1
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Ghosh N, Santoni D, Saha I, Felici G. Predicting Transcription Factor Binding Sites with Deep Learning. Int J Mol Sci 2024; 25:4990. [PMID: 38732207 PMCID: PMC11084193 DOI: 10.3390/ijms25094990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Prediction of binding sites for transcription factors is important to understand how the latter regulate gene expression and how this regulation can be modulated for therapeutic purposes. A consistent number of references address this issue with different approaches, Machine Learning being one of the most successful. Nevertheless, we note that many such approaches fail to propose a robust and meaningful method to embed the genetic data under analysis. We try to overcome this problem by proposing a bidirectional transformer-based encoder, empowered by bidirectional long-short term memory layers and with a capsule layer responsible for the final prediction. To evaluate the efficiency of the proposed approach, we use benchmark ChIP-seq datasets of five cell lines available in the ENCODE repository (A549, GM12878, Hep-G2, H1-hESC, and Hela). The results show that the proposed method can predict TFBS within the five different cell lines very well; moreover, cross-cell predictions provide satisfactory results as well. Experiments conducted across cell lines are reinforced by the analysis of five additional lines used only to test the model trained using the others. The results confirm that prediction across cell lines remains very high, allowing an extensive cross-transcription factor analysis to be performed from which several indications of interest for molecular biology may be drawn.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha ’O’ Anusandhan (Deemed to be University), Bhubaneswar 751030, India
| | - Daniele Santoni
- Institute for System Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, 00185 Rome, Italy; (D.S.); (G.F.)
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata 700106, India;
| | - Giovanni Felici
- Institute for System Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, 00185 Rome, Italy; (D.S.); (G.F.)
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2
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Shang S, Gao F, Zhang Q, Song T, Wang W, Liu D, Gong Y, Lu X. 0.263 terahertz irradiation induced genes expression changes in Caenorhabditis elegans. iScience 2024; 27:109391. [PMID: 38532884 PMCID: PMC10963221 DOI: 10.1016/j.isci.2024.109391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/18/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
The biosafety of terahertz (THz) waves has emerged as a new area of concern with the gradual application of terahertz radiation. Even though many studies have been conducted to investigate the influence of THz radiation on living organisms, the biological effects of terahertz waves have not yet been fully revealed. In this study, Caenorhabditis elegans (C. elegans) was used to evaluate the biological consequences of whole-body exposure to 0.263 THz irradiation. The integration of transcriptome sequencing and behavioral tests of C. elegans revealed that high-power THz irradiation damaged the epidermal ultrastructures, inhibited the expression of the cuticle collagen genes, and impaired the movement of C. elegans. Moreover, the genes involved in the immune system and the neural system were dramatically down-regulated by high-power THz irradiation. Our findings offer fresh perspectives on the biological impacts of high-power THz radiation that could cause epidermal damage and provoke a systemic response.
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Affiliation(s)
- Sen Shang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P.R. China
| | - Fei Gao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P.R. China
| | - Qi Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P.R. China
| | - Tao Song
- Terahertz Science and Technology Research Center, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Wei Wang
- Terahertz Science and Technology Research Center, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Diwei Liu
- Terahertz Science and Technology Research Center, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yubin Gong
- Terahertz Science and Technology Research Center, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaoyun Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P.R. China
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3
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Bishop AR, Alexandrov B, Usheva A. Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575935. [PMID: 38293094 PMCID: PMC10827174 DOI: 10.1101/2024.01.16.575935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA's biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) data in vivo involving 690 TF-DNA binding events in human genome, our model significantly improves prediction performance in over 660 binding events, with up to 9.6% increase in AUROC metric compared to the baseline model when using no DNA biophysical properties explicitly. Further, we expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (SELEX) and Protein Binding Microarray (PBM) datasets, comparing our model with established frameworks. The inclusion of DNA breathing features consistently improved TF binding predictions across different cell lines in these datasets. Notably, for complex ChIP-Seq datasets, integrating DNABERT2 with a cross-attention mechanism provided greater predictive capabilities and insights into the mechanisms of disease-related non-coding variants found in genome-wide association studies. This work highlights the importance of DNA biophysical characteristics in TF binding and the effectiveness of multi-modal deep learning models in gene regulation studies.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
- Department of Computer Science, George Mason University, 4400 University Dr, 22030, VA, USA
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, 4400 University Dr, 22030, VA, USA
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, USA
| | - Anny Usheva
- Department of Surgery, Brown University, 69 Brown St Box 1822, 02912, RI, USA
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4
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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5
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov B. Examining DNA breathing with pyDNA-EPBD. Bioinformatics 2023; 39:btad699. [PMID: 37991847 PMCID: PMC10681863 DOI: 10.1093/bioinformatics/btad699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
MOTIVATION The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Anny Usheva
- Department of Surgery, Brown University, Providence, RI 02912, United States
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
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6
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov BS. Examining DNA Breathing with pyDNA-EPBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557010. [PMID: 37745370 PMCID: PMC10515784 DOI: 10.1101/2023.09.09.557010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Motivation The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Amarda Shehu
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Anny Usheva
- Brown University, 69 Brown St Box 1822, Providence, RI 02912
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
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7
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Bubble Relaxation Dynamics in Homopolymer DNA Sequences. Molecules 2023; 28:molecules28031041. [PMID: 36770707 PMCID: PMC9920605 DOI: 10.3390/molecules28031041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.
