1
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Kolbin D, Locatelli M, Stanton J, Kesselman K, Kokkanti A, Li J, Yeh E, Bloom K. Centromeres are stress-induced fragile sites. Curr Biol 2025; 35:1197-1210.e4. [PMID: 39970915 PMCID: PMC11945498 DOI: 10.1016/j.cub.2025.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 12/12/2024] [Accepted: 01/27/2025] [Indexed: 02/21/2025]
Abstract
Centromeres are unique loci on eukaryotic chromosomes and are complexed with centromere-specific histone H3 molecules (CENP-A in mammals, Cse4 in yeast). The centromere provides the binding site for the kinetochore that captures microtubules and provides the mechanical linkage required for chromosome segregation. Centromeres encounter fluctuations in force as chromosomes jockey for position on the metaphase spindle. We have developed biological assays to examine the response of centromeres to high force. Torsional stress is induced on covalently closed DNA circles from supercoiling. Plasmid-borne centromeres with single-nucleotide inactivating mutations exhibit a high conversion frequency to plasmid dimer species. Conversion to dimers is dependent on the activity of the Rad1 single-strand endonuclease, indicative of unwinding a region of the centromere sequence in the absence of a functional kinetochore. To determine the region of unwinding, we used conditionally functional dicentric chromosomes to exert tension. Centromere DNA is exquisitely sensitive to cleavage following activation of the dicentric chromosome. Cleavage is dependent on the action of Rad1, highlighting the propensity of centromeres to unwind in response to supercoiling or mechanical stress. These studies provide mechanistic insights into the evolution of AT-rich pericentromere DNA throughout phylogeny and suggest a mechanism for stress-induced error correction at the centromere.
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Affiliation(s)
- Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Maëlle Locatelli
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John Stanton
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katie Kesselman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aryan Kokkanti
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jinghan Li
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elaine Yeh
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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2
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Burman M, Noy A. Atomic Description of the Reciprocal Action between Supercoils and Melting Bubbles on Linear DNA. PHYSICAL REVIEW LETTERS 2025; 134:038403. [PMID: 39927957 DOI: 10.1103/physrevlett.134.038403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/18/2024] [Indexed: 02/11/2025]
Abstract
Although the mechanical response of DNA to physiological torsion and tension is well characterized, the detailed structures are not yet known. By using molecular dynamics simulations on linear DNA with 300 base-pairs, we provide, for the first time, the conformational phase diagram at atomic resolution. Our simulations also reveal the dynamics and diffusion of supercoils. We observe a new state in negative supercoiling, where denaturation bubbles form in adenine/thymine-rich regions independently of the underlying DNA topology. We thus propose sequence-dependent bubbles could position plectonemes in longer DNA.
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Affiliation(s)
- Matthew Burman
- University of York, School of Physics, Engineering and Technology, York YO10 5DD, United Kingdom
| | - Agnes Noy
- University of York, School of Physics, Engineering and Technology, York YO10 5DD, United Kingdom
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3
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Kiernan K, Kwon J, Merrill B, Simonović M. Structural basis of Cas9 DNA interrogation with a 5' truncated sgRNA. Nucleic Acids Res 2025; 53:gkae1164. [PMID: 39657754 PMCID: PMC11724282 DOI: 10.1093/nar/gkae1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 10/23/2024] [Accepted: 11/07/2024] [Indexed: 12/12/2024] Open
Abstract
The efficiency and accuracy of CRISPR-Cas9 targeting varies considerably across genomic targets and remains a persistent issue for using this system in cells. Studies have shown that the use of 5' truncated single guide RNAs (sgRNAs) can reduce the rate of unwanted off-target recognition while still maintaining on-target specificity. However, it is not well-understood how reducing target complementarity enhances specificity or how truncation past 15 nucleotides (nts) prevents full Cas9 activation without compromising on-target binding. Here, we use biochemistry and cryogenic electron microscopy to investigate Cas9 structure and activity when bound to a 14-nt sgRNA. Our structures reveal that the shortened path of the displaced non-target strand (NTS) sterically occludes docking of the HNH L1 linker and prevents proper positioning of the nuclease domains. We show that cleavage inhibition can be alleviated by either artificially melting the protospacer adjacent motif (PAM)-distal duplex or providing a supercoiled substrate. Even though Cas9 forms a stable complex with its target, we find that plasmid cleavage is ∼1000-fold slower with a 14-nt sgRNA than with a full-length 20-nt sgRNA. Our results provide a structural basis for Cas9 target binding with 5' truncated sgRNAs and underline the importance of PAM-distal NTS availability in promoting Cas9 activation.
