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Vilar JMG, Saiz L. The unreasonable effectiveness of equilibrium gene regulation through the cell cycle. Cell Syst 2024; 15:639-648.e2. [PMID: 38981487 DOI: 10.1016/j.cels.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 06/19/2023] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Systems like the prototypical lac operon can reliably hold repression of transcription upon DNA replication across cell cycles with just 10 repressor molecules per cell and behave as if they were at equilibrium. The origin of this phenomenology is still an unresolved question. Here, we develop a general theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation. We find a scaling law linking actual with predicted equilibrium transcription via a single kinetic parameter. We show that even the lac operon functions beyond the physical limits of naive regulation through compensatory mechanisms that suppress non-equilibrium effects. Synthetic systems without adjuvant activators, such as the cAMP receptor protein (CRP), lack this reliability. Our results provide a rationale for the function of CRP, beyond just being a tunable activator, as a mitigator of cell cycle perturbations.
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Affiliation(s)
- Jose M G Vilar
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, 451 E. Health Sciences Drive, Davis, CA 95616, USA; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany.
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2
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Gautam P, Kumar Sinha S. Anticipating response function in gene regulatory networks. J R Soc Interface 2021; 18:20210206. [PMID: 34062105 DOI: 10.1098/rsif.2021.0206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein-DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitative prediction of genetic response and the correlation between the mechanism and the response curve is poorly understood. Here, we report in silico binding studies of GR systems to show that the transcription factor (TF) binds to multiple DNA sites with high cooperativity spreads from specific binding sites into adjacent non-specific DNA and bends the DNA. Our analysis is not limited only to the isolated model system but also can be applied to a system containing multiple interacting genes. The controlling role of TF oligomerization, TF-ligand interactions, and DNA looping for gene expression has been also characterized. The predictions are validated against detailed grand canonical Monte Carlo simulations and published data for the lac operon system. Overall, our study reveals that the expression of target genes can be quantitatively controlled by modulating TF-ligand interactions and the bending energy of DNA.
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Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology, Ropar 140001, India
| | - Sudipta Kumar Sinha
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology, Ropar 140001, India
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3
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Jeddi I, Saiz L. Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate. Sci Rep 2021; 11:10984. [PMID: 34040012 PMCID: PMC8155018 DOI: 10.1038/s41598-021-88796-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/14/2021] [Indexed: 11/09/2022] Open
Abstract
Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs-including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions-and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5' terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.
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Affiliation(s)
- Iman Jeddi
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA
| | - Leonor Saiz
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.
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Xiong X, Han J, Chen Y, Li S, Xiao W, Shi Q. DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment. NANOTECHNOLOGY 2021; 32:055601. [PMID: 33179606 DOI: 10.1088/1361-6528/abb507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The evolution of single-stranded DNA (ssDNA) assembly on octadecylamine (ODA) modified highly oriented pyrolytic graphite (HOPG) surface by heating and ultrasonic treatment has been studied for the first time. We have observed that DNA on the ODA coated HOPG surface underwent dramatic morphological changes as a function of heating and ultrasonic treatment. Ordered DNA firstly changed to random aggregates by heating and then changed to three-dimensional (3D) networks by ultrasonic treatment. This finding points to previously unknown factors that impact graphite-DNA interaction and opens new opportunities to control the deposition of DNA onto graphitic substrates. In this way, we built a cost-effective method to produce large-scale 3D ssDNA networks. All of these studies pave the way to understand the properties of DNA-solid interface, design novel nanomaterials, and improve the sensitivity of DNA biosensors.
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Affiliation(s)
- Xiaolu Xiong
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Junfeng Han
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yu Chen
- Institute of High Energy Physics, CAS. 19B Yuquan Road, Shijingshan District, Beijing 100081, People's Republic of China
| | - Shanshan Li
- Department of Rheumatology, China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Wende Xiao
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Qingfan Shi
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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Iida K, Obata N, Kimura Y. Quantifying heterogeneity of stochastic gene expression. J Theor Biol 2019; 465:56-62. [PMID: 30611711 DOI: 10.1016/j.jtbi.2019.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/27/2018] [Accepted: 01/03/2019] [Indexed: 11/20/2022]
Abstract
The heterogeneity of stochastic gene expression, which refers to the temporal fluctuation in a gene product and its cell-to-cell variation, has attracted considerable interest from biologists, physicists, and mathematicians. The dynamics of protein production and degradation have been modeled as random processes with transition probabilities. However, there is a gap between theory and phenomena, particularly in terms of analytical formulation and parameter estimation. In this study, we propose a theoretical framework in which we present a basic model of a gene regulatory system, derive a steady-state solution, and provide a Bayesian approach for estimating the model parameters from single-cell experimental data. The proposed framework is demonstrated to be applicable for various scales of single-cell experiments at both the mRNA and protein levels and is useful for comparing kinetic parameters across species, genomes, and cell strains.
