1
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Szavits-Nossan J, Grima R. Uncovering the effect of RNA polymerase steric interactions on gene expression noise: Analytical distributions of nascent and mature RNA numbers. Phys Rev E 2023; 108:034405. [PMID: 37849194 DOI: 10.1103/physreve.108.034405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/24/2023] [Indexed: 10/19/2023]
Abstract
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of nascent RNA numbers. These solutions are routinely used for the analysis of single-cell data, including the inference of transcriptional parameters. However, these models neglect important mechanistic features of transcription elongation, such as the stochastic movement of RNA polymerases and their steric (excluded-volume) interactions. Here we construct a model of gene expression describing promoter switching between inactive and active states, binding of RNA polymerases in the active state, their stochastic movement including steric interactions along the gene, and their unbinding leading to a mature transcript that subsequently decays. We derive the steady-state distributions of the nascent and mature RNA numbers in two important limiting cases: constitutive expression and slow promoter switching. We show that RNA fluctuations are suppressed by steric interactions between RNA polymerases, and that this suppression can in some instances even lead to sub-Poissonian fluctuations; these effects are most pronounced for nascent RNA and less prominent for mature RNA, since the latter is not a direct sensor of transcription. We find a relationship between the parameters of our microscopic mechanistic model and those of the standard models that ensures excellent consistency in their prediction of the first and second RNA number moments over vast regions of parameter space, encompassing slow, intermediate, and rapid promoter switching, provided the RNA number distributions are Poissonian or super-Poissonian. Furthermore, we identify the limitations of inference from mature RNA data, specifically showing that it cannot differentiate between highly distinct RNA polymerase traffic patterns on a gene.
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Affiliation(s)
- Juraj Szavits-Nossan
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
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2
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Midha T, Mallory JD, Kolomeisky AB, Igoshin OA. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy. J Phys Chem Lett 2023; 14:3422-3429. [PMID: 37010247 DOI: 10.1021/acs.jpclett.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cleavage of dinucleotides after the misincorporational pauses serves as a proofreading mechanism that increases transcriptional elongation accuracy. The accuracy is further improved by accessory proteins such as GreA and TFIIS. However, it is not clear why RNAP pauses and why cleavage-factor-assisted proofreading is necessary despite transcriptional errors in vitro being of the same order as those in downstream translation. Here, we developed a chemical-kinetic model that incorporates most relevant features of transcriptional proofreading and uncovers how the balance between speed and accuracy is achieved. We found that long pauses are essential for high accuracy, whereas cleavage-factor-stimulated proofreading optimizes speed. Moreover, in comparison to the cleavage of a single nucleotide or three nucleotides, RNAP backtracking and dinucleotide cleavage improve both speed and accuracy. Our results thereby show how the molecular mechanism and the kinetic parameters of the transcriptional process were evolutionarily optimized to achieve maximal speed and tolerable accuracy.
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Affiliation(s)
- Tripti Midha
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
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3
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Qureshi B, Juritz J, Poulton JM, Beersing-Vasquez A, Ouldridge TE. A universal method for analyzing copolymer growth. J Chem Phys 2023; 158:104906. [PMID: 36922142 DOI: 10.1063/5.0133489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerization has been studied theoretically in a number of contexts, often by considering a Markov process in which monomers are added or removed from the growing tip of a long copolymer. To date, the analysis of the most general models of this class has necessitated simulation. We present a general method for analyzing such processes without resorting to simulation. Our method can be applied to models with an arbitrary network of sub-steps prior to addition or removal of a monomer, including non-equilibrium kinetic proofreading cycles. Moreover, the approach allows for a dependency of addition and removal reactions on the neighboring site in the copolymer and thermodynamically self-consistent models in which all steps are assumed to be microscopically reversible. Using our approach, thermodynamic quantities such as chemical work; kinetic quantities such as time taken to grow; and statistical quantities such as the distribution of monomer types in the growing copolymer can be directly derived either analytically or numerically from the model definition.
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Affiliation(s)
- Benjamin Qureshi
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | | | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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4
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [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: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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5
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Zuo X, Chou T. Density- and elongation speed-dependent error correction in RNA polymerization. Phys Biol 2021; 19. [PMID: 34937012 DOI: 10.1088/1478-3975/ac45e2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which usually happens when the polymerase tries to incorporate a noncognate or "mismatched" nucleotide triphosphate. Previous models have made simplifying assumptions such as neglecting the trailing polymerase behind the backtracking polymerase or assuming that the trailing polymerase is stationary. We derive exact analytic solutions of a stochastic model that includes locally interacting RNAPs by explicitly showing how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. We also provide two related methods for computing the mean times for error correction and incorporation given an initial local RNAP configuration. Using these results, we propose an effective interacting-RNAP lattice that can be readily simulated.
