1
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Battaglia C, Michieletto D. Loops are geometric catalysts for DNA integration. Nucleic Acids Res 2024; 52:8184-8192. [PMID: 38864388 DOI: 10.1093/nar/gkae484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024] Open
Abstract
The insertion of DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of DNA insertions are not random and the physical mechanisms underlying the integration site selection are poorly understood. Here, we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as viral DNA or transposons, into naked DNA or chromatin substrates. More specifically, we explore the role of loops within the polymeric substrate and discover that they act as 'geometric catalysts' for DNA integration by reducing the energy barrier for substrate deformation. Additionally, we discover that the 1D pattern and 3D conformation of loops have a marked effect on the distribution of integration sites. Finally, we show that loops may compete with nucleosomes to attract DNA integrations. These results may be tested in vitro and they may help to understand patterns of DNA insertions with implications in genome evolution and engineering.
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Affiliation(s)
- Cleis Battaglia
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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2
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Jin MJ, Wang ZL, Wu ZH, He XJ, Zhang Y, Huang Q, Zhang LZ, Wu XB, Yan WY, Zeng ZJ. Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications. iScience 2023; 26:106308. [PMID: 36942051 PMCID: PMC10024153 DOI: 10.1016/j.isci.2023.106308] [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: 05/23/2022] [Revised: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Phenotypic dimorphism between queens and workers is an important biological characteristic of honeybees that has been the subject of intensive research. The enormous differences in morphology, lifespan, physiology, and behavior between queens and workers are caused by a complicated set of factors. Epigenetic modifications are considered to play an important role in this process. In this study, we analyzed the differences in chromosome interactions and H3K27ac and H3K4me1 modifications between the queens and workers using high-throughput chromosome conformation capture (Hi-C) and Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) technologies. We found that the queens contain more chromosome interactions and more unique H3K27ac modifications than workers; in contrast, workers have more H3K4me1 modifications than queens. Moreover, we identified Map3k15 as a potential caste gene in queen-worker differentiation. Our results suggest that chromosomal conformation and H3K27ac and H3K4me1 modifications are involved in regulating queen-worker differentiation, which reveals that the queen-worker phenotypic dimorphism is regulated by multiple epigenetic modifications.
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Affiliation(s)
- Meng Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Hao Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Yong Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
- Corresponding author
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3
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Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L. Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops. Nucleic Acids Res 2022; 50:2826-2835. [PMID: 35188572 PMCID: PMC8934669 DOI: 10.1093/nar/gkac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022] Open
Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
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Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
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4
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Yan Y, Xu W, Kumar S, Zhang A, Leng F, Dunlap D, Finzi L. Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time. Nucleic Acids Res 2021; 49:11550-11559. [PMID: 34723343 PMCID: PMC8599721 DOI: 10.1093/nar/gkab946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
Protein-mediated DNA looping is fundamental to gene regulation and such loops occur stochastically in purified systems. Additional proteins increase the probability of looping, but these probabilities maintain a broad distribution. For example, the probability of lac repressor-mediated looping in individual molecules ranged 0–100%, and individual molecules exhibited representative behavior only in observations lasting an hour or more. Titrating with HU protein progressively compacted the DNA without narrowing the 0–100% distribution. Increased negative supercoiling produced an ensemble of molecules in which all individual molecules more closely resembled the average. Furthermore, in only 12 min of observation, well within the doubling time of the bacterium, most molecules exhibited the looping probability of the ensemble. DNA supercoiling, an inherent feature of all genomes, appears to impose time-constrained, emergent behavior on otherwise random molecular activity.
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Affiliation(s)
- Yan Yan
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Sandip Kumar
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Alexander Zhang
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA 30322, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA 30322, USA
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5
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Vemulapalli S, Hashemi M, Kolomeisky AB, Lyubchenko YL. DNA Looping Mediated by Site-Specific SfiI-DNA Interactions. J Phys Chem B 2021; 125:4645-4653. [PMID: 33914533 DOI: 10.1021/acs.jpcb.1c00763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions between distant DNA segments play important roles in various biological processes, such as DNA recombination. Certain restriction enzymes create DNA loops when two sites are held together and then cleave the DNA. DNA looping is important during DNA synapsis. Here we investigated the mechanisms of DNA looping by restriction enzyme SfiI by measuring the properties of the system at various temperatures. Different sized loop complexes, mediated by SfiI-DNA interactions, were visualized with AFM. The experimental results revealed that small loops are more favorable compared to other loop sizes at all temperatures. Our theoretical model found that entropic cost dominates at all conditions, which explains the preference for short loops. Furthermore, specific loop sizes were predicted as favorable from an energetic point of view. These predictions were tested by experiments with transiently assembled SfiI loops on a substrate with a single SfiI site.
