1
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Wang L. RNA polymerase collisions and their role in transcription. Transcription 2024; 15:38-47. [PMID: 38357902 DOI: 10.1080/21541264.2024.2316972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
RNA polymerases are the central enzymes of gene expression and function frequently in either a head-on or co-directional manner on the busy DNA track. Whether and how these collisions between RNA polymerases contribute to transcriptional regulation is mysterious. Increasing evidence from biochemical and single-molecule studies suggests that RNA polymerase collisions function as an important regulator to fine-tune transcription, rather than creating deleterious "traffic jams". This review summarizes the recent progress on elucidating the consequences of RNA polymerase collisions during transcription and highlights the significance of cooperation and coordination between RNA polymerases.
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Affiliation(s)
- Ling Wang
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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2
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Hao N, Donnelly AJ, Dodd IB, Shearwin KE. When push comes to shove - RNA polymerase and DNA-bound protein roadblocks. Biophys Rev 2023; 15:355-366. [PMID: 37396453 PMCID: PMC10310618 DOI: 10.1007/s12551-023-01064-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Alana J. Donnelly
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
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3
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Kujirai T, Ehara H, Sekine SI, Kurumizaka H. Structural Transition of the Nucleosome during Transcription Elongation. Cells 2023; 12:1388. [PMID: 37408222 DOI: 10.3390/cells12101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
In eukaryotes, genomic DNA is tightly wrapped in chromatin. The nucleosome is a basic unit of chromatin, but acts as a barrier to transcription. To overcome this impediment, the RNA polymerase II elongation complex disassembles the nucleosome during transcription elongation. After the RNA polymerase II passage, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly. Nucleosome disassembly-reassembly processes play a central role in preserving epigenetic information, thus ensuring transcriptional fidelity. The histone chaperone FACT performs key functions in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies of transcribing RNA polymerase II complexed with nucleosomes have provided structural insights into transcription elongation on chromatin. Here, we review the structural transitions of the nucleosome during transcription.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-Ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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4
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Wang L, Watters JW, Ju X, Lu G, Liu S. Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. Mol Cell 2023; 83:1153-1164.e4. [PMID: 36917983 PMCID: PMC10081963 DOI: 10.1016/j.molcel.2023.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/03/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Genomic DNA is a crowded track where motor proteins frequently collide. It remains underexplored whether these collisions carry physiological function. In this work, we develop a single-molecule assay to visualize the trafficking of individual E. coli RNA polymerases (RNAPs) on DNA. Based on transcriptomic data, we hypothesize that RNAP collisions drive bidirectional transcription termination of convergent gene pairs. Single-molecule results show that the head-on collision between two converging RNAPs is necessary to prevent transcriptional readthrough but insufficient to release the RNAPs from the DNA. Remarkably, co-directional collision of a trailing RNAP into the head-on collided complex dramatically increases the termination efficiency. Furthermore, stem-loop structures formed in the nascent RNA are required for collisions to occur at well-defined positions between convergent genes. These findings suggest that physical collisions between RNAPs furnish a mechanism for transcription termination and that programmed genomic conflicts can be exploited to co-regulate the expression of multiple genes.
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Affiliation(s)
- Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
| | - John W Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Xiangwu Ju
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Genzhe Lu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
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5
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Hall PM, Inman JT, Fulbright RM, Le TT, Brewer JJ, Lambert G, Darst SA, Wang MD. Polarity of the CRISPR roadblock to transcription. Nat Struct Mol Biol 2022; 29:1217-1227. [PMID: 36471058 PMCID: PMC9758054 DOI: 10.1038/s41594-022-00864-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/12/2022] [Indexed: 12/12/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) utility relies on a stable Cas effector complex binding to its target site. However, a Cas complex bound to DNA may be removed by motor proteins carrying out host processes and the mechanism governing this removal remains unclear. Intriguingly, during CRISPR interference, RNA polymerase (RNAP) progression is only fully blocked by a bound endonuclease-deficient Cas (dCas) from the protospacer adjacent motif (PAM)-proximal side. By mapping dCas-DNA interactions at high resolution, we discovered that the collapse of the dCas R-loop allows Escherichia coli RNAP read-through from the PAM-distal side for both Sp-dCas9 and As-dCas12a. This finding is not unique to RNAP and holds for the Mfd translocase. This mechanistic understanding allowed us to modulate the dCas R-loop stability by modifying the guide RNAs. This work highlights the importance of the R-loop in dCas-binding stability and provides valuable mechanistic insights for broad applications of CRISPR technology.
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Affiliation(s)
- Porter M Hall
- Biophysics Program, Cornell University, Ithaca, NY, USA
| | - James T Inman
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Robert M Fulbright
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
| | - Tung T Le
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Joshua J Brewer
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Guillaume Lambert
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA.
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.
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6
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RNase HI Depletion Strongly Potentiates Cell Killing by Rifampicin in Mycobacteria. Antimicrob Agents Chemother 2022; 66:e0209121. [PMID: 36154174 DOI: 10.1128/aac.02091-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant (MDR) tuberculosis (TB) is defined by the resistance of Mycobacterium tuberculosis, the causative organism, to the first-line antibiotics rifampicin and isoniazid. Mitigating or reversing resistance to these drugs offers a means of preserving and extending their use in TB treatment. R-loops are RNA/DNA hybrids that are formed in the genome during transcription, and they can be lethal to the cell if not resolved. RNase HI is an enzyme that removes R-loops, and this activity is essential in M. tuberculosis: knockouts of rnhC, the gene encoding RNase HI, are nonviable. This essentiality makes it a candidate target for the development of new antibiotics. In the model organism Mycolicibacterium smegmatis, RNase HI activity is provided by two enzymes, RnhA and RnhC. We show that the partial depletion of RNase HI activity in M. smegmatis, by knocking out either of the genes encoding RnhA or RnhC, led to the accumulation of R-loops. The sensitivity of the knockout strains to the antibiotics moxifloxacin, streptomycin, and rifampicin was increased, the latter by a striking near 100-fold. We also show that R-loop accumulation accompanies partial transcriptional inhibition, suggesting a mechanistic basis for the synergy between RNase HI depletion and rifampicin. A model of how transcriptional inhibition can potentiate R-loop accumulation is presented. Finally, we identified four small molecules that inhibit recombinant RnhC activity and that also potentiated rifampicin activity in whole-cell assays against M. tuberculosis, supporting an on-target mode of action and providing the first step in developing a new class of antimycobacterial drug.
