1
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Pandey G, Budhathoki A, Spille JH. Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In Vivo. Methods Mol Biol 2023; 2563:425-445. [PMID: 36227487 DOI: 10.1007/978-1-0716-2663-4_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fluorescence microscopy assays enable the investigation of endogenous biomolecular condensates directly in their cellular context. With appropriate experimental designs, these assays yield quantitative information on condensate material properties and inform on biophysical mechanisms of condensate formation. Single-molecule super-resolution and tracking experiments grant access to the smallest condensates and early condensation stages not resolved by conventional imaging approaches. Here, we discuss considerations for using single-molecule assays to extract quantitative information about biomolecular condensates directly in their cellular context.
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Affiliation(s)
- Ganesh Pandey
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA
| | - Alisha Budhathoki
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
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2
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Williams MR, Xiaokang Y, Hathaway NA, Kireev D. A simulation model of heterochromatin formation at submolecular detail. iScience 2022; 25:104590. [PMID: 35800764 PMCID: PMC9254115 DOI: 10.1016/j.isci.2022.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/16/2021] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
Heterochromatin is a physical state of the chromatin fiber that maintains gene repression during cell development. Although evidence exists on molecular mechanisms involved in heterochromatin formation, a detailed structural mechanism of heterochromatin formation needs a better understanding. We made use of a simple Monte Carlo simulation model with explicit representation of key molecular events to observe molecular self-organization leading to heterochromatin formation. Our simulations provide a structural interpretation of several important traits of the heterochromatinization process. In particular, this study provides a depiction of how small amounts of HP1 are able to induce a highly condensed chromatin state through HP1 dimerization and bridging of sequence-remote nucleosomes. It also elucidates structural roots of a yet poorly understood phenomenon of a nondeterministic nature of heterochromatin formation and subsequent gene repression. Experimental chromatin in vivo assay provides an unbiased estimate of time scale of repressive response to a heterochromatin-triggering event.
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Affiliation(s)
- Michael R. Williams
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Yan Xiaokang
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
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3
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Papale A, Smrek J, Rosa A. Nanorheology of active-passive polymer mixtures differentiates between linear and ring polymer topology. SOFT MATTER 2021; 17:7111-7117. [PMID: 34254620 DOI: 10.1039/d1sm00665g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We study the motion of dispersed nanoprobes in entangled active-passive polymer mixtures. By comparing the two architectures of linear vs. unconcatenated and unknotted circular polymers, we demonstrate that novel, rich physics emerge. For both polymer architectures, nanoprobes of size smaller than the entanglement threshold of the solution move faster as activity is increased and more energy is pumped in the system. For larger nanoprobes, a surprising phenomenon occurs: while in linear solutions they move qualitatively as before, in active-passive ring solutions nanoprobes decelerate with respect to the purely passive conditions. We rationalize this effect in terms of the non-equilibrium, topology-dependent association (clustering) of nanoprobes to the cold component of the ring mixture reminiscent of the recently discovered [Weber et al., Phys. Rev. Lett., 2016, 116, 058301] phase separation in scalar active-passive mixtures. We conclude with a potential connection to the microrheology of the chromatin in the nuclei of the cells.
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Affiliation(s)
- Andrea Papale
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
| | - Angelo Rosa
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
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4
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Felipe C, Shin J, Kolomeisky AB. DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search. J Phys Chem B 2021; 125:1727-1734. [PMID: 33570939 DOI: 10.1021/acs.jpcb.0c09599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein searching and binding to specific sites on DNA is a fundamentally important process that marks the beginning of all major cellular transformations. While the dynamics of protein-DNA interactions in in vitro settings is well investigated, the situation is much more complex for in vivo conditions because the DNA molecules in live cells are packed into chromosomal structures where they are undergoing strong dynamic and conformational fluctuations. In this work, we present a theoretical investigation on the role of DNA looping and DNA conformational fluctuations in the protein target search. It is based on a discrete-state stochastic analysis that allows for explicit calculations of dynamic properties, which is also supplemented by Monte Carlo computer simulations. It is found that for stronger nonspecific interactions between DNA and proteins the search occurs faster on the DNA looped conformation in comparison with the unlooped conformation, and the fastest search is observed when the loop is formed near the target site. It is also shown that DNA fluctuations between the looped and unlooped conformations influence the search dynamics, and this depends on the magnitude of conformational transition rates and on which conformation is more energetically stable. Physical-chemical arguments explaining these observations are presented. Our theoretical study suggests that the geometry and conformational changes in DNA are additional factors that might efficiently control the gene regulation processes.
