401
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Abstract
The biochemical processes leading to the synthesis of new proteins are random, as they typically involve a small number of diffusing molecules. They lead to fluctuations in the number of proteins in a single cell as a function of time and to cell-to-cell variability of protein abundances. These in turn can lead to phenotypic heterogeneity in a population of genetically identical cells. Phenotypic heterogeneity may have important consequences for the development of multicellular organisms and the fitness of bacterial colonies, raising the question of how it is regulated. Here we review the experimental evidence that transcriptional regulation affects noise in gene expression, and discuss how the noise strength is encoded in the architecture of the promoter region. We discuss how models based on specific molecular mechanisms of gene regulation can make experimentally testable predictions for how changes to the promoter architecture are reflected in gene expression noise.
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Affiliation(s)
- Alvaro Sanchez
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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402
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Hensel Z, Xiao J. Single-molecule methods for studying gene regulation in vivo. Pflugers Arch 2013; 465:383-95. [PMID: 23430319 PMCID: PMC3595547 DOI: 10.1007/s00424-013-1243-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/25/2023]
Abstract
The recent emergence of new experimental tools employing sensitive fluorescence detection in vivo has made it possible to visualize various aspects of gene regulation at the single-molecule level in the native, intracellular context. In this review, we will first describe general considerations for in vivo, single-molecule fluorescence detection of DNA, mRNA, and protein molecules involved in gene regulation. We will then give an overview of the rapidly evolving suite of molecular tools available for observing gene regulation in vivo and discuss new insights they have brought into gene regulation.
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Affiliation(s)
- Zach Hensel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
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403
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Wolters S, Schumacher B. Genome maintenance and transcription integrity in aging and disease. Front Genet 2013; 4:19. [PMID: 23443494 PMCID: PMC3580961 DOI: 10.3389/fgene.2013.00019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/03/2013] [Indexed: 12/21/2022] Open
Abstract
DNA damage contributes to cancer development and aging. Congenital syndromes that affect DNA repair processes are characterized by cancer susceptibility, developmental defects, and accelerated aging (Schumacher et al., 2008). DNA damage interferes with DNA metabolism by blocking replication and transcription. DNA polymerase blockage leads to replication arrest and can gives rise to genome instability. Transcription, on the other hand, is an essential process for utilizing the information encoded in the genome. DNA damage that interferes with transcription can lead to apoptosis and cellular senescence. Both processes are powerful tumor suppressors (Bartek and Lukas, 2007). Cellular response mechanisms to stalled RNA polymerase II complexes have only recently started to be uncovered. Transcription-coupled DNA damage responses might thus play important roles for the adjustments to DNA damage accumulation in the aging organism (Garinis et al., 2009). Here we review human disorders that are caused by defects in genome stability to explore the role of DNA damage in aging and disease. We discuss how the nucleotide excision repair system functions at the interface of transcription and repair and conclude with concepts how therapeutic targeting of transcription might be utilized in the treatment of cancer.
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Affiliation(s)
- Stefanie Wolters
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
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404
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The SWI/SNF chromatin remodeling complex influences transcription by RNA polymerase I in Saccharomyces cerevisiae. PLoS One 2013; 8:e56793. [PMID: 23437238 PMCID: PMC3577654 DOI: 10.1371/journal.pone.0056793] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/15/2013] [Indexed: 01/22/2023] Open
Abstract
SWI/SNF is a chromatin remodeling complex that affects transcription initiation and elongation by RNA polymerase II. Here we report that SWI/SNF also plays a role in transcription by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Deletion of the genes encoding the Snf6p or Snf5p subunits of SWI/SNF was lethal in combination with mutations that impair Pol I transcription initiation and elongation. SWI/SNF physically associated with ribosomal DNA (rDNA) within the coding region, with an apparent peak near the 5' end of the gene. In snf6Δ cells there was a ∼2.5-fold reduction in rRNA synthesis rate compared to WT, but there was no change in average polymerase occupancy per gene, the number of rDNA gene repeats, or the percentage of transcriptionally active rDNA genes. However, both ChIP and EM analyses showed a small but reproducible increase in Pol I density in a region near the 5' end of the gene. Based on these data, we conclude that SWI/SNF plays a positive role in Pol I transcription, potentially by modifying chromatin structure in the rDNA repeats. Our findings demonstrate that SWI/SNF influences the most robust transcription machinery in proliferating cells.
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405
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Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level. Int J Mol Sci 2013; 14:3961-92. [PMID: 23429188 PMCID: PMC3588080 DOI: 10.3390/ijms14023961] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/13/2013] [Accepted: 02/04/2013] [Indexed: 12/13/2022] Open
Abstract
The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model.
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406
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Dadiani M, van Dijk D, Segal B, Field Y, Ben-Artzi G, Raveh-Sadka T, Levo M, Kaplow I, Weinberger A, Segal E. Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res 2013; 23:966-76. [PMID: 23403035 PMCID: PMC3668364 DOI: 10.1101/gr.149096.112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Individual cells from a genetically identical population exhibit substantial variation in gene expression. A significant part of this variation is due to noise in the process of transcription that is intrinsic to each gene, and is determined by factors such as the rate with which the promoter transitions between transcriptionally active and inactive states, and the number of transcripts produced during the active state. However, we have a limited understanding of how the DNA sequence affects such promoter dynamics. Here, we used single-cell time-lapse microscopy to compare the effect on transcriptional dynamics of two distinct types of sequence changes in the promoter that can each increase the mean expression of a cell population by similar amounts but through different mechanisms. We show that increasing expression by strengthening a transcription factor binding site results in slower promoter dynamics and higher noise as compared with increasing expression by adding nucleosome-disfavoring sequences. Our results suggest that when achieving the same mean expression, the strategy of using stronger binding sites results in a larger number of transcripts produced from the active state, whereas the strategy of adding nucleosome-disfavoring sequences results in a higher frequency of promoter transitions between active and inactive states. In the latter strategy, this increased sampling of the active state likely reduces the expression variability of the cell population. Our study thus demonstrates the effect of cis-regulatory elements on expression variability and points to concrete types of sequence changes that may allow partial decoupling of expression level and noise.