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7
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Kor R, Mohammad-Rafiee F. Theoretical study of RNA-polymerase behavior considering the backtracking state. SOFT MATTER 2022; 18:5979-5988. [PMID: 35920142 DOI: 10.1039/d2sm00232a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The dynamical behavior of the RNA polymerase in the transcription process is vital to gene expression. During the transcription process, the 3' end of the transcribed RNA can be dislocated from the active site of the enzyme and as a result, the RNA polymerase goes to the backtracked state. Here, we develop a theoretical model to study the transcription process considering the backtracking state. We aim at describing the behavior of the enzyme in the backtracking state in the presence of an external force, which leads to two possibilities: (i) rescuing from the backtracking state and, (ii) the arresting of the enzyme. We study the probability and the rate of the mentioned processes. In addition, we find that entering the backtracking state behaves like the Brownian ratchet mechanism. This model could shed some light on the modeling of the transcription process and further studies on the energy landscape of the backtracking channel and the gene regulation.
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Affiliation(s)
- Razieh Kor
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
| | - Farshid Mohammad-Rafiee
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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8
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Lu Y, Voros Z, Borjas G, Hendrickson C, Shearwin K, Dunlap D, Finzi L. RNA polymerase efficiently transcribes DNA-scaffolded, cooperative bacteriophage repressor complexes. FEBS Lett 2022; 596:1994-2006. [PMID: 35819073 PMCID: PMC9491066 DOI: 10.1002/1873-3468.14447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/07/2022]
Abstract
DNA can act as a scaffold for the cooperative binding of protein oligomers. For example, the phage 186 CI repressor forms a wheel of seven dimers wrapped in DNA with specific binding sites, while phage λ CI repressor dimers bind to two well-separated sets of operators, forming a DNA loop. Atomic force microscopy was used to measure transcription elongation by E. coli RNA polymerase through these protein complexes. 186 CI, or λ CI, bound along unlooped DNA negligibly interfered with transcription by RNAP. Wrapped and looped topologies induced by these scaffolded, cooperatively bound repressor oligomers did not form significantly better roadblocks to transcription. Thus, despite binding with high affinity, these repressors are not effective roadblocks to transcription.
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Affiliation(s)
- Yue Lu
- Physics Department, Emory University, Atlanta, GA, USA
| | | | | | | | - Keith Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
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9
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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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10
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Chatterjee P, Goldenfeld N, Kim S. DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis. PHYSICAL REVIEW LETTERS 2021; 127:218101. [PMID: 34860091 PMCID: PMC9034659 DOI: 10.1103/physrevlett.127.218101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/18/2021] [Indexed: 05/20/2023]
Abstract
Transcription of genes can be affected by both biochemical and mechanical factors. Recent experiments suggested that the mechanical stress associated with transcription-induced DNA supercoiling is responsible for the transition from cooperative to antagonistic group dynamics of RNA polymerases (RNAPs) upon promoter repression. To underpin the mechanism behind this drastic transition, we developed a continuum deterministic model for transcription under torsion. In our model, the speed of an RNAP is affected by the local DNA supercoiling, as well as two global factors: (i) the number of RNAPs on the gene affecting the torsional stress experienced by individual RNAPs and (ii) transcription factors blocking the diffusion of DNA supercoils. Our minimal model can successfully reproduce the experimental findings and helps elucidate the interplay of mechanical and biological factors in the collective dynamics of molecular machines involved in gene expression.
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11
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Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways. DNA Repair (Amst) 2021; 108:103229. [PMID: 34601381 DOI: 10.1016/j.dnarep.2021.103229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
Helicases involved in genomic maintenance are a class of nucleic-acid dependent ATPases that convert the energy of ATP hydrolysis into physical work to execute irreversible steps in DNA replication, repair, and recombination. Prokaryotic helicases provide simple models to understand broadly conserved molecular mechanisms involved in manipulating nucleic acids during genome maintenance. Our understanding of the catalytic properties, mechanisms of regulation, and roles of prokaryotic helicases in DNA metabolism has been assembled through a combination of genetic, biochemical, and structural methods, further refined by single-molecule approaches. Together, these investigations have constructed a framework for understanding the mechanisms that maintain genomic integrity in cells. This review discusses recent single-molecule insights into molecular mechanisms of prokaryotic helicases and translocases.
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12
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Qian J, Xu W, Dunlap D, Finzi L. Single-molecule insights into torsion and roadblocks in bacterial transcript elongation. Transcription 2021; 12:219-231. [PMID: 34719335 PMCID: PMC8632135 DOI: 10.1080/21541264.2021.1997315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
During transcription, RNA polymerase (RNAP) translocates along the helical template DNA while maintaining high transcriptional fidelity. However, all genomes are dynamically twisted, writhed, and decorated by bound proteins and motor enzymes. In prokaryotes, proteins bound to DNA, specifically or not, frequently compact DNA into conformations that may silence genes by obstructing RNAP. Collision of RNAPs with these architectural proteins, may result in RNAP stalling and/or displacement of the protein roadblock. It is important to understand how rapidly transcribing RNAPs operate under different levels of supercoiling or in the presence of roadblocks. Given the broad range of asynchronous dynamics exhibited by transcriptional complexes, single-molecule assays, such as atomic force microscopy, fluorescence detection, optical and magnetic tweezers, etc. are well suited for detecting and quantifying activity with adequate spatial and temporal resolution. Here, we summarize current understanding of the effects of torsion and roadblocks on prokaryotic transcription, with a focus on single-molecule assays that provide real-time detection and readout.