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Affiliation(s)
- Sridhar Vemulapalli
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry-MS60, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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6
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Hao N, Sullivan AE, Shearwin KE, Dodd IB. The loopometer: a quantitative in vivo assay for DNA-looping proteins. Nucleic Acids Res 2021; 49:e39. [PMID: 33511418 PMCID: PMC8053113 DOI: 10.1093/nar/gkaa1284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/22/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Adrienne E Sullivan
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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7
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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8
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Hao N, Shearwin KE, Dodd IB. Positive and Negative Control of Enhancer-Promoter Interactions by Other DNA Loops Generates Specificity and Tunability. Cell Rep 2020; 26:2419-2433.e3. [PMID: 30811991 DOI: 10.1016/j.celrep.2019.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/08/2019] [Accepted: 02/01/2019] [Indexed: 12/15/2022] Open
Abstract
Enhancers are ubiquitous and critical gene-regulatory elements. However, quantitative understanding of the role of DNA looping in the regulation of enhancer action and specificity is limited. We used the Escherichia coli NtrC enhancer-σ54 promoter system as an in vivo model, finding that NtrC activation is highly sensitive to the enhancer-promoter (E-P) distance in the 300-6,000 bp range. DNA loops formed by Lac repressor were able to strongly regulate enhancer action either positively or negatively, recapitulating promoter targeting and insulation. A single LacI loop combining targeting and insulation produced a strong shift in specificity for enhancer choice between two σ54 promoters. A combined kinetic-thermodynamic model was used to quantify the effect of DNA-looping interactions on promoter activity and revealed that sensitivity to E-P distance and to control by other loops is itself dependent on enhancer and promoter parameters that may be subject to regulation.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia; CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia.
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9
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Velasco-Berrelleza V, Burman M, Shepherd JW, Leake MC, Golestanian R, Noy A. SerraNA: a program to determine nucleic acids elasticity from simulation data. Phys Chem Chem Phys 2020; 22:19254-19266. [DOI: 10.1039/d0cp02713h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly.
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Affiliation(s)
| | | | | | - Mark C. Leake
- Department of Physics
- University of York
- York
- UK
- Department of Biology
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS)
- Göttingen
- Germany
- Rudolf Peierls Center for Theoretical Physics
- University of Oxford
| | - Agnes Noy
- Department of Physics
- University of York
- York
- UK
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10
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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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11
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Yan Y, Ding Y, Leng F, Dunlap D, Finzi L. Protein-mediated loops in supercoiled DNA create large topological domains. Nucleic Acids Res 2019. [PMID: 29538766 PMCID: PMC5961096 DOI: 10.1093/nar/gky153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure. To characterize the extent of constrained supercoiling, 400 bp, lac repressor-secured loops were formed in extensively over- or under-wound DNA under gentle tension in a magnetic tweezer. The protein-mediated loops constrained variable amounts of supercoiling that often exceeded the maximum writhe expected for a 400 bp plectoneme. Loops with such high levels of supercoiling appear to be entangled with flanking domains. Thus, loop-mediating proteins operating on supercoiled substrates can establish topological domains that may coordinate gene regulation and other DNA transactions across spans in the genome that are larger than the separation between the binding sites.
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Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Yue Ding
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
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12
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Yan Y, Leng F, Finzi L, Dunlap D. Protein-mediated looping of DNA under tension requires supercoiling. Nucleic Acids Res 2019; 46:2370-2379. [PMID: 29365152 PMCID: PMC5861448 DOI: 10.1093/nar/gky021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023] Open
Abstract
Protein-mediated DNA looping is ubiquitous in chromatin organization and gene regulation, but to what extent supercoiling or nucleoid associated proteins promote looping is poorly understood. Using the lac repressor (LacI), a paradigmatic loop-mediating protein, we measured LacI-induced looping as a function of either supercoiling or the concentration of the HU protein, an abundant nucleoid protein in Escherichia coli. Negative supercoiling to physiological levels with magnetic tweezers easily drove the looping probability from 0 to 100% in single DNA molecules under slight tension that likely exists in vivo. In contrast, even saturating (micromolar) concentrations of HU could not raise the looping probability above 30% in similarly stretched DNA or 80% in DNA without tension. Negative supercoiling is required to induce significant looping of DNA under any appreciable tension.