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Affiliation(s)
- Xinzhe Zuo
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
| | - Tom Chou
- Department of Mathematics, University of California - Los Angeles, Los Angeles, CA 90095-1555, USA, Los Angeles, California, 90095, UNITED STATES
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6
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Sahoo M, N A, Baral PR, Klumpp S. Accuracy and speed of elongation in a minimal model of DNA replication. Phys Rev E 2021; 104:034417. [PMID: 34654207 DOI: 10.1103/physreve.104.034417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022]
Abstract
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination of the polymerization and exonuclease activity of DNA polymerase. Here, we propose and analyze a minimal kinetic model of DNA replication and determine exact expressions for the velocity of elongation and the accuracy of replication. We first analyze the case without exonuclease activity. In that case, accuracy is determined by a kinetic competition between stepping and unbinding, with discrimination between correct and incorrect nucleotides in both transitions. We then include exonuclease activity and ask how different modes of additional discrimination in the exonuclease pathway can improve the accuracy while limiting the detrimental effect of exonuclease on the speed of replication. In this way, we ask how the kinetic parameters of the model have to be set to coordinate the two activities of the enzyme for high accuracy and high speed. The analysis also shows that the design of a replication system does not universally have to follow the speed-accuracy trade-off rule, although it does in the biologically realized parameter range. The accuracy of the process is mainly controlled by the crucial role of stepping after erroneous incorporation, which has impact on both polymerase and exonuclease activities of DNA polymerase.
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Affiliation(s)
- M Sahoo
- Department of Physics, University of Kerala, Kariavattom Campus 695581, India.,School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram-695551, India
| | - Arsha N
- Department of Physics, University of Kerala, Kariavattom Campus 695581, India
| | - P R Baral
- School of Physics, Indian Institute of Science Education and Research, Thiruvananthapuram-695551, India
| | - S Klumpp
- Institute for the Dynamics of Complex Systems, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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7
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Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size. Curr Biol 2020; 30:1217-1230.e7. [DOI: 10.1016/j.cub.2020.01.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/01/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
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8
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Iyer S, Le D, Park BR, Kim M. Distinct mechanisms coordinate transcription and translation under carbon and nitrogen starvation in Escherichia coli. Nat Microbiol 2018; 3:741-748. [PMID: 29760462 DOI: 10.1038/s41564-018-0161-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 04/16/2018] [Indexed: 11/09/2022]
Abstract
Bacteria adapt to environmental stress by producing proteins that provide stress protection. However, stress can severely perturb the kinetics of gene expression, disrupting protein production. Here, we characterized how Escherichia coli mitigates such perturbations under nutrient stress through the kinetic coordination of transcription and translation. We observed that, when translation became limiting under nitrogen starvation, transcription elongation slowed accordingly. This slowdown was mediated by (p)ppGpp, the alarmone whose primary role is thought to be promoter regulation. This kinetic coordination by (p)ppGpp was critical for the robust synthesis of gene products. Surprisingly, under carbon starvation, (p)ppGpp was dispensable for robust synthesis. Characterization of the underlying kinetics revealed that under carbon starvation, transcription became limiting, and translation aided transcription elongation. This mechanism naturally coordinated transcription with translation, alleviating the need for (p)ppGpp as a mediator. These contrasting mechanisms for coordination resulted in the condition-dependent effects of (p)ppGpp on global protein synthesis and starvation survival. Our findings reveal a kinetic aspect of gene expression plasticity, establishing (p)ppGpp as a condition-dependent global effector of gene expression.
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Affiliation(s)
- Sukanya Iyer
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Dai Le
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Bo Ryoung Park
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, USA. .,Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, USA. .,Emory Antibiotic Resistance Center, Emory University, Atlanta, GA, USA.
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9
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Mellenius H, Ehrenberg M. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Res 2017; 45:11582-11593. [PMID: 29036494 PMCID: PMC5714138 DOI: 10.1093/nar/gkx849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/10/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
We suggest a novel two-step proofreading mechanism with two sequential rounds of proofreading selection in mRNA transcription. It is based on the previous experimental observations that the proofreading RNA polymerase cleaves off transcript fragments of at least 2 nt and that transcript elongation after a nucleotide misincorporation is anomalously slow. Taking these results into account, we extend the description of the accuracy of template guided nucleotide selection beyond previous models of RNA polymerase-dependent DNA transcription. The model derives the accuracy of initial and proofreading base selection from experimentally estimated nearest-neighbor parameters. It is also used to estimate the small accuracy enhancement of polymerase revisiting of previous positions following transcript cleavage.