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Affiliation(s)
- Jin Qian
- Emory University, Atlanta, GA, USA
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13
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Gamarra N, Narlikar GJ. Collaboration through chromatin: motors of transcription and chromatin structure. J Mol Biol 2021; 433:166876. [PMID: 33556407 PMCID: PMC8989640 DOI: 10.1016/j.jmb.2021.166876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Packaging of the eukaryotic genome into chromatin places fundamental physical constraints on transcription. Clarifying how transcription operates within these constraints is essential to understand how eukaryotic gene expression programs are established and maintained. Here we review what is known about the mechanisms of transcription on chromatin templates. Current models indicate that transcription through chromatin is accomplished by the combination of an inherent nucleosome disrupting activity of RNA polymerase and the action of ATP-dependent chromatin remodeling motors. Collaboration between these two types of molecular motors is proposed to occur at all stages of transcription through diverse mechanisms. Further investigation of how these two motors combine their basic activities is essential to clarify the interdependent relationship between genome structure and transcription.
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Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; TETRAD Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
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14
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Bustamante CJ, Chemla YR, Liu S, Wang MD. Optical tweezers in single-molecule biophysics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:25. [PMID: 34849486 PMCID: PMC8629167 DOI: 10.1038/s43586-021-00021-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.
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Affiliation(s)
- Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
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15
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Huynh MT, Yadav SP, Reese JC, Lee TH. Nucleosome Dynamics during Transcription Elongation. ACS Chem Biol 2020; 15:3133-3142. [PMID: 33263994 DOI: 10.1021/acschembio.0c00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nucleosome is the basic packing unit of the eukaryotic genome. Dynamic interactions between DNA and histones in the nucleosome are the molecular basis of gene accessibility regulation that governs the kinetics of various DNA-templated processes such as transcription elongation by RNA Polymerase II (Pol II). On the basis of single-molecule FRET measurements with chemically modified histones, we investigated the nucleosome dynamics during transcription elongation and how it is affected by histone acetylation at H3 K56 and the histone chaperone Nap1, both of which can affect DNA-histone interactions. We observed that H3K56 acetylation dramatically shortens the pause duration of Pol II near the entry region of the nucleosome, while Nap1 induces no noticeable difference. We also found that the elongation rate of Pol II through the nucleosome is unaffected by the acetylation or Nap1. These results indicate that H3K56 acetylation facilitates Pol II translocation through the nucleosome by assisting paused Pol II to resume and that Nap1 does not affect Pol II progression. Following transcription, only a small fraction of nucleosomes remain intact, which is unaffected by H3K56 acetylation or Nap1. These results suggest that (i) spontaneous nucleosome opening enables Pol II progression, (ii) Pol II mediates nucleosome reassembly very inefficiently, and (iii) Nap1 in the absence of other factors does not promote nucleosome disassembly or reassembly during transcription.
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16
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Bendandi A, Patelli AS, Diaspro A, Rocchia W. The role of histone tails in nucleosome stability: An electrostatic perspective. Comput Struct Biotechnol J 2020; 18:2799-2809. [PMID: 33133421 PMCID: PMC7575852 DOI: 10.1016/j.csbj.2020.09.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/20/2023] Open
Abstract
We propose a methodology for the study of protein-DNA electrostatic interactions and apply it to clarify the effect of histone tails in nucleosomes. This method can be used to correlate electrostatic interactions to structural and functional features of protein-DNA systems, and can be combined with coarse-grained representations. In particular, we focus on the electrostatic field and resulting forces acting on the DNA. We investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilization upon histone tail truncation, and the role of specific arginines and lysines undergoing Post-Translational Modifications. We find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. Small conformational variations in the often overlooked H2A C-terminal tails had significant electrostatic repercussions near the DNA entry and exit sites. The H2A N-terminal tail exerts attractive electrostatic forces towards the histone core in positions where Polymerase II halts its progress. We validate our results with comparisons to previous experimental and computational observations.
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Affiliation(s)
- Artemi Bendandi
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Alessandro S Patelli
- LCVMM, Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Alberto Diaspro
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Walter Rocchia
- Concept Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
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17
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Kim S, Beltran B, Irnov I, Jacobs-Wagner C. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling. Cell 2020; 179:106-119.e16. [PMID: 31539491 DOI: 10.1016/j.cell.2019.08.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
| | - Bruno Beltran
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
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18
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Cardiello JF, Sanchez GJ, Allen MA, Dowell RD. Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. Transcription 2019; 11:3-18. [PMID: 31856658 DOI: 10.1080/21541264.2019.1704128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nascent transcription assays, such as global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), have uncovered a myriad of unstable RNAs being actively produced from numerous sites genome-wide. These transcripts provide a more complete and immediate picture of the impact of regulatory events. Transcription factors recruit RNA polymerase II, effectively initiating the process of transcription; repressors inhibit polymerase recruitment. Efficiency of recruitment is dictated by sequence elements in and around the RNA polymerase loading zone. A combination of sequence elements and RNA binding proteins subsequently influence the ultimate stability of the resulting transcript. Some of these transcripts are capable of providing feedback on the process, influencing subsequent transcription. By monitoring RNA polymerase activity, nascent assays provide insights into every step of the regulated process of transcription.