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Affiliation(s)
- Cayke Felipe
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jaeoh Shin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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5
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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6
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Di Stefano M, Paulsen J, Jost D, Marti-Renom MA. 4D nucleome modeling. Curr Opin Genet Dev 2020; 67:25-32. [PMID: 33253996 PMCID: PMC8098745 DOI: 10.1016/j.gde.2020.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 02/01/2023]
Abstract
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced over the last ten years, many new experimental techniques, mainly based on microscopy and chromosome conformation capture, have been introduced to study the genome in space and time. Owing to the increasing complexity of these cutting-edge techniques, computational approaches have become of paramount importance to interpret, contextualize, and complement such experiments with new insights. Hence, it is becoming crucial for experimental biologists to have a clear understanding of the diverse theoretical modeling approaches available and the biological information each of them can provide.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
| | - Jonas Paulsen
- EVOGENE, Department of Biosciences, Faculty of Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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7
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Hansen AS. CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism. Nucleus 2020; 11:132-148. [PMID: 32631111 PMCID: PMC7566886 DOI: 10.1080/19491034.2020.1782024] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 01/10/2023] Open
Abstract
Mammalian genome structure is closely linked to function. At the scale of kilobases to megabases, CTCF and cohesin organize the genome into chromatin loops. Mechanistically, cohesin is proposed to extrude chromatin loops bidirectionally until it encounters occupied CTCF DNA-binding sites. Curiously, loops form predominantly between CTCF binding sites in a convergent orientation. How CTCF interacts with and blocks cohesin extrusion in an orientation-specific manner has remained a mechanistic mystery. Here, we review recent papers that have shed light on these processes and suggest a multi-step interaction between CTCF and cohesin. This interaction may first involve a pausing step, where CTCF halts cohesin extrusion, followed by a stabilization step of the CTCF-cohesin complex, resulting in a chromatin loop. Finally, we discuss our own recent studies on an internal RNA-Binding Region (RBRi) in CTCF to elucidate its role in regulating CTCF clustering, target search mechanisms and chromatin loop formation and future challenges.
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Affiliation(s)
- Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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Shaban HA, Barth R, Bystricky K. Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription. Genome Biol 2020; 21:278. [PMID: 33203432 PMCID: PMC7670612 DOI: 10.1186/s13059-020-02185-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
The eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber at appropriate sites in a timely manner. We describe how recent advances in quantitative imaging techniques overcome caveats of sequencing-based methods (Hi-C and related) by enabling direct visualization of transcription factors and chromatin at high resolution, from single genes to the whole nucleus. We discuss the contribution of fluorescence imaging to deciphering the principles underlying this coordination within the crowded nuclear space in living cells and discuss challenges ahead.
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Affiliation(s)
- Haitham A Shaban
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, Cairo, 12622, Egypt.
- Current Address: Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
- Institut Universitaire de France (IUF), Paris, France.
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9
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Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome? Int J Mol Sci 2020; 21:ijms21218360. [PMID: 33171795 PMCID: PMC7664663 DOI: 10.3390/ijms21218360] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of the genetic information. Nowadays, 8-oxoG is also considered as an oxidative stress-sensor with a putative role in transcription regulation. In mammalian cells, the modified base is excised by the 8-oxoguanine DNA glycosylase (OGG1), initiating the base excision repair (BER) pathway. OGG1 confronts the massive challenge that is finding rare occurrences of 8-oxoG among a million-fold excess of normal guanines. Here, we review the current knowledge on the search and discrimination mechanisms employed by OGG1 to find its substrate in the genome. While there is considerable data from in vitro experiments, much less is known on how OGG1 is recruited to chromatin and scans the genome within the cellular nucleus. Based on what is known of the strategies used by proteins searching for rare genomic targets, we discuss the possible scenarios allowing the efficient detection of 8-oxoG by OGG1.
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10
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Agbleke AA, Amitai A, Buenrostro JD, Chakrabarti A, Chu L, Hansen AS, Koenig KM, Labade AS, Liu S, Nozaki T, Ovchinnikov S, Seeber A, Shaban HA, Spille JH, Stephens AD, Su JH, Wadduwage D. Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields. Mol Cell 2020; 79:881-901. [PMID: 32768408 PMCID: PMC7888594 DOI: 10.1016/j.molcel.2020.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
Nucleosomes package genomic DNA into chromatin. By regulating DNA access for transcription, replication, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes. In addition, dynamic organization of chromatin underlies both regulation of gene expression and evolution of chromosomes into individualized sister objects, which can segregate cleanly to different daughter cells at anaphase. This collaborative review shines a spotlight on technologies that will be crucial to interrogate key questions in chromatin and chromosome biology including state-of-the-art microscopy techniques, tools to physically manipulate chromatin, single-cell methods to measure chromatin accessibility, computational imaging with neural networks and analytical tools to interpret chromatin structure and dynamics. In addition, this review provides perspectives on how these tools can be applied to specific research fields such as genome stability and developmental biology and to test concepts such as phase separation of chromatin.