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8
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Barbero-Aparicio JA, Cuesta-Lopez S, García-Osorio CI, Pérez-Rodríguez J, García-Pedrajas N. Nonlinear physics opens a new paradigm for accurate transcription start site prediction. BMC Bioinformatics 2022; 23:565. [PMID: 36585618 PMCID: PMC9801560 DOI: 10.1186/s12859-022-05129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learning (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors.
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Affiliation(s)
- José Antonio Barbero-Aparicio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Santiago Cuesta-Lopez
- grid.23520.360000 0000 8569 1592Universidad de Burgos, Hospital del Rey, s/n, 09001 Burgos, Spain ,ICAMCyL Foundation, Internacional Center for Advanced Materials and Raw Materials of Castilla y León, León Technology Park, main building, first floor, offices 106-108, C/Julia Morros s/n, Armunia, 24009 León, Spain
| | - César Ignacio García-Osorio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Javier Pérez-Rodríguez
- grid.449008.10000 0004 1795 4150Departamento de Métodos Cuantitativos, Universidad de Loyola Andalucía, Escritor Castilla Aguayo, 4, 14004 Córdoba, Spain
| | - Nicolás García-Pedrajas
- grid.411901.c0000 0001 2183 9102Department of Computing and Numerical Analysis, University of Córdoba, Edificio Albert Einstein, Campus de Rabanales, 14071 Córdoba, Spain
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9
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Han K, Shen LC, Zhu YH, Xu J, Song J, Yu DJ. MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Brief Bioinform 2021; 23:6399874. [PMID: 34664074 DOI: 10.1093/bib/bbab445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/06/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
Accurate identification of transcription factor binding sites is of great significance in understanding gene expression, biological development and drug design. Although a variety of methods based on deep-learning models and large-scale data have been developed to predict transcription factor binding sites in DNA sequences, there is room for further improvement in prediction performance. In addition, effective interpretation of deep-learning models is greatly desirable. Here we present MAResNet, a new deep-learning method, for predicting transcription factor binding sites on 690 ChIP-seq datasets. More specifically, MAResNet combines the bottom-up and top-down attention mechanisms and a state-of-the-art feed-forward network (ResNet), which is constructed by stacking attention modules that generate attention-aware features. In particular, the multi-scale attention mechanism is utilized at the first stage to extract rich and representative sequence features. We further discuss the attention-aware features learned from different attention modules in accordance with the changes as the layers go deeper. The features learned by MAResNet are also visualized through the TMAP tool to illustrate that the method can extract the unique characteristics of transcription factor binding sites. The performance of MAResNet is extensively tested on 690 test subsets with an average AUC of 0.927, which is higher than that of the current state-of-the-art methods. Overall, this study provides a new and useful framework for the prediction of transcription factor binding sites by combining the funnel attention modules with the residual network.
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Affiliation(s)
- Ke Han
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Long-Chen Shen
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Yi-Heng Zhu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Jian Xu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China
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10
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Hillebrand M, Kalosakas G, Bishop AR, Skokos C. Bubble lifetimes in DNA gene promoters and their mutations affecting transcription. J Chem Phys 2021; 155:095101. [PMID: 34496591 DOI: 10.1063/5.0060335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.