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Affiliation(s)
| | - Gilson J Sanchez
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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19
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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20
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Singh AK, Jaiswal A, Kodgire P. AID preferentially targets the top strand in nucleosome sequences. Mol Immunol 2019; 112:198-205. [DOI: 10.1016/j.molimm.2019.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/29/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
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21
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The base pair-scale diffusion of nucleosomes modulates binding of transcription factors. Proc Natl Acad Sci U S A 2019; 116:12161-12166. [PMID: 31147470 DOI: 10.1073/pnas.1815424116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The structure of promoter chromatin determines the ability of transcription factors (TFs) to bind to DNA and therefore has a profound effect on the expression levels of genes. However, the role of spontaneous nucleosome movements in this process is not fully understood. Here, we developed a single-molecule optical tweezers assay capable of simultaneously characterizing the base pair-scale diffusion of a nucleosome on DNA and the binding of a TF, using the luteinizing hormone β subunit gene (Lhb) promoter and Egr-1 as a model system. Our results demonstrate that nucleosomes undergo confined diffusion, and that the incorporation of the histone variant H2A.Z serves to partially relieve this confinement, inducing a different type of nucleosome repositioning. The increase in diffusion leads to exposure of a TF's binding site and facilitates its association with the DNA, which, in turn, biases the subsequent movement of the nucleosome. Our findings suggest the use of mobile nucleosomes as a general transcriptional regulatory mechanism.
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22
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Belitsky V, Schütz G. RNA Polymerase interactions and elongation rate. J Theor Biol 2019; 462:370-380. [DOI: 10.1016/j.jtbi.2018.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
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23
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Zananiri R, Malik O, Rudnizky S, Gaydar V, Kreiserman R, Henn A, Kaplan A. Synergy between RecBCD subunits is essential for efficient DNA unwinding. eLife 2019; 8:e40836. [PMID: 30601118 PMCID: PMC6338465 DOI: 10.7554/elife.40836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/01/2019] [Indexed: 12/12/2022] Open
Abstract
The subunits of the bacterial RecBCD act in coordination, rapidly and processively unwinding DNA at the site of a double strand break. RecBCD is able to displace DNA-binding proteins, suggesting that it generates high forces, but the specific role of each subunit in the force generation is unclear. Here, we present a novel optical tweezers assay that allows monitoring the activity of RecBCD's individual subunits, when they are part of an intact full complex. We show that RecBCD and its subunits are able to generate forces up to 25-40 pN without a significant effect on their velocity. Moreover, the isolated RecD translocates fast but is a weak helicase with limited processivity. Experiments at a broad range of [ATP] and forces suggest that RecD unwinds DNA as a Brownian ratchet, rectified by ATP binding, and that the presence of the other subunits shifts the ratchet equilibrium towards the post-translocation state.
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Affiliation(s)
- Rani Zananiri
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Omri Malik
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Russell Berrie Nanotechnology InstituteTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Sergei Rudnizky
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Vera Gaydar
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Roman Kreiserman
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Faculty of PhysicsTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Arnon Henn
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Ariel Kaplan
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
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24
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Belitsky V, Schütz GM. Stationary RNA polymerase fluctuations during transcription elongation. Phys Rev E 2019; 99:012405. [PMID: 30780341 DOI: 10.1103/physreve.99.012405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Indexed: 06/09/2023]
Abstract
We study fluctuation effects of nonsteric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track during transcription elongation. Based on a stochastic model that allows for the exact analytical computation of the stationary distribution of RNAPs as a function of their density, interaction strength, nucleoside triphosphate concentration, and rate of pyrophosphate release we predict an almost geometric headway distribution of subsequent RNAP transcribing on the same DNA segment. The localization length which characterizes the decay of the headway distribution depends directly only the average density of RNAP and the interaction strength, but not on specific single-RNAP properties. Density correlations are predicted to decay exponentially with the distance (in units of DNA base pairs), with a correlation length that is significantly shorter than the localization length.
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Affiliation(s)
- V Belitsky
- Instituto de Matemática e Estátistica, Universidade de São Paulo, Rua do Matão, 1010, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - G M Schütz
- Institute of Complex Systems II, Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, 52425 Jülich, Germany
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25
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Le TT, Wang MD. Molecular Highways—Navigating Collisions of DNA Motor Proteins. J Mol Biol 2018; 430:4513-4524. [DOI: 10.1016/j.jmb.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023]
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26
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The interaction landscape between transcription factors and the nucleosome. Nature 2018; 562:76-81. [PMID: 30250250 PMCID: PMC6173309 DOI: 10.1038/s41586-018-0549-5] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 08/06/2018] [Indexed: 01/01/2023]
Abstract
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.