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Affiliation(s)
- Maya Dadiani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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407
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Schwabe A, Rybakova KN, Bruggeman FJ. Transcription stochasticity of complex gene regulation models. Biophys J 2013; 103:1152-61. [PMID: 22995487 DOI: 10.1016/j.bpj.2012.07.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/05/2012] [Indexed: 11/28/2022] Open
Abstract
Transcription is regulated by a multitude of factors that concertedly induce genes to switch between activity states. Eukaryotic transcription involves a multitude of complexes that sequentially assemble on chromatin under the influence of transcription factors and the dynamic state of chromatin. Prokaryotic transcription depends on transcription factors, sigma-factors, and, in some cases, on DNA looping. We present a stochastic model of transcription that considers these complex regulatory mechanisms. We coarse-grain the molecular details in such a way that the model can describe a broad class of gene-regulation mechanisms. We solve this model analytically for various measures of stochastic transcription and compare alternative gene-regulation designs. We find that genes with complex multiprotein regulation can have peaked burst-size distributions in contrast to the geometric distributions found for simple models of transcription regulation. Burst-size distributions are, in addition, shaped by mRNA degradation during transcription bursts. We derive the stochastic properties of genes in the limit of deterministic switch times. These genes typically have reduced transcription noise. Severe timescale separation between gene regulation and transcription initiation enhances noise and leads to bimodal mRNA copy number distributions. In general, complex mechanisms for gene regulation lead to nonexponential waiting-time distributions for gene switching and transcription initiation, which typically reduce noise in mRNA copy numbers and burst size. Finally, we discuss that qualitatively different gene regulation models can often fit the same experimental data on single-cell mRNA abundance even though they have qualitatively different burst-size statistics and regulatory parameters.
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Affiliation(s)
- Anne Schwabe
- Life Sciences, Centre for Mathematics and Computer Science (Centrum Wiskunde & Informatica), Amsterdam, The Netherlands
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408
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Veksler A, Kolomeisky AB. Speed-selectivity paradox in the protein search for targets on DNA: is it real or not? J Phys Chem B 2013; 117:12695-701. [PMID: 23316873 DOI: 10.1021/jp311466f] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein search for targets on DNA starts all major biological processes. Although significant experimental and theoretical efforts have been devoted to investigation of these phenomena, mechanisms of protein-DNA interactions during the search remain not fully understood. One of the most surprising observations is known as a speed-selectivity paradox. It suggests that experimentally observed fast findings of targets require smooth protein-DNA binding potentials, while the stability of the specific protein-DNA complex imposes a large energy gap which should significantly slow down the protein molecule. We developed a discrete-state stochastic approach that allowed us to investigate explicitly target search phenomena and to analyze the speed-selectivity paradox. A general dynamic phase diagram for different search regimes is constructed. The effect of the target position on search dynamics is investigated. Using experimentally observed parameters, it is found that slow protein diffusion on DNA does not lead to an increase in the search times. Thus, our theory resolves the speed-selectivity paradox by arguing that it does not exist. It is just an artifact of using approximate continuum theoretical models for analyzing protein search in the region of the parameter space beyond the range of validity of these models. In addition, the presented method, for the first time, provides an explanation for fast target search at the level of single protein molecules. Our theoretical predictions agree with all available experimental observations, and extensive Monte Carlo computer simulations are performed to support analytical calculations.
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Affiliation(s)
- Alex Veksler
- Department of Chemistry, Rice University , Houston, Texas 77005, United States
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409
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Andrews BT, Capraro DT, Sulkowska JI, Onuchic JN, Jennings PA. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. J Phys Chem Lett 2013; 4:180-188. [PMID: 23525263 PMCID: PMC3601837 DOI: 10.1021/jz301893w] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of the proteins. Oftentimes these regions are introduced into the protein scaffold for function and increase frustration in the otherwise smooth-funneled landscape. Interestingly, while functional regions add complexity to folding landscapes, they may also contribute to a unique behavior referred to as hysteresis. While hysteresis is predicted to be rare, it is observed in various proteins, including proteins containing a unique peptide cyclization to form a fluorescent chromophore as well as proteins containing a knotted topology in their native fold. Here, hysteresis is demonstrated to be a consequence of the decoupling of unfolding events from the isomerization or hula-twist of a chromophore in one protein and the untying of the knot in a second protein system. The question now is- can hysteresis be a marker for the interplay of landscapes where complex folding and functional regions overlap?
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Affiliation(s)
| | - Dominique T. Capraro
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA
| | | | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston TX 77005
| | - Patricia A. Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA
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410
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Abstract
Single-cell studies of gene regulation suggest that transcription dynamics play a fundamental role in determining expression heterogeneity within a population. In addition, the three-dimensional organization of the nucleus seems to both reflect and influence expression patterns in the cell. Therefore, to gain a holistic understanding of transcriptional regulation, it is necessary to develop methods for studying transcription of single genes in living cells with high spatial and temporal resolution. In this chapter, we describe a recently developed approach for visualizing and quantifying pre-mRNA synthesis at a single active gene in the nucleus. The approach is based on the high-affinity interaction between MS2/PP7 bacteriophage coat proteins and RNA hairpins which are transcribed by the gene of interest. The MS2/PP7 coat protein is fused to a fluorescent protein and binds the nascent mRNA, allowing for detection of single transcription events in the fluorescence microscope. By time-lapse fluorescence imaging and quantitative image analysis, one can generate a time trace of fluorescence intensity at the site of transcription. By temporal autocorrelation analysis, one can determine enzymatic activities of RNAP such as initiation rate and elongation rate. In this protocol, we summarize the experimental concept, design, and execution for real-time observation of transcription in living cells.