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Affiliation(s)
- M Hillebrand
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - A R Bishop
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Ch Skokos
- Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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11
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Shang S, Wu X, Zhang Q, Zhao J, Hu E, Wang L, Lu X. 0.1 THz exposure affects primary hippocampus neuron gene expression via alternating transcription factor binding. BIOMEDICAL OPTICS EXPRESS 2021; 12:3729-3742. [PMID: 34221691 PMCID: PMC8221933 DOI: 10.1364/boe.426928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/09/2021] [Accepted: 05/24/2021] [Indexed: 05/15/2023]
Abstract
In recent years, many studies have been conducted to investigate the influence of terahertz (THz) radiation on the gene expression in various cell types, but the underling molecular mechanism has not yet been fully revealed. In this study, we explored the effects of 0.1 THz radiation on the gene expression in primary neuron cells through RNA-seq analysis. 111 up-regulated and 54 down-regulated genes were identified. Several biomolecule binding related categories such as "long-chain fatty acid binding", "tropomyosin binding", "BMP receptor binding", as well as "GTPase binding" and "phospholipid binding" were enriched by GO analysis. Moreover, the GSEA analysis indicated that genes encoding protein biosynthetic machinery ribosome were up-regulated by 0.1 THz irradiation. In addition, we demonstrated that the binding efficiency of a transcription factor (TF) AP-1 with its transcription factor binding site (TFBS) in DNA was reduced by THz irradiation, which suggested that THz irradiation might affect the interaction between TFs with DNA and consequently regulate the gene expression. Our results provide new insights into the biological effects of terahertz irradiation.
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12
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Yakushevich LV, Krasnobaeva LA. Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics. Biophys Rev 2021; 13:315-338. [PMID: 34178171 PMCID: PMC8214655 DOI: 10.1007/s12551-021-00801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12551-021-00801-0.
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Affiliation(s)
- Ludmila V. Yakushevich
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Larisa A. Krasnobaeva
- Siberian State Medical University, Tomsk, Russia
- Tomsk State University, Tomsk, Russia
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13
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Chen B, Huang Q, Qu Z, Li C, Li Q, Shi J, Fan C, Wang L, Zuo X, Shen J, Li J. Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer. Angew Chem Int Ed Engl 2021; 60:6624-6630. [PMID: 33314629 DOI: 10.1002/anie.202014466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Indexed: 12/17/2022]
Abstract
Variation of DNA conformation is important in regulating gene expression and mediating drug-DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label-free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i-motifs, G-quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label-free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells.
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Affiliation(s)
- Bin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
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14
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Chen B, Huang Q, Qu Z, Li C, Li Q, Shi J, Fan C, Wang L, Zuo X, Shen J, Li J. Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Chen
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Cong Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
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15
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Menssen RJ, Kimmel GJ, Tokmakoff A. Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations. J Chem Phys 2021; 154:045101. [PMID: 33514113 DOI: 10.1063/5.0035187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The model is designed to be accessible to experimental researchers in terms of both computational simplicity and expense while providing detailed insights beyond those provided by experimental methods. The model is an extension of a thermodynamic lattice model for DNA hybridization utilizing the formalism of the nucleation-zipper mechanism. Association and dissociation trajectories were generated utilizing the Gillespie algorithm and parameters determined via fitting the association and dissociation timescales to previously published experimental data. Terminal end fraying, experimentally observed following a rapid T-jump, in the sequence 5'-ATATGCATAT-3' was replicated by the model that also demonstrated that experimentally observed fast dynamics in the sequences 5'-C(AT)nG-3', where n = 2-6, were also due to terminal end fraying. The dominant association pathways, isolated by transition pathway theory, showed two primary motifs: initiating at or next to a G:C base pair, which is enthalpically favorable and related to the increased strength of G:C base pairs, and initiating in the center of the sequence, which is entropically favorable and related to minimizing the penalty associated with the decrease in configurational entropy due to hybridization.
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Affiliation(s)
- Ryan J Menssen
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gregory J Kimmel
- Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida 33612, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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16
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Hillebrand M, Kalosakas G, Skokos C, Bishop AR. Distributions of bubble lifetimes and bubble lengths in DNA. Phys Rev E 2020; 102:062114. [PMID: 33465959 DOI: 10.1103/physreve.102.062114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.
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Affiliation(s)
- M Hillebrand
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - Ch Skokos
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - A R Bishop
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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17
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Liebl K, Zacharias M. How global DNA unwinding causes non-uniform stress distribution and melting of DNA. PLoS One 2020; 15:e0232976. [PMID: 32413048 PMCID: PMC7228070 DOI: 10.1371/journal.pone.0232976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
- * E-mail:
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18
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Martis B S, Forquet R, Reverchon S, Nasser W, Meyer S. DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria? Comput Struct Biotechnol J 2019; 17:1047-1055. [PMID: 31452857 PMCID: PMC6700405 DOI: 10.1016/j.csbj.2019.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/28/2022] Open
Abstract
DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.