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27
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Ide H, Nakano T, Salem AMH, Shoulkamy MI. DNA-protein cross-links: Formidable challenges to maintaining genome integrity. DNA Repair (Amst) 2018; 71:190-197. [PMID: 30177436 DOI: 10.1016/j.dnarep.2018.08.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DNA is associated with proteins that are involved in its folding and transaction processes. When cells are exposed to chemical cross-linking agents or free radical-generating ionizing radiation, DNA-associated proteins are covalently trapped within the DNA to produce DNA-protein cross-links (DPCs). DPCs produced by these agents contain cross-linked proteins in an undisrupted DNA strand. Some DNA-metabolizing enzymes that form covalent reaction intermediates can also be irreversibly trapped in the presence of inhibitors or DNA damage to give rise to abortive DPCs. The abortive DPCs often contain cross-linked proteins attached to the 5' or 3' end of a DNA strand break. In vitro studies show that steric hindrance caused by cross-linked proteins impedes the progression of DNA helicases and polymerases and of RNA polymerases. The modes and consequences by which DPCs impede replication and transcription processes are considerably different from those with conventional DNA lesions. Thus, DPCs are formidable challenges to maintaining genome integrity and faithful gene expression. Current models of DPC repair involve direct and indirect removal of DPCs. The direct mechanism works for DPCs that contain topoisomerase 2 attached to the 5' end of DNA. The Mre11-Rad50-Nbs1 complex cleaves the site internal to the DPC and directly releases a DPC-containing oligonucleotide. The indirect mechanism involves degradation of cross-linked proteins by proteasomes or the recently identified DPC proteases Wss1 and Sprtn to relieve steric hindrance of DPCs. The resulting peptide-cross-links might be processed by translesion synthesis or other canonical repair mechanisms: however, the exact mechanism remains to be elucidated.
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Affiliation(s)
- Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Amir M H Salem
- Department of Pathology, Medical Research Division, National Research Centre, El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Mahmoud I Shoulkamy
- Department of Zoology, Biological Science Building, Faculty of Science, Minia University, Minia 61519, Egypt
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28
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Helicase promotes replication re-initiation from an RNA transcript. Nat Commun 2018; 9:2306. [PMID: 29899338 PMCID: PMC5997990 DOI: 10.1038/s41467-018-04702-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/30/2018] [Indexed: 11/12/2022] Open
Abstract
To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances, the associated DNAP also moves forward. The presence of the DNAP increases both helicase’s processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicase’s novel role in replication re-initiation. During DNA replication, replicative helicases play an essential role for DNA unwinding to occur. Here the authors find that bacteriophage T7 helicase is also involved in replication re-initiation by interacting with a non-replicating DNAP and increasing unwinding rate.
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29
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Bameta T, Das D, Padinhateeri R. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer. Nucleic Acids Res 2018; 46:4991-5000. [PMID: 29850895 PMCID: PMC6007630 DOI: 10.1093/nar/gky207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/09/2018] [Indexed: 01/09/2023] Open
Abstract
Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich ‘phase diagram’ having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.
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Affiliation(s)
- Tripti Bameta
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
- To whom correspondence should be addressed. Tel: +91 22 25767761; Fax: +91 22 25767760; . Correspondence may also be addressed to Tripti Bameta.
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- To whom correspondence should be addressed. Tel: +91 22 25767761; Fax: +91 22 25767760; . Correspondence may also be addressed to Tripti Bameta.
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30
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Abstract
Optical tweezers are flexible and powerful single-molecule tools that have been extensively utilized in biophysical studies. With their ability to stretch and twist DNA, and measure its force and torque simultaneously, they provide excellent opportunities to gain novel insights into the function of protein motors and protein-DNA interactions. Recently, a novel DNA supercoiling assay using an angular optical tweezers (AOT) has been developed to investigate torque generation during transcription. Here, we provide a detailed and practical guide to performing this technique. Using bacterial RNA polymerase (RNAP) as an example, we present protocols for constructing and calibrating an AOT instrument, preparing DNA templates, and acquiring and analyzing real-time data for transcription under DNA supercoiling. While these protocols were initially developed with E. coli RNAP, they can be readily adapted to study other DNA-based motor proteins.
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31
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Le TT, Yang Y, Tan C, Suhanovsky MM, Fulbright RM, Inman JT, Li M, Lee J, Perelman S, Roberts JW, Deaconescu AM, Wang MD. Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism. Cell 2017; 172:344-357.e15. [PMID: 29224782 DOI: 10.1016/j.cell.2017.11.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/21/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022]
Abstract
The bacterial Mfd ATPase is increasingly recognized as a general transcription factor that participates in the resolution of transcription conflicts with other processes/roadblocks. This function stems from Mfd's ability to preferentially act on stalled RNA polymerases (RNAPs). However, the mechanism underlying this preference and the subsequent coordination between Mfd and RNAP have remained elusive. Here, using a novel real-time translocase assay, we unexpectedly discovered that Mfd translocates autonomously on DNA. The speed and processivity of Mfd dictate a "release and catch-up" mechanism to efficiently patrol DNA for frequently stalled RNAPs. Furthermore, we showed that Mfd prevents RNAP backtracking or rescues a severely backtracked RNAP, allowing RNAP to overcome stronger obstacles. However, if an obstacle's resistance is excessive, Mfd dissociates the RNAP, clearing the DNA for other processes. These findings demonstrate a remarkably delicate coordination between Mfd and RNAP, allowing efficient targeting and recycling of Mfd and expedient conflict resolution.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Yi Yang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Chuang Tan
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Margaret M Suhanovsky
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | | | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ming Li
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Sarah Perelman
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexandra M Deaconescu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
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32
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van den Berg AA, Depken M. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes. Nucleic Acids Res 2017; 45:7623-7632. [PMID: 28586463 PMCID: PMC5737439 DOI: 10.1093/nar/gkx513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/03/2017] [Indexed: 12/20/2022] Open
Abstract
During eukaryotic transcription, RNA polymerase (RNAP) translocates along DNA molecules covered with nucleosomes and other DNA binding proteins. Though the interactions between a single nucleosome and RNAP are by now fairly well understood, this understanding has not been synthesized into a description of transcription on crowded genes, where multiple RNAP transcribe through nucleosomes while preserving the nucleosome coverage. We here take a deductive modeling approach to establish the consequences of RNAP–nucleosome interactions for transcription in crowded environments. We show that under physiologically crowded conditions, the interactions of RNAP with nucleosomes induce a strong kinetic attraction between RNAP molecules, causing them to self-organize into stable and moving pelotons. The peloton formation quantitatively explains the observed nucleosome and RNAP depletion close to the initiation site on heavily transcribed genes. Pelotons further translate into short-timescale transcriptional bursts at termination, resulting in burst characteristics consistent with instances of bursty transcription observed in vivo. To facilitate experimental testing of our proposed mechanism, we present several analytic relations that make testable quantitative predictions.