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Affiliation(s)
- Matthew L. Ferguson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD 20892
| | - Daniel R. Larson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD 20892
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411
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Ren R, Wang H, Liu R, Zhang S. Direct visualization of the reaction transformation and signal amplification in a DNA molecular machine with total internal reflection fluorescence microscopy. Front Chem 2013; 1:23. [PMID: 24790951 PMCID: PMC3982516 DOI: 10.3389/fchem.2013.00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/26/2013] [Indexed: 11/13/2022] Open
Abstract
In this study, as a proof of concept, the signal amplification in an artificial DNA molecular machine was directly visualized via total internal reflection fluorescence microscopy (TIRFM). The molecular machine brought about obvious morphology change in DNA nanostructures as well as signal amplifications. On one hand, through a triggered and autonomically repeated RCA, a DNA nano-complex featuring a "locked" circular DNA template (serving as raw feed) was converted into a long periodically repeated strand, i.e., the RCA products. On the other hand, this RCA was repeated in three controllable reaction phases, bring about progressive signal amplification. It was testified that the RCA products (presented as long thread-like fluorescent objects) can be easily distinguished from the inputted DNA probes (presented as fluorescent dots), thus the transformation in reaction can be visualized. Also, by quantitive counting of the aforementioned fluorescence objects, the progress of the reaction through the phases, along with time, and over the lysozyme concentration can be demonstrated through TIRFM visualization. Overall, it was demonstrated that TIRFM is an efficient approach to quantitatively visualize the biochemical processes at single-molecule level.
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Affiliation(s)
- Rui Ren
- School of Chemistry and Chemical Engineering, Linyi University , Linyi, China ; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Haiyan Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Rui Liu
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
| | - Shusheng Zhang
- School of Chemistry and Chemical Engineering, Linyi University , Linyi, China ; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, China
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412
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Chubb JR, Stevense M, Cannon D, Muramoto T, Corrigan AM. Imaging nascent RNA dynamics in Dictyostelium. Methods Mol Biol 2013; 1042:101-13. [PMID: 23980003 DOI: 10.1007/978-1-62703-526-2_8] [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] [Indexed: 01/25/2023]
Abstract
Dictyostelium cells have great utility for live imaging of single gene transcriptional dynamics. The cells allow efficient molecular genetics, for targeting of RNA reporters and fluorescent proteins to individual, defined loci. Dictyostelium cells share many signalling, chromatin and nuclear characteristics of larger eukaryotes, yet the cells have a relatively simple scattered differentiation programme, allowing imaging of transcriptional events in the context of stochastic developmental choices. This review will detail the methods and considerations for imaging nascent RNA dynamics at single genes in living Dictyostelium cells.
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Affiliation(s)
- Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology, Department of Cell and Developmental Biology, University College London, London, UK
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413
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Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat Methods 2012; 10:119-21. [PMID: 23263691 DOI: 10.1038/nmeth.2305] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 11/21/2012] [Indexed: 01/11/2023]
Abstract
Live-cell imaging of mRNA yields important insights into gene expression, but it has generally been limited to the labeling of one RNA species and has never been used to count single mRNAs over time in yeast. We demonstrate a two-color imaging system with single-molecule resolution using MS2 and PP7 RNA labeling. We use this methodology to measure intrinsic noise in mRNA levels and RNA polymerase II kinetics at a single gene.
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414
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Katz ZB, Wells AL, Park HY, Wu B, Shenoy SM, Singer RH. β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes Dev 2012; 26:1885-90. [PMID: 22948660 DOI: 10.1101/gad.190413.112] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Directed cell motility is at the basis of biological phenomena such as development, wound healing, and metastasis. It has been shown that substrate attachments mediate motility by coupling the cell's cytoskeleton with force generation. However, it has been unclear how the persistence of cell directionality is facilitated. We show that mRNA localization plays an important role in this process, but the mechanism of action is still unknown. In this study, we show that the zipcode-binding protein 1 transports β-actin mRNA to the focal adhesion compartment, where it dwells for minutes, suggesting a means for associating its localization with motility through the formation of stable connections between adhesions and newly synthesized actin filaments. In order to demonstrate this, we developed an approach for assessing the functional consequences of β-actin mRNA and protein localization by tethering the mRNA to a specific location-in this case, the focal adhesion complex. This approach will have a significant impact on cell biology because it is now possible to forcibly direct any mRNA and its cognate protein to specific locations in the cell. This will reveal the importance of localized protein translation on various cellular processes.
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Affiliation(s)
- Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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415
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Chao JA, Yoon YJ, Singer RH. Imaging translation in single cells using fluorescent microscopy. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a012310. [PMID: 22960595 DOI: 10.1101/cshperspect.a012310] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The regulation of translation provides a mechanism to control not only the abundance of proteins, but also the precise time and subcellular location that they are synthesized. Much of what is known concerning the molecular basis for translational control has been gleaned from experiments (e.g., luciferase assays and polysome analysis) that measure average changes in the protein synthesis of a population of cells, however, mechanistic insights can be obscured in ensemble measurements. The development of fluorescent microscopy techniques and reagents has allowed translation to be studied within its cellular context. Here we highlight recent methodologies that can be used to study global changes in protein synthesis or regulation of specific mRNAs in single cells. Imaging of translation has provided direct evidence for local translation of mRNAs at synapses in neurons and will become an important tool for studying translational control.