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Affiliation(s)
- Kaitlyn A Kiernan
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, 900 S Ashland Ave, Chicago, IL 60607, USA
| | - Jieun Kwon
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, 900 S Ashland Ave, Chicago, IL 60607, USA
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, 900 S Ashland Ave, Chicago, IL 60607, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, 900 S Ashland Ave, Chicago, IL 60607, USA
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4
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Muskhelishvili G, Sobetzko P, Travers A. Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle? Biomolecules 2022; 12:biom12060831. [PMID: 35740956 PMCID: PMC9221221 DOI: 10.3390/biom12060831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023] Open
Abstract
In this article we describe the bacterial growth cycle as a closed, self-reproducing, or autopoietic circuit, reestablishing the physiological state of stationary cells initially inoculated in the growth medium. In batch culture, this process of self-reproduction is associated with the gradual decline in available metabolic energy and corresponding change in the physiological state of the population as a function of "travelled distance" along the autopoietic path. We argue that this directional alteration of cell physiology is both reflected in and supported by sequential gene expression along the chromosomal OriC-Ter axis. We propose that during the E. coli growth cycle, the spatiotemporal order of gene expression is established by coupling the temporal gradient of supercoiling energy to the spatial gradient of DNA thermodynamic stability along the chromosomal OriC-Ter axis.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Biology Program, Agricultural University of Georgia, 0159 Tbilisi, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Synmikro, Loewe Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
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5
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Tripathi S, Brahmachari S, Onuchic JN, Levine H. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Res 2021; 50:1269-1279. [PMID: 34951454 PMCID: PMC8860607 DOI: 10.1093/nar/gkab1252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.,Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics and Astronomy, Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
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6
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Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 2021; 12:5683. [PMID: 34584096 PMCID: PMC8478907 DOI: 10.1038/s41467-021-25936-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
DNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.
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Affiliation(s)
- Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Houston, TX, USA
| | - Allison K Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
| | - Erik Stricker
- Department of Molecular Virology and Microbiology, Houston, TX, USA
| | - Hilda L Chan
- Graduate Program in Immunology and Microbiology, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Houston, TX, USA.
- Graduate Program in Immunology and Microbiology, Houston, TX, USA.
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7
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Spakman D, Bakx JAM, Biebricher AS, Peterman EJG, Wuite GJL, King GA. Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches. Nucleic Acids Res 2021; 49:5470-5492. [PMID: 33963870 PMCID: PMC8191776 DOI: 10.1093/nar/gkab239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
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Affiliation(s)
- Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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8
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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9
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Putative Cooperative ATP-DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly. Int J Mol Sci 2021; 22:ijms22126643. [PMID: 34205762 PMCID: PMC8235120 DOI: 10.3390/ijms22126643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 01/03/2023] Open
Abstract
oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the mode of orisome assembly differ in distantly related bacteria. In this work, we characterized oriC of Helicobacter pylori, which consists of two DnaA box clusters and a DNA unwinding element (DUE); the latter can be subdivided into a GC-rich region, a DnaA-trio and an AT-rich region. We show that the DnaA-trio submodule is crucial for DNA unwinding, possibly because it enables proper DnaA oligomerization on ssDNA. However, we also observed the reverse effect: DNA unwinding, enabling subsequent DnaA-ssDNA oligomer formation-stabilized DnaA binding to box ts1. This suggests the interplay between DnaA binding to ssDNA and dsDNA upon DNA unwinding. Further investigation of the ts1 DnaA box revealed that this box, together with the newly identified c-ATP DnaA box in oriC1, constitute a new class of ATP-DnaA boxes. Indeed, in vitro ATP-DnaA unwinds H. pylori oriC more efficiently than ADP-DnaA. Our results expand the understanding of H. pylori orisome formation, indicating another regulatory pathway of H. pylori orisome assembly.