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Affiliation(s)
| | - Assaf Amitai
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Aditi Chakrabarti
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Lingluo Chu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristen M Koenig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; JHDSF Program, Harvard University, Cambridge, MA 02138, USA
| | - Ajay S Labade
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sirui Liu
- FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Tadasu Nozaki
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sergey Ovchinnikov
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Andrew Seeber
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA.
| | - Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA; Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew D Stephens
- Biology Department, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | - Jun-Han Su
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dushan Wadduwage
- JHDSF Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
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11
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Saxton MJ. Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model. Biophys J 2020; 118:2151-2167. [PMID: 32294478 PMCID: PMC7203007 DOI: 10.1016/j.bpj.2020.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/28/2020] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
Single-particle tracking experiments have measured escape times of DNA-binding species diffusing in living cells: CRISPR-Cas9, TetR, and LacI. The observed distribution is a truncated power law. Working backward from the experimental results, the observed distribution appears inconsistent with a Gaussian distribution of binding energies. Working forward, the observed distribution leads to transient anomalous subdiffusion, in which diffusion is anomalous at short times and normal at long times, here only mildly anomalous. Monte Carlo simulations are used to characterize the time-dependent diffusion coefficient D(t) in terms of the anomalous exponent α, the crossover time tcross, and the limits D(0) and D(∞) and to relate these quantities to the escape time distribution. The simplest interpretations identify the escape time as the actual binding time to DNA or the period of one-dimensional diffusion on DNA in the standard model combining one-dimensional and three-dimensional search, but a more complicated interpretation may be required. The model has several implications for cell biophysics. 1) The initial anomalous regime represents the search of the DNA-binding species for its target DNA sequence. 2) Non-target DNA sites have a significant effect on search kinetics. False positives in bioinformatic searches of the genome are potentially rate-determining in vivo. For simple binding, the search would be speeded if false-positive sequences were eliminated from the genome. 3) Both binding and obstruction affect diffusion. Obstruction ought to be measured directly, using as the primary probe the DNA-binding species with the binding site inactivated and eGFP as a calibration standard among laboratories and cell types. 4) Overexpression of the DNA-binding species reduces anomalous subdiffusion because the deepest binding sites are occupied and unavailable. 5) The model provides a coarse-grained phenomenological description of diffusion of a DNA-binding species, useful in larger-scale modeling of kinetics, FCS, and FRAP.
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Affiliation(s)
- Michael J Saxton
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California.
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12
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Hansen AS, Amitai A, Cattoglio C, Tjian R, Darzacq X. Guided nuclear exploration increases CTCF target search efficiency. Nat Chem Biol 2019; 16:257-266. [PMID: 31792445 PMCID: PMC7036004 DOI: 10.1038/s41589-019-0422-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022]
Abstract
The enormous size of mammalian genomes means that for a DNA-binding protein, the number of non-specific, off-target sites vastly exceeds the number of specific, cognate sites. How mammalian DNA-binding proteins overcome this challenge to efficiently locate their target sites is not known. Here through live-cell single-molecule tracking, we show that CCCTC-binding factor, CTCF, is repeatedly trapped in small zones that likely correspond to CTCF clusters, in a manner that is largely dependent on an internal RNA-binding region (RBRi). We develop a new theoretical model, Anisotropic Diffusion through transient Trapping in Zones (ADTZ), to explain CTCF dynamics. Functionally, transient RBRi-mediated trapping increases the efficiency of CTCF target search by ~2.5 fold. Overall, our results suggest a “guided” mechanism where CTCF clusters concentrate diffusing CTCF proteins near cognate binding sites, thus increasing the local ON-rate. We suggest that local guiding may allow DNA-binding proteins to more efficiently locate their target sites.
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Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Assaf Amitai
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA. .,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA, USA. .,CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.