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Affiliation(s)
- Jeffrey A Chao
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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416
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Nicholson P, Joncourt R, Mühlemann O. Analysis of nonsense-mediated mRNA decay in mammalian cells. CURRENT PROTOCOLS IN CELL BIOLOGY 2012; Chapter 27:Unit27.4. [PMID: 22733442 DOI: 10.1002/0471143030.cb2704s55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway acts to selectively identify and degrade mRNAs that contain a premature translation termination codon (PTC), and hence reduce the accumulation of potentially toxic truncated proteins. NMD is one of the best studied mRNA quality-control mechanisms in eukaryotes, and it has become clear during recent years that many physiological mRNAs are also NMD substrates, signifying a role for NMD beyond mRNA quality control as a translation-dependent post-transcriptional regulator of gene expression. Despite a great deal of scientific research for over twenty years, the process of NMD is far from being fully understood with regard to its physiological relevance to the cell, the molecular mechanisms that underpin this pathway, all of the factors that are involved, and the exact cellular locations of NMD. This unit details some of the fundamental RNA based approaches taken to examine aspects of NMD, such as creating PTC+ reporter genes, knocking down key NMD factors via RNAi, elucidating the important functions of NMD factors by complementation assays or Tethered Function Assays, and measuring RNA levels by reverse-transcription quantitative PCR.
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417
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Mischo HE, Proudfoot NJ. Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:174-85. [PMID: 23085255 PMCID: PMC3793857 DOI: 10.1016/j.bbagrm.2012.10.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/29/2022]
Abstract
Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Hannah E Mischo
- Cancer Research UK London Research Institute, Blanche Lane South Mimms, Herts, UK.
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418
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Toplak T, Pandzic E, Chen L, Vicente-Manzanares M, Horwitz AR, Wiseman PW. STICCS reveals matrix-dependent adhesion slipping and gripping in migrating cells. Biophys J 2012; 103:1672-82. [PMID: 23083710 DOI: 10.1016/j.bpj.2012.08.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/16/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022] Open
Abstract
Two-color spatio-temporal image cross-correlation spectroscopy (STICCS) is a new, to our knowledge, image analysis method that calculates space-time autocorrelation and cross-correlation functions from fluorescence intensity fluctuations. STICCS generates cellular flow and diffusion maps that reveal interactions and cotransport of two distinct molecular species labeled with different fluorophores. Here we use computer simulations to map the capabilities and limitations of STICCS for measurements in complex heterogeneous environments containing micro- and macrostructures. We then use STICCS to analyze the co-flux of adhesion components in migrating cells imaged using total internal reflection fluorescence microscopy. The data reveal a robust, time-dependent co-fluxing of certain integrins and paxillin in adhesions in protrusions when they pause, and in adhesions that are sliding and disassembling, demonstrating that the molecules in these adhesions move as a complex. In these regions, both α6β1- or αLβ2-integrins, expressed in CHO.B2 cells, co-flux with paxillin; an analogous cotransport was seen for α6β1-integrin and α-actinin in U2OS. This contrasts with the behavior of the α5β1-integrin and paxillin, which do not co-flux. Our results clearly show that integrins can move in complexes with adhesion proteins in protrusions that are retracting.
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Affiliation(s)
- Tim Toplak
- Department of Physics, McGill University, Montréal, Québec, Canada
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419
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Abstract
Proper timing of gene expression requires that transcription factors (TFs) efficiently locate and bind their target sites within a genome. Theoretical studies have long proposed that one-dimensional sliding along DNA while simultaneously reading its sequence can accelerate TF's location of target sites. Sliding by prokaryotic and eukaryotic TFs were subsequently observed. More recent theoretical investigations have argued that simultaneous reading and sliding is not possible for TFs without their possessing at least two DNA-binding modes. The tumor suppressor p53 has been shown to slide on DNA, and recent experiments have offered structural and single molecule support for a two-mode model for the protein. If the model is applicable to p53, then the requirement that TFs be able to read while sliding implies that noncognate sites will affect p53's mobility on DNA, which will thus be generally sequence-dependent. Here, we confirm this prediction with single-molecule microscopy measurements of p53's local diffusivity on noncognate DNA. We show how a two-mode model accurately predicts the variation in local diffusivity, while a single-mode model does not. We further determine that the best model of sequence-specific binding energy includes terms for "hemi-specific" binding, with one dimer of tetrameric p53 binding specifically to a half-site and the other binding nonspecifically to noncognate DNA. Our work provides evidence that the recognition by p53 of its targets and the timing thereof can depend on its noncognate binding properties and its ability to change between multiple modes of binding, in addition to the much better-studied effects of cognate-site binding.
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420
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Zhou J, Schweikhard V, Block SM. Single-molecule studies of RNAPII elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:29-38. [PMID: 22982192 DOI: 10.1016/j.bbagrm.2012.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 01/22/2023]
Abstract
Elongation, the transcriptional phase in which RNA polymerase (RNAP) moves processively along a DNA template, occurs via a fundamental enzymatic mechanism that is thought to be universally conserved among multi-subunit polymerases in all kingdoms of life. Beyond this basic mechanism, a multitude of processes are integrated into transcript elongation, among them fidelity control, gene regulatory interactions involving elongation factors, RNA splicing or processing factors, and regulatory mechanisms associated with chromatin structure. Many kinetic and molecular details of the mechanism of the nucleotide addition cycle and its regulation, however, remain elusive and generate continued interest and even controversy. Recently, single-molecule approaches have emerged as powerful tools for the study of transcription in eukaryotic organisms. Here, we review recent progress and discuss some of the unresolved questions and ongoing debates, while anticipating future developments in the field. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
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Affiliation(s)
- Jing Zhou
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
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421
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Steffen PA, Fonseca JP, Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012; 34:901-13. [PMID: 22911103 DOI: 10.1002/bies.201200076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.