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Affiliation(s)
- Keita Iida
- Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan.
| | - Nobuaki Obata
- Graduate School of Information Sciences, Tohoku University, Sendai 980-8579, Japan.
| | - Yoshitaka Kimura
- Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan.
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Jeddi I, Saiz L. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. Sci Rep 2017; 7:1178. [PMID: 28446765 PMCID: PMC5430850 DOI: 10.1038/s41598-017-01348-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/24/2017] [Indexed: 12/11/2022] Open
Abstract
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
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Affiliation(s)
- Iman Jeddi
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA
| | - Leonor Saiz
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.
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Abstract
Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed "phase-space sampling," we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332-0430, USA
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9
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Vilar JMG, Saiz L. Suppression and enhancement of transcriptional noise by DNA looping. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:062703. [PMID: 25019810 DOI: 10.1103/physreve.89.062703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 06/03/2023]
Abstract
DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of transcriptional noise in terms of the molecular parameters and elucidate the role of DNA looping. Our results rationalize paradoxical experimental observations and provide the first quantitative explanation of landmark individual-cell measurements at the single molecule level on the classical lac operon genetic system [Choi, L. Cai, K. Frieda, and X. S. Xie, Science 322, 442 (2008)].
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Affiliation(s)
- Jose M G Vilar
- Biophysics Unit (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, P.O. Box 644, 48080 Bilbao, Spain and IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, California 95616, USA
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10
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Petrosyan KG, Hu CK. Oscillations in probability distributions for stochastic gene expression. J Chem Phys 2014; 140:205104. [PMID: 24880335 DOI: 10.1063/1.4875800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The phenomenon of oscillations in probability distribution functions of number of components is found for a model of stochastic gene expression. It takes place in cases of low levels of molecules or strong intracellular noise. The oscillations distinguish between more probable even and less probable odd number of particles. The even-odd symmetry restores as the number of molecules increases with the probability distribution function tending to Poisson distribution. We discuss the possibility of observation of the phenomenon in gene, protein, and mRNA expression experiments.
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Affiliation(s)
- K G Petrosyan
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
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11
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Wang B, Xu B. Transition model for ricin-aptamer interactions with multiple pathways and energy barriers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022720. [PMID: 25353521 DOI: 10.1103/physreve.89.022720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Indexed: 06/04/2023]
Abstract
We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.
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Affiliation(s)
- Bin Wang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia 30602, USA
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia 30602, USA
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12
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Vilar JMG, Saiz L. Systems biophysics of gene expression. Biophys J 2014; 104:2574-85. [PMID: 23790365 DOI: 10.1016/j.bpj.2013.04.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/08/2013] [Accepted: 04/12/2013] [Indexed: 01/16/2023] Open
Abstract
Gene expression is a process central to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular and extracellular changes. This diversity in scales poses fundamental challenges to the use of traditional approaches to fully understand even the simplest gene expression systems. Recent advances in computational systems biophysics have provided promising avenues to reliably integrate the molecular detail of biophysical process into the system behavior. Here, we review recent advances in the description of gene regulation as a system of biophysical processes that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. There is now basic mechanistic understanding on how promoters controlled by multiple, local and distal, DNA binding sites for transcription factors can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including precision and flexibility of the transcriptional responses.
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Affiliation(s)
- Jose M G Vilar
- Biophysics Unit CSIC-UPV/EHU and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain.
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Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K. Taking into account nucleosomes for predicting gene expression. Methods 2013; 62:26-38. [PMID: 23523656 DOI: 10.1016/j.ymeth.2013.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 03/10/2013] [Indexed: 01/10/2023] Open
Abstract
The eukaryotic genome is organized in a chain of nucleosomes that consist of 145-147 bp of DNA wrapped around a histone octamer protein core. Binding of transcription factors (TF) to nucleosomal DNA is frequently impeded, which makes it a challenging task to calculate TF occupancy at a given regulatory genomic site for predicting gene expression. Here, we review methods to calculate TF binding to DNA in the presence of nucleosomes. The main theoretical problems are (i) the computation speed that is becoming a bottleneck when partial unwrapping of DNA from the nucleosome is considered, (ii) the perturbation of the binding equilibrium by the activity of ATP-dependent chromatin remodelers, which translocate nucleosomes along the DNA, and (iii) the model parameterization from high-throughput sequencing data and fluorescence microscopy experiments in living cells. We discuss strategies that address these issues to efficiently compute transcription factor binding in chromatin.
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Affiliation(s)
- Vladimir B Teif
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum-DKFZ & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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