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Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
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13
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Kovari DT, Yan Y, Finzi L, Dunlap D. Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors. Methods Mol Biol 2018; 1665:317-340. [PMID: 28940077 DOI: 10.1007/978-1-4939-7271-5_17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tethered Particle Motion (TPM) is a versatile in vitro technique for monitoring the conformations a linear macromolecule, such as DNA, can exhibit. The technique involves monitoring the diffusive motion of a particle anchored to a fixed point via the macromolecule of interest, which acts as a tether. In this chapter, we provide an overview of TPM, review the fundamental principles that determine the accuracy with which effective tether lengths can be used to distinguish different tether conformations, present software tools that assist in capturing and analyzing TPM data, and provide a protocol which uses TPM to characterize lac repressor-induced DNA looping. Critical to any TPM assay is the understanding of the timescale over which the diffusive motion of the particle must be observed to accurately distinguish tether conformations. Approximating the tether as a Hookean spring, we show how to estimate the diffusion timescale and discuss how it relates to the confidence with which tether conformations can be distinguished. Applying those estimates to a lac repressor titration assay, we describe how to perform a TPM experiment. We also provide graphically driven software which can be used to speed up data collection and analysis. Lastly, we detail how TPM data from the titration assay can be used to calculate relevant molecular descriptors such as the J factor for DNA looping and lac repressor-operator dissociation constants. While the included protocol is geared toward studying DNA looping, the technique, fundamental principles, and analytical methods are more general and can be adapted to a wide variety of molecular systems.
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Affiliation(s)
- Daniel T Kovari
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA, 30322, USA
| | - Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA, 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA, 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA, 30322, USA.
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14
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Hao N, Shearwin KE, Dodd IB. Programmable DNA looping using engineered bivalent dCas9 complexes. Nat Commun 2017; 8:1628. [PMID: 29158476 PMCID: PMC5696343 DOI: 10.1038/s41467-017-01873-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022] Open
Abstract
DNA looping is a ubiquitous and critical feature of gene regulation. Although DNA looping can be efficiently detected, tools to readily manipulate DNA looping are limited. Here we develop CRISPR-based DNA looping reagents for creation of programmable DNA loops. Cleavage-defective Cas9 proteins of different specificity are linked by heterodimerization or translational fusion to create bivalent complexes able to link two separate DNA regions. After model-directed optimization, the reagents are validated using a quantitative DNA looping assay in E. coli. Looping efficiency is ~15% for a 4.7 kb loop, but is significantly improved by loop multiplexing with additional guides. Bivalent dCas9 complexes are also used to activate endogenous norVW genes by rewiring chromosomal DNA to bring distal enhancer elements to the gene promoters. Such reagents should allow manipulation of DNA looping in a variety of cell types, aiding understanding of endogenous loops and enabling creation of new regulatory connections. DNA loops are a ubiquitious feature of gene regulation across the kingdoms of life. Here the authors design a Cas9-based dimerization system for inducing DNA loops in E. coli, allowing activation and rewiring of gene expression.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Keith E Shearwin
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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15
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Huang L, Liu P, Yuan Z, Zhou T, Yu J. The free-energy cost of interaction between DNA loops. Sci Rep 2017; 7:12610. [PMID: 28974770 PMCID: PMC5626758 DOI: 10.1038/s41598-017-12765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
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Affiliation(s)
- Lifang Huang
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Peijiang Liu
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Zhanjiang Yuan
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China.
| | - Jianshe Yu
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China.
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16
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Hao N, Sneppen K, Shearwin KE, Dodd IB. Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements. Nucleic Acids Res 2017; 45:5074-5085. [PMID: 28160597 PMCID: PMC5435920 DOI: 10.1093/nar/gkx069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/25/2017] [Indexed: 11/15/2022] Open
Abstract
Genes are frequently regulated by interactions between proteins that bind to the DNA near the gene and proteins that bind to DNA sites located far away, with the intervening DNA looped out. But it is not understood how efficient looping can occur when the sites are very far apart. We develop a simple theoretical framework that relates looping efficiency to the energetic cost and benefit of looping, allowing prediction of the efficiency of single or multiple nested loops at different distances. Measurements of absolute loop efficiencies for Lac repressor and λ CI using gene expression reporters in Escherichia coli cells show that, as predicted by the model, long-range DNA looping between a pair of sites can be strongly enhanced by the use of nested DNA loops or by the use of additional protein-binding sequences. A combination of these approaches was able to generate efficient DNA looping at a 200 kb distance.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Cellular Biology, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen Ø 2100, Denmark
| | - Keith E Shearwin
- Department of Molecular and Cellular Biology, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Cellular Biology, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
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17
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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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18
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Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
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Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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Benedetti F, Japaridze A, Dorier J, Racko D, Kwapich R, Burnier Y, Dietler G, Stasiak A. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. Nucleic Acids Res 2015; 43:2390-9. [PMID: 25653164 PMCID: PMC4344501 DOI: 10.1093/nar/gkv055] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Aleksandre Japaridze
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 845 41 Bratislava, Slovakia
| | - Robert Kwapich
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland Department of Medical Physics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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