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422
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Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG. A benchmark for chromatin binding measurements in live cells. Nucleic Acids Res 2012; 40:e119. [PMID: 22844090 PMCID: PMC3424588 DOI: 10.1093/nar/gks701] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult to mimic in vitro. However, different studies have yielded widely discrepant predictions, and so it remains uncertain how to make the measurements accurately. To establish a benchmark we measured binding of the transcription factor p53 to chromatin by three approaches: fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and single-molecule tracking (SMT). Using new procedures to analyze the SMT data and to guide the FRAP and FCS analysis, we show how all three approaches yield similar estimates for both the fraction of p53 molecules bound to chromatin (only about 20%) and the residence time of these bound molecules (∼1.8 s). We also apply these procedures to mutants in p53 chromatin binding. Our results support the model that p53 locates specific sites by first binding at sequence-independent sites.
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Affiliation(s)
- Davide Mazza
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA
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423
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Yushchenko DA, Zhang M, Yan Q, Waggoner AS, Bruchez MP. Genetically targetable and color-switching fluorescent probe. Chembiochem 2012; 13:1564-8. [PMID: 22777954 DOI: 10.1002/cbic.201200334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Indexed: 11/10/2022]
Abstract
Color bind: We have developed a probe TMR-para-MG that switches its fluorescence emission upon binding to a fluorogen-activating protein (FAP). In cells that express FAP, this dye labels target sites in one color and mitochondria in another color, thus it might be a suitable tool for monitoring changes in mitochondrial membrane potential.
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Affiliation(s)
- Dmytro A Yushchenko
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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424
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Stavreva DA, Varticovski L, Hager GL. Complex dynamics of transcription regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:657-66. [PMID: 22484099 PMCID: PMC3371156 DOI: 10.1016/j.bbagrm.2012.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 03/10/2012] [Accepted: 03/15/2012] [Indexed: 01/10/2023]
Abstract
Transcription is a tightly regulated cellular function which can be triggered by endogenous (intrinsic) or exogenous (extrinsic) signals. The development of novel techniques to examine the dynamic behavior of transcription factors and the analysis of transcriptional activity at the single cell level with increased temporal resolution has revealed unexpected elements of stochasticity and dynamics of this process. Emerging research reveals a complex picture, wherein a wide range of time scales and temporal transcription patterns overlap to generate transcriptional programs. The challenge now is to develop a perspective that can guide us to common underlying mechanisms, and consolidate these findings. Here we review the recent literature on temporal dynamics and stochastic gene regulation patterns governed by intrinsic or extrinsic signals, utilizing the glucocorticoid receptor (GR)-mediated transcriptional model to illustrate commonality of these emerging concepts. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Building 41, B507, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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425
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Abstract
Transcription by RNA polymerase II is the process that copies DNA into RNA leading to the expression of a specific gene. Averaged estimates of polymerase elongation rates in mammalian cells have been shown to vary between 1 and 4 kilobases per minute. However, recent advances in live cell imaging allowed direct measurements of RNA biogenesis from a single gene exceeded 50 kb·min(-1) . This unexpected finding opens novel and intriguing perspectives on the control of metazoan transcription.
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Affiliation(s)
- Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
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426
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Wu B, Chao JA, Singer RH. Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells. Biophys J 2012; 102:2936-44. [PMID: 22735544 DOI: 10.1016/j.bpj.2012.05.017] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/01/2012] [Accepted: 05/07/2012] [Indexed: 01/12/2023] Open
Abstract
Imaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous β-actin mRNA, which has 24xMS2 binding sites inserted into the 3' untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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427
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Owen-Hughes T, Gkikopoulos T. Making sense of transcribing chromatin. Curr Opin Cell Biol 2012; 24:296-304. [PMID: 22410403 PMCID: PMC3432231 DOI: 10.1016/j.ceb.2012.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 11/03/2022]
Abstract
Eukaryotic cells package their genomes into a nucleoprotein form called chromatin. The basic unit of chromatin is the nucleosome, formed by the wrapping of ∼147bp of DNA around an octameric complex of core histones. Advances in genomic technologies have enabled the locations of nucleosomes to be mapped across genomes. This has revealed a striking organisation with respect to transcribed genes in a diverse range of eukaryotes. This consists of a nucleosome depleted region upstream of promoters, with an array of well spaced nucleosomes extending into coding regions. This observation reinforces the links between chromatin organisation and transcription. Central to this is the paradox that while chromatin is required by eukaryotes to restrict inappropriate access to DNA, this must be overcome in order for genetic information to be expressed. This conundrum is at its most flagrant when considering the need for nucleic acid polymerase's to transit 1000's of based pairs of DNA wrapped as arrays of nucleosomes.
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Affiliation(s)
- Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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428
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Montes M, Becerra S, Sánchez-Álvarez M, Suñé C. Functional coupling of transcription and splicing. Gene 2012; 501:104-17. [DOI: 10.1016/j.gene.2012.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 01/13/2023]
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429
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Aquino T, Abranches E, Nunes A. Stochastic single-gene autoregulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061913. [PMID: 23005133 DOI: 10.1103/physreve.85.061913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/07/2012] [Indexed: 06/01/2023]
Abstract
A detailed stochastic model of single-gene autoregulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness that are intrinsic to the autoregulation process and it considers both transcriptional and post-transcriptional regulation. The time-scale separation allows the derivation of analytic expressions for the equilibrium distributions of protein and mRNA. These distributions are generally well described in the continuous approximation, which is used to discuss the qualitative features of the protein equilibrium distributions as a function of the biological parameters in the fast mRNA regime. The performance of the time-scale approximation is assessed by comparison with simulations of the full stochastic system, and a good quantitative agreement is found for a wide range of parameter values. We show that either unimodal or bimodal equilibrium protein distributions can arise, and we discuss the autoregulation mechanisms associated with bimodality.