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Affiliation(s)
- Harriet Mellenius
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 752 37, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 752 37, Sweden
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10
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Heberling T, Davis L, Gedeon J, Morgan C, Gedeon T. A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases. PLoS Comput Biol 2016; 12:e1005069. [PMID: 27517607 PMCID: PMC4982667 DOI: 10.1371/journal.pcbi.1005069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/20/2016] [Indexed: 11/19/2022] Open
Abstract
In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.
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Affiliation(s)
- Tamra Heberling
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jakub Gedeon
- Computer Science Department, Montana State University, Bozeman, Montana, United States of America
| | - Charles Morgan
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
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11
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Roldán É, Lisica A, Sánchez-Taltavull D, Grill SW. Stochastic resetting in backtrack recovery by RNA polymerases. Phys Rev E 2016; 93:062411. [PMID: 27415302 DOI: 10.1103/physreve.93.062411] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/07/2022]
Abstract
Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random walk along the DNA template. Recovery of polymerases from the transcriptionally inactive backtracked state is determined by a kinetic competition between one-dimensional diffusion and RNA cleavage. Here we describe backtrack recovery as a continuous-time random walk, where the time for a polymerase to recover from a backtrack of a given depth is described as a first-passage time of a random walker to reach an absorbing state. We represent RNA cleavage as a stochastic resetting process and derive exact expressions for the recovery time distributions and mean recovery times from a given initial backtrack depth for both continuous and discrete-lattice descriptions of the random walk. We show that recovery time statistics do not depend on the discreteness of the DNA lattice when the rate of one-dimensional diffusion is large compared to the rate of cleavage.
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Affiliation(s)
- Édgar Roldán
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Center for Advancing Electronics Dresden, cfaed, Dresden, Germany.,GISC - Grupo Interdisciplinar de Sistemas Complejos, Madrid, Spain
| | - Ana Lisica
- BIOTEC, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | | | - Stephan W Grill
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,BIOTEC, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
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12
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Abstract
During DNA transcription, RNA polymerases often adopt inactive backtracked states. Recovery from backtracks can occur by 1D diffusion or cleavage of backtracked RNA, but how polymerases make this choice is unknown. Here, we use single-molecule optical tweezers experiments and stochastic theory to show that the choice of a backtrack recovery mechanism is determined by a kinetic competition between 1D diffusion and RNA cleavage. Notably, RNA polymerase I (Pol I) and Pol II recover from shallow backtracks by 1D diffusion, use RNA cleavage to recover from intermediary depths, and are unable to recover from extensive backtracks. Furthermore, Pol I and Pol II use distinct mechanisms to avoid nonrecoverable backtracking. Pol I is protected by its subunit A12.2, which decreases the rate of 1D diffusion and enables transcript cleavage up to 20 nt. In contrast, Pol II is fully protected through association with the cleavage stimulatory factor TFIIS, which enables rapid recovery from any depth by RNA cleavage. Taken together, we identify distinct backtrack recovery strategies of Pol I and Pol II, shedding light on the evolution of cellular functions of these key enzymes.
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13
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Wang J, Pfeuty B, Thommen Q, Romano MC, Lefranc M. Minimal model of transcriptional elongation processes with pauses. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:050701. [PMID: 25493724 DOI: 10.1103/physreve.90.050701] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 06/04/2023]
Abstract
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of nonequilibrium statistical physics, the totally asymmetric exclusion principle (TASEP). This model describes particles hopping between sites of a one-dimensional lattice, with the particle current determining the transcription or translation rate. An open problem is how to analyze a TASEP where particles can pause randomly, as has been observed during transcription. In this work, we report that surprisingly, a simple mean-field model predicts well the particle current for all values of the average pause duration, using a simple description of blocking behind paused particles.
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Affiliation(s)
- Jingkui Wang
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - Benjamin Pfeuty
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - Quentin Thommen
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - M Carmen Romano
- SUPA, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom and Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Marc Lefranc
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
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14
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Abstract
Nucleotide excision repair (NER) is a key component of the DNA damage response (DDR) and it is essential to safeguard genome integrity against genotoxic insults. The regulation of NER is primarily mediated by protein post-translational modifications (PTMs). The NER machinery removes a wide spectrum of DNA helix distorting lesions, including those induced by solar radiation, through two sub-pathways: global genome nucleotide excision repair (GG-NER) and transcription coupled nucleotide excision repair (TC-NER). Severe clinical consequences associated with inherited NER defects, including premature ageing, neurodegeneration and extreme cancer-susceptibility, underscore the biological relevance of NER. In the last two decades most of the core NER machinery has been elaborately described, shifting attention to molecular mechanisms that either facilitate NER in the context of chromatin or promote the timely and accurate interplay between NER factors and various post-translational modifications. In this review, we summarize and discuss the latest findings in NER. In particular, we focus on emerging factors and novel molecular mechanisms by which NER is regulated.
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