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Affiliation(s)
- Aafke A van den Berg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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33
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Single molecule high-throughput footprinting of small and large DNA ligands. Nat Commun 2017; 8:304. [PMID: 28824174 PMCID: PMC5563512 DOI: 10.1038/s41467-017-00379-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 06/20/2017] [Indexed: 02/04/2023] Open
Abstract
Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation. Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.
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34
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Vörös Z, Yan Y, Kovari DT, Finzi L, Dunlap D. Proteins mediating DNA loops effectively block transcription. Protein Sci 2017; 26:1427-1438. [PMID: 28295806 PMCID: PMC5477534 DOI: 10.1002/pro.3156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
Abstract
Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop‐mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.
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Affiliation(s)
- Zsuzsanna Vörös
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Yan Yan
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Daniel T Kovari
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, Georgia, 30322
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35
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Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV. Partially Assembled Nucleosome Structures at Atomic Detail. Biophys J 2016; 112:460-472. [PMID: 28038734 DOI: 10.1016/j.bpj.2016.10.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/06/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022] Open
Abstract
The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.
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Affiliation(s)
- Georgy N Rychkov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Igor B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey V Shvetsov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Applied Mathematics and Mechanics, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Dmitry V Lebedev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexander Y Konev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Vladimir V Isaev-Ivanov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Tech, Blacksburg, Virginia.
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36
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Brennan LD, Forties RA, Patel SS, Wang MD. DNA looping mediates nucleosome transfer. Nat Commun 2016; 7:13337. [PMID: 27808093 PMCID: PMC5097161 DOI: 10.1038/ncomms13337] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023] Open
Abstract
Proper cell function requires preservation of the spatial organization of chromatin modifications. Maintenance of this epigenetic landscape necessitates the transfer of parental nucleosomes to newly replicated DNA, a process that is stringently regulated and intrinsically linked to replication fork dynamics. This creates a formidable setting from which to isolate the central mechanism of transfer. Here we utilized a minimal experimental system to track the fate of a single nucleosome following its displacement, and examined whether DNA mechanics itself, in the absence of any chaperones or assembly factors, may serve as a platform for the transfer process. We found that the nucleosome is passively transferred to available dsDNA as predicted by a simple physical model of DNA loop formation. These results demonstrate a fundamental role for DNA mechanics in mediating nucleosome transfer and preserving epigenetic integrity during replication.
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Affiliation(s)
- Lucy D Brennan
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Robert A Forties
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Michelle D Wang
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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37
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Sun B, Wang MD. Single-Molecule Optical-Trapping Techniques to Study Molecular Mechanisms of a Replisome. Methods Enzymol 2016; 582:55-84. [PMID: 28062045 DOI: 10.1016/bs.mie.2016.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The replisome is a multiprotein molecular machinery responsible for the replication of DNA. It is composed of several specialized proteins each with dedicated enzymatic activities, and in particular, helicase unwinds double-stranded DNA and DNA polymerase catalyzes the synthesis of DNA. Understanding how a replisome functions in the process of DNA replication requires methods to dissect the mechanisms of individual proteins and of multiproteins acting in concert. Single-molecule optical-trapping techniques have proved to be a powerful approach, offering the unique ability to observe and manipulate biomolecules at the single-molecule level and providing insights into the mechanisms of molecular motors and their interactions and coordination in a complex. Here, we describe a practical guide to applying these techniques to study the dynamics of individual proteins in the bacteriophage T7 replisome, as well as the coordination among them. We also summarize major findings from these studies, including nucleotide-specific helicase slippage and new lesion bypass pathway in T7 replication.
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Affiliation(s)
- B Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, PR China
| | - M D Wang
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, United States; Howard Hughes Medical Institute, Cornell University, Ithaca, NY, United States.
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38
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Ordu O, Lusser A, Dekker NH. Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophys Rev 2016; 8:33-49. [PMID: 28058066 PMCID: PMC5167136 DOI: 10.1007/s12551-016-0212-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the regulation of essential nuclear processes such as replication, transcription, and repair by controlling the accessibility of DNA. Thus, knowledge of this fundamental DNA-protein complex is crucial for understanding the mechanisms of gene control. While structural and biochemical studies over the past few decades have provided key insights into both the molecular composition and functional aspects of nucleosomes, these approaches necessarily average over large populations and times. In contrast, single-molecule methods are capable of revealing features of subpopulations and dynamic changes in the structure or function of biomolecules, rendering them a powerful complementary tool for probing mechanistic aspects of DNA-protein interactions. In this review, we highlight how these single-molecule approaches have recently yielded new insights into nucleosomal and subnucleosomal structures and dynamics.