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Affiliation(s)
- Tomás Aquino
- Centro de Física da Matéria Condensada and Departamento de Física, Faculdade de Ciências da Universidade de Lisboa, P-1649-003 Lisboa, Portugal
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430
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Meyer B, Bénichou O, Kafri Y, Voituriez R. Geometry-induced bursting dynamics in gene expression. Biophys J 2012; 102:2186-91. [PMID: 22824283 PMCID: PMC3341560 DOI: 10.1016/j.bpj.2012.03.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 11/17/2022] Open
Abstract
In prokaryotes and eukaryotes, genes are transcribed stochastically according to various temporal patterns that range from simple first-order kinetics to marked bursts, resulting in temporal and cell-to-cell variations of mRNA and protein levels. Here, we consider the effect of the transport of regulatory molecules on the noise in gene expression by taking into account explicitly the dynamics of a finite number of transcription factors confined in the cell. We calculate analytically time-dependent correlation functions of mRNA levels for a wide range of transport mechanisms and find that in the limit of small-transcription-factor copy number, the results differ significantly from standard approaches, which ignore confinement. It is shown how such dynamical quantities, which can now be obtained experimentally, can be used to identify the underlying mechanisms of transcription. Of particular importance, it is demonstrated that the geometry of transcription-factor trajectories in the cellular environment plays a key role in transcription kinetics, and can intrinsically generate the observed various transcription patterns ranging from simple first-order kinetics to bursts.
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Affiliation(s)
- B. Meyer
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
| | - O. Bénichou
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
| | - Y. Kafri
- Department of Physics, Technion, Haifa, Israel
| | - R. Voituriez
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
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431
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Benabbas A, Karunakaran V, Youn H, Poulos TL, Champion PM. Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA. J Biol Chem 2012; 287:21729-40. [PMID: 22544803 DOI: 10.1074/jbc.m112.345090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role.
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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432
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Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A 2012; 109:7350-5. [PMID: 22529358 DOI: 10.1073/pnas.1117603109] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription of genes can be discontinuous, occurring in pulses or bursts. It is not clear how properties of transcriptional pulses vary between different genes. We compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells. Each gene displayed its own transcriptional signature, differing in probability of firing and pulse duration, frequency, and intensity. In contrast to the prevailing view from both prokaryotes and eukaryotes that transcription displays binary behavior, strongly expressed housekeeping genes altered the magnitude of their transcriptional pulses during development. These nonbinary "tunable" responses may be better suited than stochastic switch behavior for housekeeping functions. Analysis of RNA synthesis kinetics using fluorescence recovery after photobleaching implied modulation of housekeeping-gene pulse strength occurs at the level of transcription initiation rather than elongation. In addition, disparities between single cell and population measures of transcript production suggested differences in RNA stability between gene classes. Analysis of stability using RNAseq revealed no major global differences in stability between developmental and housekeeping transcripts, although strongly induced RNAs showed unusually rapid decay, indicating tight regulation of expression.
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433
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Hoskins AA, Moore MJ. The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem Sci 2012; 37:179-88. [PMID: 22480731 DOI: 10.1016/j.tibs.2012.02.009] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 01/22/2023]
Abstract
With more than a hundred individual RNA and protein parts and a highly dynamic assembly and disassembly pathway, the spliceosome is arguably the most complicated macromolecular machine in the eukaryotic cell. This complexity has made kinetic and mechanistic analysis of splicing incredibly challenging. Yet, recent technological advances are now providing tools for understanding this process in much greater detail. Ranging from genome-wide analyses of splicing and creation of an orthogonal spliceosome in vivo, to purification of active spliceosomes and observation of single molecules in vitro, such new experimental approaches are yielding significant insight into the inner workings of this remarkable machine. These experiments are rewriting the textbooks, with a new picture emerging of a dynamic, malleable machine heavily influenced by the identity of its pre-mRNA substrate.
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Affiliation(s)
- Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA.
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434
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Abstract
Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent microscopy experiments have been able to monitor transcription from single genes in individual cells. These observations have revealed two striking features: transcriptional activity can vary markedly from one cell to another, and is subject to large changes over time, sometimes within minutes. How the chromatin structure, transcription machinery assembly and signalling networks generate such patterns is still unclear. In this review, we present the techniques used to investigate transcription from single genes, introduce quantitative modelling tools, and discuss transcription mechanisms and their implications for gene expression regulation.
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435
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Guo J, Ju J, Turro NJ. Fluorescent hybridization probes for nucleic acid detection. Anal Bioanal Chem 2012; 402:3115-25. [PMID: 22086400 PMCID: PMC6609299 DOI: 10.1007/s00216-011-5526-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/19/2011] [Indexed: 01/09/2023]
Abstract
Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.
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Affiliation(s)
- Jia Guo
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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436
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Transcription factories: genetic programming in three dimensions. Curr Opin Genet Dev 2012; 22:110-4. [PMID: 22365496 DOI: 10.1016/j.gde.2012.01.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 01/23/2012] [Indexed: 11/21/2022]
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437
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Palangat M, Larson DR. Complexity of RNA polymerase II elongation dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:667-72. [PMID: 22480952 DOI: 10.1016/j.bbagrm.2012.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 12/24/2022]
Abstract
Transcription of protein-coding genes by RNA polymerase II can be regulated at multiple points during the process of RNA synthesis, including initiation, elongation, and termination. In vivo data suggests that elongating polymerases exhibit heterogeneity throughout the gene body, suggestive of changes in elongation rate and/or pausing. Here, we review evidence from a variety of different experimental approaches for understanding regulation of transcription elongation. We compare steady-state measurements of nascent RNA density and polymerase occupancy to time-resolved measurements and point out areas of disagreement. Finally, we discuss future avenues of investigation for understanding this critically important step in gene regulation. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Murali Palangat
- Center for Cancer Research, National Cancer Institute, National Institues of Health, Bethesda, MD, USA
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438
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Trujillo C, Cooper MM, Klymkowsky MW. Using graph-based assessments within socratic tutorials to reveal and refine students' analytical thinking about molecular networks. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 40:100-107. [PMID: 22419590 DOI: 10.1002/bmb.20585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 11/10/2011] [Indexed: 05/31/2023]
Abstract
Biological systems, from the molecular to the ecological, involve dynamic interaction networks. To examine student thinking about networks we used graphical responses, since they are easier to evaluate for implied, but unarticulated assumptions. Senior college level molecular biology students were presented with simple molecular level scenarios; surprisingly, most students failed to articulate the basic assumptions needed to generate reasonable graphical representations; their graphs often contradicted their explicit assumptions. We then developed a tiered Socratic tutorial based on leading questions designed to provoke metacognitive reflection. The activity is characterized by leading questions (prompts) designed to provoke meta-cognitive reflection. When applied in a group or individual setting, there was clear improvement in targeted areas. Our results highlight the promise of using graphical responses and Socratic prompts in a tutorial context as both a formative assessment for students and an informative feedback system for instructors, in part because graphical responses are relatively easy to evaluate for implied, but unarticulated assumptions.
