects the kinetics of transcription. We present a theoretical model for the stochastic kinetics of nascent RNA, which we solve to obtain the probability distribution of nascent RNA per gene. The model allows us to evaluate the kinetic parameters of transcription from single-cell measurements of nascent RNA. The model also predicts surprising discontinuities in the distribution of nascent RNA, a feature which we verify experimentally.
Collapse
Affiliation(s)
- Heng Xu
- Center for Theoretical Biological Physics, Rice University, Houston,
Texas, USA
- Center for the Physics of Living Cells, University of Illinois at
Urbana-Champaign, Urbana, Illinois, USA
- Verna & Marrs McLean Department of Biochemistry and Molecular
Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Samuel O. Skinner
- Center for Theoretical Biological Physics, Rice University, Houston,
Texas, USA
- Center for the Physics of Living Cells, University of Illinois at
Urbana-Champaign, Urbana, Illinois, USA
- Verna & Marrs McLean Department of Biochemistry and Molecular
Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Anna Marie Sokac
- Verna & Marrs McLean Department of Biochemistry and Molecular
Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ido Golding
- Center for Theoretical Biological Physics, Rice University, Houston,
Texas, USA
- Center for the Physics of Living Cells, University of Illinois at
Urbana-Champaign, Urbana, Illinois, USA
- Verna & Marrs McLean Department of Biochemistry and Molecular
Biology, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
7
|
Sherman MS, Lorenz K, Lanier MH, Cohen BA. Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression. Cell Syst 2015; 1:315-325. [PMID: 26623441 DOI: 10.1016/j.cels.2015.10.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Random fluctuations in gene expression lead to wide cell-to-cell differences in RNA and protein counts. Most efforts to understand stochastic gene expression focus on local (intrinisic) fluctuations, which have an exact theoretical representation. However, no framework exists to model global (extrinsic) mechanisms of stochasticity. We address this problem by dissecting the sources of stochasticity that influence the expression of a yeast heat shock gene, SSA1. Our observations suggest that extrinsic stochasticity does not influence every step of gene expression, but rather arises specifically from cell-to-cell differences in the propensity to transcribe RNA. This led us to propose a framework for stochastic gene expression where transcription rates vary globally in combination with local, gene-specific fluctuations in all steps of gene expression. The proposed model better explains total expression stochasticity than the prevailing ON-OFF model and offers transcription as the specific mechanism underlying correlated fluctuations in gene expression.
Collapse
Affiliation(s)
- Marc S Sherman
- Computational and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, United States. ; Center for Genome Sciences, Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States
| | - Kim Lorenz
- Center for Genome Sciences, Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States
| | - M Hunter Lanier
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Barak A Cohen
- Center for Genome Sciences, Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States
| |
Collapse
|