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10
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Buglione E, Salerno D, Marrano CA, Cassina V, Vesco G, Nardo L, Dacasto M, Rigo R, Sissi C, Mantegazza F. Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene. Nucleic Acids Res 2021; 49:4564-4573. [PMID: 33849064 PMCID: PMC8096272 DOI: 10.1093/nar/gkab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.
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Affiliation(s)
- Enrico Buglione
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Guglielmo Vesco
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Luca Nardo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro (PD), Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35121 Padova (PD), Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
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11
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Single-molecule micromanipulation studies of methylated DNA. Biophys J 2021; 120:2148-2155. [PMID: 33838135 DOI: 10.1016/j.bpj.2021.03.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylated at the five-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in longer contour length and increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded "bubbles" of DNA under physiologically relevant stretching forces and supercoiling densities. The flexibility and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.
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12
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Liebl K, Zacharias M. How global DNA unwinding causes non-uniform stress distribution and melting of DNA. PLoS One 2020; 15:e0232976. [PMID: 32413048 PMCID: PMC7228070 DOI: 10.1371/journal.pone.0232976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
- * E-mail:
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13
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The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes. PLoS Genet 2020; 16:e1008645. [PMID: 32226006 PMCID: PMC7145188 DOI: 10.1371/journal.pgen.1008645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 04/09/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023] Open
Abstract
The gene products that drive early development are critical for setting up developmental trajectories in all animals. The earliest stages of development are fueled by maternally provided mRNAs until the zygote can take over transcription of its own genome. In early development, both maternally deposited and zygotically transcribed gene products have been well characterized in model systems. Previously, we demonstrated that across the genus Drosophila, maternal and zygotic mRNAs are largely conserved but also showed a surprising amount of change across species, with more differences evolving at the zygotic stage than the maternal stage. In this study, we use comparative methods to elucidate the regulatory mechanisms underlying maternal deposition and zygotic transcription across species. Through motif analysis, we discovered considerable conservation of regulatory mechanisms associated with maternal transcription, as compared to zygotic transcription. We also found that the regulatory mechanisms active in the maternal and zygotic genomes are quite different. For maternally deposited genes, we uncovered many signals that are consistent with transcriptional regulation at the level of chromatin state through factors enriched in the ovary, rather than precisely controlled gene-specific factors. For genes expressed only by the zygotic genome, we found evidence for previously identified regulators such as Zelda and GAGA-factor, with multiple analyses pointing toward gene-specific regulation. The observed mechanisms of regulation are consistent with what is known about regulation in these two genomes: during oogenesis, the maternal genome is optimized to quickly produce a large volume of transcripts to provide to the oocyte; after zygotic genome activation, mechanisms are employed to activate transcription of specific genes in a spatiotemporally precise manner. Thus the genetic architecture of the maternal and zygotic genomes, and the specific requirements for the transcripts present at each stage of embryogenesis, determine the regulatory mechanisms responsible for transcripts present at these stages.
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14
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Shepherd JW, Greenall RJ, Probert M, Noy A, Leake M. The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA. Nucleic Acids Res 2020; 48:1748-1763. [PMID: 31930331 PMCID: PMC7038985 DOI: 10.1093/nar/gkz1227] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/26/2022] Open
Abstract
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.
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Affiliation(s)
- Jack W Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York,YO10 5NG, UK
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15
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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16
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Marin-Gonzalez A, Vilhena JG, Moreno-Herrero F, Perez R. DNA Crookedness Regulates DNA Mechanical Properties at Short Length Scales. PHYSICAL REVIEW LETTERS 2019; 122:048102. [PMID: 30768347 DOI: 10.1103/physrevlett.122.048102] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 05/13/2023]
Abstract
Sequence-dependent DNA conformation and flexibility play a fundamental role in the specificity of DNA-protein interactions. Here we quantify the DNA crookedness: a sequence-dependent deformation of DNA that consists of periodic bends of the base pair centers chain. Using extensive 100 μs-long, all-atom molecular dynamics simulations, we found that DNA crookedness and its associated flexibility are bijective, which unveils a one-to-one relation between DNA structure and dynamics. This allowed us to build a predictive model to compute the stretch moduli of different DNA sequences from solely their structure. Sequences with very little crookedness show extremely high stretching stiffness and have been previously shown to form unstable nucleosomes and promote gene expression. Interestingly, the crookedness can be tailored by epigenetic modifications, known to affect gene expression. Our results rationalize the idea that the DNA sequence is not only a chemical code, but also a physical one that allows finely regulating its mechanical properties and, possibly, its 3D arrangement inside the cell.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH 4056 Basel, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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17
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Kim SH, Ganji M, Kim E, van der Torre J, Abbondanzieri E, Dekker C. DNA sequence encodes the position of DNA supercoils. eLife 2018; 7:e36557. [PMID: 30523779 PMCID: PMC6301789 DOI: 10.7554/elife.36557] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.