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Affiliation(s)
- Caleb Trujillo
- Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, Boulder, Colorado 80309, USA
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439
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Chalancon G, Ravarani CNJ, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM. Interplay between gene expression noise and regulatory network architecture. Trends Genet 2012; 28:221-32. [PMID: 22365642 DOI: 10.1016/j.tig.2012.01.006] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/23/2012] [Accepted: 01/26/2012] [Indexed: 01/24/2023]
Abstract
Complex regulatory networks orchestrate most cellular processes in biological systems. Genes in such networks are subject to expression noise, resulting in isogenic cell populations exhibiting cell-to-cell variation in protein levels. Increasing evidence suggests that cells have evolved regulatory strategies to limit, tolerate or amplify expression noise. In this context, fundamental questions arise: how can the architecture of gene regulatory networks generate, make use of or be constrained by expression noise? Here, we discuss the interplay between expression noise and gene regulatory network at different levels of organization, ranging from a single regulatory interaction to entire regulatory networks. We then consider how this interplay impacts a variety of phenomena, such as pathogenicity, disease, adaptation to changing environments, differential cell-fate outcome and incomplete or partial penetrance effects. Finally, we highlight recent technological developments that permit measurements at the single-cell level, and discuss directions for future research.
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Affiliation(s)
- Guilhem Chalancon
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK.
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440
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Abstract
RNA:DNA hybrids in the genome are constantly being generated as a by-product of transcription; in this issue, two papers, from Helmrich et al. (2011) and Wahba et al. (2011), provide insight into how RNA:DNA hybrids lead to genetic instability.
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Affiliation(s)
- Catherine J Potenski
- Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
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441
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Trcek T, Larson DR, Moldón A, Query CC, Singer RH. Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell 2012; 147:1484-97. [PMID: 22196726 DOI: 10.1016/j.cell.2011.11.051] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 07/27/2011] [Accepted: 11/22/2011] [Indexed: 12/29/2022]
Abstract
Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.
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Affiliation(s)
- Tatjana Trcek
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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442
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Normanno D, Dahan M, Darzacq X. Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:482-93. [PMID: 22342464 DOI: 10.1016/j.bbagrm.2012.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/26/2012] [Accepted: 02/03/2012] [Indexed: 12/26/2022]
Abstract
Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Davide Normanno
- Institut de Biologie de l'Ecole normale supérieure (IBENS), CNRS UMR 8197, Ecole normale supérieure, 46, Rue d'Ulm, 75005 Paris, France.
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443
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Golubev A. Genes at work in random bouts: stochastically discontinuous gene activity makes cell cycle duration and cell fate decisions variable, thus providing for stem cells plasticity. Bioessays 2012; 34:311-9. [PMID: 22323313 DOI: 10.1002/bies.201100119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell interdivision periods (IDP) in homogenous cell populations vary stochastically. Another aspect of probabilistic cell behavior is randomness in cell differentiation. These features are suggested to result from competing stochastic events of assembly/disassembly of the transcription pre-initiation complex (PIC) at gene promoters. The time needed to assemble a proper PIC from different proteins, which must be numerous enough to make their combination gene specific, may be comparable to the IDP. Nascent mRNA visualization at defined genes and inferences from protein level fluctuations in single cells suggest that some genes do operate in this way. The onset of mRNA production by such genes may miss the time windows provided by the cell cycle, resulting in cells differentiating into those in which the respective mRNAs are either present or absent. This creates a way to generate cell phenotype diversity in multicellular organisms.
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Affiliation(s)
- Alexey Golubev
- Research Institute for Experimental Medicine, Saint-Petersburg, Russia.