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13
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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14
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Murugan R. Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks. Biophys J 2019; 114:2516-2529. [PMID: 29874603 DOI: 10.1016/j.bpj.2018.04.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/13/2018] [Accepted: 04/24/2018] [Indexed: 01/19/2023] Open
Abstract
We show that nucleosomes exert a maximal amount of hindrance to the one-dimensional diffusion of transcription factors (TFs) when they are present between TFs and their cognate sites on DNA. The effective one-dimensional diffusion coefficient of TFs (χTF) decreases with a rise in the free-energy barrier (μNU) of the sliding of nucleosomes as χTF∝exp(-μNU). The average time (ηL) required by TFs to slide over L sites on DNA increases with μNU as ηL∝exp(μNU). When TFs move close to nucleosomes, then they exhibit typical subdiffusion. Nucleosomes can enhance the search dynamics of TFs when TFs are present between nucleosomes and TF binding sites. These results suggest that nucleosome-depleted regions around the cognate sites of TFs are mandatory for efficient site-specific binding of TFs. Remarkably, the genome-wide in vivo positioning pattern of TFs shows a maximum at their specific binding sites where the occupancy of nucleosomes shows a minimum. This could be a consequence of an increasing level of breathing dynamics of nucleosome cores and decreasing levels of fluctuations in the DNA binding domains of TFs as they move across TF binding sites. The dynamics of TFs becomes slow as they approach their cognate sites so that TFs form a tight site-specific complex, whereas the dynamics of nucleosomes becomes rapid so that they quickly pass through the cognate sites of TFs. Several in vivo data sets on the genome-wide positioning pattern of nucleosomes and TFs agree well with our arguments. The retarding effects of nucleosomes can be minimized when the degree of condensation of DNA is such that it can permit a jump size associated with the dynamics of TFs beyond ∼160-180 bp.
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Affiliation(s)
- Rajamanickam Murugan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.
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15
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McSwiggen DT, Hansen AS, Teves SS, Marie-Nelly H, Hao Y, Heckert AB, Umemoto KK, Dugast-Darzacq C, Tjian R, Darzacq X. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. eLife 2019; 8:e47098. [PMID: 31038454 PMCID: PMC6522219 DOI: 10.7554/elife.47098] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol II into membraneless domains, reminiscent of liquid-liquid phase separation. Despite sharing several properties with phase-separated condensates, we show that RCs operate via a distinct mechanism wherein unrestricted nonspecific protein-DNA interactions efficiently outcompete host chromatin, profoundly influencing the way DNA-binding proteins explore RCs. We find that the viral genome remains largely nucleosome-free, and this increase in accessibility allows Pol II and other DNA-binding proteins to repeatedly visit nearby DNA binding sites. This anisotropic behavior creates local accumulations of protein factors despite their unrestricted diffusion across RC boundaries. Our results reveal underappreciated consequences of nonspecific DNA binding in shaping gene activity, and suggest additional roles for chromatin in modulating nuclear function and organization.
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Affiliation(s)
- David Trombley McSwiggen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Anders S Hansen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Sheila S Teves
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Department of Biochemistry and Molecular BiologyUniversity of British ColumbiaVancouverCanada
| | - Hervé Marie-Nelly
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Yvonne Hao
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Alec Basil Heckert
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Kayla K Umemoto
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- California Institute of Regenerative Medicine Center of ExcellenceUniversity of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
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16
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Schuss Z, Basnayake K, Holcman D. Redundancy principle and the role of extreme statistics in molecular and cellular biology. Phys Life Rev 2019; 28:52-79. [PMID: 30691960 DOI: 10.1016/j.plrev.2019.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
The paradigm of chemical activation rates in cellular biology has been shifted from the mean arrival time of a single particle to the mean of the first among many particles to arrive at a small activation site. The activation rate is set by extremely rare events, which have drastically different time scales from the mean times between activations, and depends on different structural parameters. This shift calls for reconsideration of physical processes used in deterministic and stochastic modeling of chemical reactions that are based on the traditional forward rate, especially for fast activation processes in living cells. Consequently, the biological activation time is not necessarily exponentially distributed. We review here the physical models, the mathematical analysis and the new paradigm of setting the scale to be the shortest time for activation that clarifies the role of population redundancy in selecting and accelerating transient cellular search processes. We provide examples in cellular transduction, gene activation, cell senescence activation or spermatozoa selection during fertilization, where the rate depends on numbers. We conclude that the statistics of the minimal time to activation set kinetic laws in biology, which can be very different from the ones associated to average times.
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Affiliation(s)
- Z Schuss
- Department of Applied Mathematics, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - K Basnayake
- Computational Biology and Applied Mathematics, Ecole Normale Supérieure, Paris, France
| | - D Holcman
- Computational Biology and Applied Mathematics, Ecole Normale Supérieure, Paris, France; Churchill College, Univ. of Cambridge, CB30DS, UK.
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