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Affiliation(s)
- Orkide Ordu
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H. Dekker
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
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39
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Rudnizky S, Bavly A, Malik O, Pnueli L, Melamed P, Kaplan A. H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes. Nat Commun 2016; 7:12958. [PMID: 27653784 PMCID: PMC5036153 DOI: 10.1038/ncomms12958] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/19/2016] [Indexed: 01/17/2023] Open
Abstract
The structure and dynamics of promoter chromatin have a profound effect on the expression levels of genes. Yet, the contribution of DNA sequence, histone post-translational modifications, histone variant usage and other factors in shaping the architecture of chromatin, and the mechanisms by which this architecture modulates expression of specific genes are not yet completely understood. Here we use optical tweezers to study the roles that DNA sequence and the histone variant H2A.Z have in shaping the chromatin landscape at the promoters of two model genes, Cga and Lhb. Guided by MNase mapping of the promoters of these genes, we reconstitute nucleosomes that mimic those located near the transcriptional start site and immediately downstream (+1), and measure the forces required to disrupt these nucleosomes, and their mobility along the DNA sequence. Our results indicate that these genes are basally regulated by two distinct strategies, making use of H2A.Z to modulate separate phases of transcription, and highlight how DNA sequence, alternative histone variants and remodelling machinery act synergistically to modulate gene expression.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Adaiah Bavly
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Malik
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
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40
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Studitsky VM, Nizovtseva EV, Shaytan AK, Luse DS. Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure. ACTA ACUST UNITED AC 2016; 2. [PMID: 27754494 DOI: 10.21767/2471-8084.100017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Packaging of DNA into chromatin affects all processes on DNA. Nucleosomes present a strong barrier to transcription, raising important questions about the nature and the mechanisms of overcoming the barrier. Recently it was shown that DNA sequence, DNA-histone interactions and backtracking by RNA polymerase II (Pol II) all contribute to formation of the barrier. After partial uncoiling of nucleosomal DNA from histone octamer by Pol II and backtracking of the enzyme, nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. Histone chaperones and transcription factors TFIIS, TFIIF and FACT facilitate transcription through chromatin using different molecular mechanisms.
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Affiliation(s)
- Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111; Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Alexey K Shaytan
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Donal S Luse
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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41
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Hainer SJ, Martens JA. Regulation of chaperone binding and nucleosome dynamics by key residues within the globular domain of histone H3. Epigenetics Chromatin 2016; 9:17. [PMID: 27134679 PMCID: PMC4851828 DOI: 10.1186/s13072-016-0066-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Nucleosomes have an important role in modulating access of DNA by regulatory factors. The role specific histone residues have in this process has been shown to be an important mechanism of transcription regulation. Previously, we identified eight amino acids in histones H3 and H4 that are required for nucleosome occupancy over highly transcribed regions of the genome. RESULTS We investigate the mechanism through which three of these previously identified histone H3 amino acids regulate nucleosome architecture. We find that histone H3 K122, Q120, and R49 are required for Spt2, Spt6, and Spt16 occupancies at genomic locations where transcription rates are high, but not over regions of low transcription rates. Furthermore, substitution at one residue, K122, located on the dyad axis of the nucleosome, results in improper reassembly and disassembly of nucleosomes, likely accounting for the transcription rate-dependent regulation by these mutant histones. CONCLUSIONS These data show that when specific amino acids of histone proteins are substituted, Spt2, Spt6, and Spt16 occupancies are reduced and nucleosome dynamics are altered. Therefore, these data support a mechanism for histone chaperone binding where these factors interact with histone proteins to promote their activities during transcription.
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Affiliation(s)
- Sarah J Hainer
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, LRB 560D, Worcester, MA 01604 USA ; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Joseph A Martens
- Shady Side Academy Senior School, 423 Fox Chapel Road, Pittsburgh, PA 15238 USA ; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
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42
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Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nat Commun 2016; 7:11244. [PMID: 27091704 PMCID: PMC4838855 DOI: 10.1038/ncomms11244] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation. RNA Polymerase II can detect and cleave mis-incorporated nucleotides by a proofreading mechanism that requires backtracking of the enzyme. Here the authors show that Pol II backtracking occurs in a stepwise mode that involves two intermediate states where the fraying of the terminal RNA nucleotide is a prerequisite.
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43
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Sun B, Pandey M, Inman JT, Yang Y, Kashlev M, Patel SS, Wang MD. T7 replisome directly overcomes DNA damage. Nat Commun 2015; 6:10260. [PMID: 26675048 PMCID: PMC4703881 DOI: 10.1038/ncomms10260] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/22/2015] [Indexed: 11/09/2022] Open
Abstract
Cells and viruses possess several known ‘restart' pathways to overcome lesions during DNA replication. However, these ‘bypass' pathways leave a gap in replicated DNA or require recruitment of accessory proteins, resulting in significant delays to fork movement or even cell division arrest. Using single-molecule and ensemble methods, we demonstrate that the bacteriophage T7 replisome is able to directly replicate through a leading-strand cyclobutane pyrimidine dimer (CPD) lesion. We show that when a replisome encounters the lesion, a substantial fraction of DNA polymerase (DNAP) and helicase stay together at the lesion, the replisome does not dissociate and the helicase does not move forward on its own. The DNAP is able to directly replicate through the lesion by working in conjunction with helicase through specific helicase–DNAP interactions. These observations suggest that the T7 replisome is fundamentally permissive of DNA lesions via pathways that do not require fork adjustment or replisome reassembly. Genomic instability can result from stalled or collapsed replication fork at sites of unrepaired DNA lesions. Here the authors uncover a new lesion bypass pathway for the T7 replisome, where leading strand template lesions can be overcome through interaction between the replisome's helicase and polymerase components.
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Affiliation(s)
- Bo Sun
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - James T Inman
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
| | - Yi Yang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
| | - Mikhail Kashlev
- NCI Center for Cancer Research, Frederick, Maryland 21702, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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44
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Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. J Mol Biol 2015; 428:221-237. [PMID: 26699921 DOI: 10.1016/j.jmb.2015.12.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/16/2022]
Abstract
An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Grigoriy A Armeev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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45
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Abstract
Thousands of human and Drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. However, the molecular mechanisms of formation of the nucleosomal barrier to transcribing RNA polymerase II (Pol II) and nucleosome survival during/after transcription remain unknown. Here we show that both DNA-histone interactions and Pol II backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely occurs through allosterically stabilized histone-histone interactions. Structural analysis indicates that after Pol II encounters the barrier, the enzyme backtracks and nucleosomal DNA recoils on the octamer, locking Pol II in the arrested state. DNA is displaced from one of the H2A/H2B dimers that remains associated with the octamer. The data reveal the importance of intranucleosomal DNA-protein and protein-protein interactions during conformational changes in the nucleosome structure on transcription. Mechanisms of nucleosomal barrier formation and nucleosome survival during transcription are proposed.