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444
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Shukla S, Oberdoerffer S. Co-transcriptional regulation of alternative pre-mRNA splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:673-83. [PMID: 22326677 DOI: 10.1016/j.bbagrm.2012.01.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 12/22/2022]
Abstract
While studies of alternative pre-mRNA splicing regulation have typically focused on RNA-binding proteins and their target sequences within nascent message, it is becoming increasingly evident that mRNA splicing, RNA polymerase II (pol II) elongation and chromatin structure are intricately intertwined. The majority of introns in higher eukaryotes are excised prior to transcript release in a manner that is dependent on transcription through pol II. As a result of co-transcriptional splicing, variations in pol II elongation influence alternative splicing patterns, wherein a slower elongation rate is associated with increased inclusion of alternative exons within mature mRNA. Physiological barriers to pol II elongation, such as repressive chromatin structure, can thereby similarly impact splicing decisions. Surprisingly, pre-mRNA splicing can reciprocally influence pol II elongation and chromatin structure. Here, we highlight recent advances in co-transcriptional splicing that reveal an extensive network of coupling between splicing, transcription and chromatin remodeling complexes. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Sanjeev Shukla
- Mouse Cancer Genetics Program, NCI- Frederick, NIH, Frederick, MD 21702, USA
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445
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Sood P, Johnston RJ, Kussell E. Stochastic de-repression of Rhodopsins in single photoreceptors of the fly retina. PLoS Comput Biol 2012; 8:e1002357. [PMID: 22319431 PMCID: PMC3271025 DOI: 10.1371/journal.pcbi.1002357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/05/2011] [Indexed: 11/18/2022] Open
Abstract
The photoreceptors of the Drosophila compound eye are a classical model for studying cell fate specification. Photoreceptors (PRs) are organized in bundles of eight cells with two major types – inner PRs involved in color vision and outer PRs involved in motion detection. In wild type flies, most PRs express a single type of Rhodopsin (Rh): inner PRs express either Rh3, Rh4, Rh5 or Rh6 and outer PRs express Rh1. In outer PRs, the K50 homeodomain protein Dve is a key repressor that acts to ensure exclusive Rh expression. Loss of Dve results in de-repression of Rhodopsins in outer PRs, and leads to a wide distribution of expression levels. To quantify these effects, we introduce an automated image analysis method to measure Rhodopsin levels at the single cell level in 3D confocal stacks. Our sensitive methodology reveals cell-specific differences in Rhodopsin distributions among the outer PRs, observed over a developmental time course. We show that Rhodopsin distributions are consistent with a two-state model of gene expression, in which cells can be in either high or basal states of Rhodopsin production. Our model identifies a significant role of post-transcriptional regulation in establishing the two distinct states. The timescale for interconversion between basal and high states is shown to be on the order of days. Our results indicate that even in the absence of Dve, the Rhodopsin regulatory network can maintain highly stable states. We propose that the role of Dve in outer PRs is to buffer against rare fluctuations in this network. Complex networks of genetic interactions govern the development of multicellular organisms. One of the best-characterized networks governs the development of the fruit-fly retina, a highly organized, three-dimensional organ composed of a hexagonal grid of eight types of photoreceptor neurons. Each photoreceptor responds to a particular wavelength of light depending on the Rhodopsin protein it expresses. We present novel computational methods to quantify cell-specific Rhodopsin levels from confocal microscopy images. We apply these methods to study the effect of the loss of a key repressor that ensures each photoreceptor expresses only one Rhodopsin. We show that this perturbation has cell-specific effects. Our measurement of the cell-type specific Rhodopsin distributions reveals differences between photoreceptor cells, which could not otherwise be detected. Using mathematical models of gene expression, we attribute this variability to stochastic events that activate Rhodopsin production.
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Affiliation(s)
- Pranidhi Sood
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Robert J. Johnston
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York, United States of America
| | - Edo Kussell
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Physics, New York University, New York, New York, United States of America
- * E-mail:
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446
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Trcek T, Chao JA, Larson DR, Park HY, Zenklusen D, Shenoy SM, Singer RH. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nat Protoc 2012; 7:408-19. [PMID: 22301778 DOI: 10.1038/nprot.2011.451] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d.
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Affiliation(s)
- Tatjana Trcek
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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447
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Bakstad D, Adamson A, Spiller DG, White MRH. Quantitative measurement of single cell dynamics. Curr Opin Biotechnol 2012; 23:103-9. [PMID: 22137453 DOI: 10.1016/j.copbio.2011.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 01/24/2023]
Abstract
Over the past 20 years luminescent and fluorescent imaging assays have been developed to report on the dynamics of transcription and protein translocation in single cells. The combination of these measurements with mathematical analysis is having an increasingly significant impact on cell biology. There is an urgent need to translate these assays to the study of cells and tissues in vivo, which requires new tools and technologies. Emergence of these new tools and techniques will further the understanding of the role of signalling and transcriptional dynamics in the generation of cellular heterogeneity and the control of cell fate.
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448
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Abstract
During transcription elongation, RNA polymerase II (Pol II) binds the general elongation factor Spt5. Spt5 contains a repetitive C-terminal region (CTR) that is required for cotranscriptional recruitment of the Paf1 complex (D. L. Lindstrom et al., Mol. Cell. Biol. 23:1368-1378, 2003; Z. Zhang, J. Fu, and D. S. Gilmour, Genes Dev. 19:1572-1580, 2005). Here we report a new role of the Spt5 CTR in the recruitment of 3' RNA-processing factors. Chromatin immunoprecipitation (ChIP) revealed that the Spt5 CTR is required for normal recruitment of pre-mRNA cleavage factor I (CFI) to the 3' ends of Saccharomyces cerevisiae genes. RNA contributes to CFI recruitment, as RNase treatment prior to ChIP further decreases CFI ChIP signals. Genome-wide ChIP profiling detected occupancy peaks of CFI subunits around 100 nucleotides downstream of the polyadenylation (pA) sites of genes. CFI recruitment to this defined region may result from simultaneous binding to the Spt5 CTR, to nascent RNA containing the pA sequence, and to the elongating Pol II isoform that is phosphorylated at serine 2 (S2) residues in its C-terminal domain (CTD). Consistent with this model, the CTR interacts with CFI in vitro but is not required for pA site recognition and transcription termination in vivo.
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449
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Nagatoishi S, Ono R, Sugimoto N. The yields of transcripts for a RNA polymerase regulated by hairpin structures in nascent RNAs. Chem Commun (Camb) 2012; 48:5121-3. [DOI: 10.1039/c2cc31657a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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450
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Reddy ASN, Day IS, Göhring J, Barta A. Localization and dynamics of nuclear speckles in plants. PLANT PHYSIOLOGY 2012; 158:67-77. [PMID: 22045923 PMCID: PMC3252098 DOI: 10.1104/pp.111.186700] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 10/31/2011] [Indexed: 05/17/2023]
Affiliation(s)
- Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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