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Affiliation(s)
- Sung Hyun Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Mahipal Ganji
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Eugene Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Jaco van der Torre
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Elio Abbondanzieri
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Cees Dekker
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
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18
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Min Y, Purohit PK. Discontinuous growth of DNA plectonemes due to atomic scale friction. SOFT MATTER 2018; 14:7759-7770. [PMID: 30209494 PMCID: PMC6158071 DOI: 10.1039/c8sm00852c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We develop a model to explain discontinuities in the increase of the length of a DNA plectoneme when the DNA filament is continuously twisted under tension. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuation. We postulate that a corrugated energy landscape that contains energy barriers is the cause of jumps in the length of the plectoneme as the number of turns is increased. Thus, our model is similar to the Prandtl-Tomlinson model of atomic scale friction. The existence of a corrugated energy landscape can be justified due to the close proximity of the neighboring pieces of DNA in a plectoneme. We assume the corrugated energy landscape to be sinusoidal since the plectoneme has a periodic helical structure and rotation of the bead is a form of periodic motion. We perform calculations with different tensile forces and ionic concentrations, and show that rotation-extension curves manifest stair-step shapes under relatively high ionic concentrations and high forces. We show that the jump in the plectonemic growth is caused by the flattening of the energy barrier in the corrugated landscape.
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Affiliation(s)
- Yifei Min
- Graduate Group in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Prashant K. Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA. Tel.:+215 898 3870; Fax: +215 573 6334.
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19
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Ordu O, Kremser L, Lusser A, Dekker NH. Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. J Chem Phys 2018; 148:123323. [PMID: 29604863 DOI: 10.1063/1.5009100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.
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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
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - 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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20
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Fosado YAG, Michieletto D, Marenduzzo D. Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting. PHYSICAL REVIEW LETTERS 2017; 119:118002. [PMID: 28949232 DOI: 10.1103/physrevlett.119.118002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Indexed: 06/07/2023]
Abstract
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular closed plasmids, is less abrupt than that of linear molecules. This finding points to an important role of topology in the physics of DNA denaturation, which is, however, poorly understood. Here, we shed light on this issue by combining large-scale Brownian dynamics simulations with an analytically solvable phenomenological Landau mean field theory. We find that the competition between melting and supercoiling leads to phase coexistence of denatured and intact phases at the single-molecule level. This coexistence occurs in a wide temperature range, thereby accounting for the broadening of the transition. Finally, our simulations show an intriguing topology-dependent scaling law governing the growth of denaturation bubbles in supercoiled plasmids, which can be understood within the proposed mean field theory.
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Affiliation(s)
- Y A G Fosado
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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Jha JK, Ramachandran R, Chattoraj DK. Opening the Strands of Replication Origins-Still an Open Question. Front Mol Biosci 2016; 3:62. [PMID: 27747216 PMCID: PMC5043065 DOI: 10.3389/fmolb.2016.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Dhruba K Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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22
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Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, K Doye JP, Louis AA, Harris SA. Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res 2016; 44:9121-9130. [PMID: 27664220 PMCID: PMC5100592 DOI: 10.1093/nar/gkw815] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/03/2016] [Indexed: 12/14/2022] Open
Abstract
It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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Affiliation(s)
- Thana Sutthibutpong
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Craig Benham
- UC Davis Genome Centre, Health Sciences Drive, Davis, CA 95616, USA
| | - Gabriel G Slade
- Department of Physics, São Paulo State University, Rua Cristovão, São José do Rio Preto, SP 15054-000, Brazil
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK .,Astbury Centre for Structural and Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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