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46
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Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. Dynamic regulation of transcription factors by nucleosome remodeling. eLife 2015; 4. [PMID: 26047462 PMCID: PMC4456607 DOI: 10.7554/elife.06249] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/11/2015] [Indexed: 12/27/2022] Open
Abstract
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes. DOI:http://dx.doi.org/10.7554/eLife.06249.001 Cells contain thousands of genes that are encoded by molecules of DNA. In yeast and other eukaryotic organisms, this DNA is wrapped around proteins called histones to make structures called nucleosomes. This compacts the DNA and allows it to fit inside the tiny nucleus within the cell. The positioning of the nucleosomes influences how tightly packed the DNA is, which in turn influences the activity of genes. Less active genes tend to be found within regions of DNA that are tightly packed, while more active genes are found in less tightly packed regions. To activate a gene, proteins called transcription factors bind to a section of DNA within the gene called the promoter. Enzymes known as ‘chromatin remodelers’ can alter the locations of nucleosomes on DNA to allow the transcription factors access to the promoters of particular genes. In yeast, the SWI/SNF family of chromatin remodelers can disassemble nucleosomes to promote gene activity, while the ISW1 family organises nucleosomes into closely spaced groups to repress gene activity. However, it is not clear if, or how, chromatin remodelers can influence transcription factors that are already bound to DNA. Here, Li et al. studied the interactions between a transcription factor and the chromatin remodelers in yeast. The experiment used a piece of DNA that contained a bound transcription factor and a single nucleosome. Li et al. used a technique called ‘single molecule DNA unzipping’, which enabled them to precisely locate the position of the nucleosome and transcription factor before and after the nucleosome was remodeled. The experiments found that a chromatin remodeler called ISW1a moved the nucleosome away from the transcription factor, while a SWI/SNF chromatin remodeler moved the nucleosome towards it. Significantly, Li et al. also found that a transcription factor is a major barrier to ISW1a's remodeling activity, suggesting that ISW1a may use transcription factors as reference points to position nucleosomes. In contrast, SWI/SNF was able to slide a nucleosome past the transcription factor, which led to the transcription factor falling off the DNA. Therefore, SWI/SNF is able to move transcription factors out of the way to deactivate genes. Li et al. propose a new model for how chromatin remodelers can move nucleosomes and regulate transcription factors to alter gene activity. A future challenge will be to observe these types of activities in living cells. DOI:http://dx.doi.org/10.7554/eLife.06249.002
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Affiliation(s)
- Ming Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Arjan Hada
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Payel Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Lola Olufemi
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michael A Hall
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Benjamin Y Smith
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Scott Forth
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Jeffrey N McKnight
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ashok Patel
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Blaine Bartholomew
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
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47
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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48
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Krasich R, Wu SY, Kuo HK, Kreuzer KN. Functions that protect Escherichia coli from DNA-protein crosslinks. DNA Repair (Amst) 2015; 28:48-59. [PMID: 25731940 DOI: 10.1016/j.dnarep.2015.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) treatment in cells overexpressing cytosine methyltransferase; hypersensitivity was verified to depend on methyltransferase expression. We isolated hypersensitive mutants that were uncovered in previous studies (recA, recBC, recG, and uvrD), hypersensitive mutants that apparently activate phage Mu Gam expression, and novel hypersensitive mutants in genes involved in DNA metabolism, cell division, and tRNA modification (dinG, ftsK, xerD, dnaJ, hflC, miaA, mnmE, mnmG, and ssrA). Inactivation of SbcCD, which can cleave DNA at protein-DNA complexes, did not cause hypersensitivity. We previously showed that tmRNA pathway defects cause aza-C hypersensitivity, implying that DPCs block coupled transcription/translation complexes. Here, we show that mutants in tRNA modification functions miaA, mnmE and mnmG cause defects in aza-C-induced tmRNA tagging, explaining their hypersensitivity. In order for tmRNA to access a stalled ribosome, the mRNA must be cleaved or released from RNA polymerase. Mutational inactivation of functions involved in mRNA processing and RNA polymerase elongation/release (RNase II, RNaseD, RNase PH, RNase LS, Rep, HepA, GreA, GreB) did not cause aza-C hypersensitivity; the mechanism of tmRNA access remains unclear.
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Affiliation(s)
- Rachel Krasich
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Sunny Yang Wu
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - H Kenny Kuo
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States
| | - Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710, United States.
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Sirbuly DJ, Friddle RW, Villanueva J, Huang Q. Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it? REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:024101. [PMID: 25629797 DOI: 10.1088/0034-4885/78/2/024101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.
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Affiliation(s)
- Donald J Sirbuly
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA. Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
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50
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Langecker M, Ivankin A, Carson S, Kinney SM, Simmel FC, Wanunu M. Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability. NANO LETTERS 2015; 15:783-90. [PMID: 25495735 PMCID: PMC4296928 DOI: 10.1021/nl504522n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/09/2014] [Indexed: 05/21/2023]
Abstract
Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.
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Affiliation(s)
- Martin Langecker
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Andrey Ivankin
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shannon
R. M. Kinney
- Department
of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, Massachusetts 01119, United States
| | - Friedrich C. Simmel
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- E-mail:
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- E-mail:
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