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Affiliation(s)
- Shiny Martis B
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 11 avenue Jean Capelle, 69621 Villeurbanne, France
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19
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Hillebrand M, Kalosakas G, Schwellnus A, Skokos C. Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model. Phys Rev E 2019; 99:022213. [PMID: 30934325 DOI: 10.1103/physreve.99.022213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 06/09/2023]
Abstract
We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.
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Affiliation(s)
- M Hillebrand
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - G Kalosakas
- Department of Materials Science, University of Patras, GR-26504 Rio, Greece
| | - A Schwellnus
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - Ch Skokos
- Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
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20
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Zdravković S, Satarić MV, Parkhomenko AY, Bugay AN. Demodulated standing solitary wave and DNA-RNA transcription. CHAOS (WOODBURY, N.Y.) 2018; 28:113103. [PMID: 30501228 DOI: 10.1063/1.5046772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA.
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Affiliation(s)
- S Zdravković
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
| | - M V Satarić
- Department of Mathematics, Physics and Geosciences, Serbian Academy of Sciences and Arts, 11000 Beograd, Serbia
| | - A Yu Parkhomenko
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
| | - A N Bugay
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
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21
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Zrimec J, Lapanje A. DNA structure at the plasmid origin-of-transfer indicates its potential transfer range. Sci Rep 2018; 8:1820. [PMID: 29379098 PMCID: PMC5789077 DOI: 10.1038/s41598-018-20157-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/10/2018] [Indexed: 11/29/2022] Open
Abstract
Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efficiently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.html.
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Affiliation(s)
- Jan Zrimec
- Institute of Metagenomics and Microbial Technologies, 1000, Ljubljana, Slovenia. .,Faculty of Health Sciences, University of Primorska, 6320, Izola, Slovenia. .,Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden.
| | - Aleš Lapanje
- Institute of Metagenomics and Microbial Technologies, 1000, Ljubljana, Slovenia. .,Department of Nanotechnology, Saratov State University, 410012, Saratov, Russian Federation. .,Department of Environmental Sciences, Institute Jožef Štefan, 1000, Ljubljana, Slovenia.
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22
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Alexandrov LB, Rasmussen KØ, Bishop AR, Alexandrov BS. Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization. Sci Rep 2017; 7:9731. [PMID: 28851939 PMCID: PMC5575098 DOI: 10.1038/s41598-017-09537-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/27/2017] [Indexed: 12/11/2022] Open
Abstract
The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded "flexible hinges" to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87545, United States of America.
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA.
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23
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Taylor RL, Cruickshank MN, Karimi M, Ng HL, Quail E, Kaufman KM, Harley JB, Abraham LJ, Tsao BP, Boackle SA, Ulgiati D. Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells. Cell Mol Immunol 2016; 13:119-31. [PMID: 25640655 PMCID: PMC4711682 DOI: 10.1038/cmi.2014.138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/05/2014] [Accepted: 12/27/2014] [Indexed: 12/13/2022] Open
Abstract
Complement receptor 2 (CR2/CD21) is predominantly expressed on the surface of mature B cells where it forms part of a coreceptor complex that functions, in part, to modulate B-cell receptor signal strength. CR2/CD21 expression is tightly regulated throughout B-cell development such that CR2/CD21 cannot be detected on pre-B or terminally differentiated plasma cells. CR2/CD21 expression is upregulated at B-cell maturation and can be induced by IL-4 and CD40 signaling pathways. We have previously characterized elements in the proximal promoter and first intron of CR2/CD21 that are involved in regulating basal and tissue-specific expression. We now extend these analyses to the CR2/CD21 core promoter. We show that in mature B cells, CR2/CD21 transcription proceeds from a focused TSS regulated by a non-consensus TATA box, an initiator element and a downstream promoter element. Furthermore, occupancy of the general transcriptional machinery in pre-B versus mature B-cell lines correlate with CR2/CD21 expression level and indicate that promoter accessibility must switch from inactive to active during the transitional B-cell window.
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Affiliation(s)
- Rhonda L Taylor
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
| | - Mahdad Karimi
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Han Leng Ng
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Elizabeth Quail
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Lawrence J Abraham
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniela Ulgiati
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
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24
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Huang HH, Seeger C, Danielson UH, Lindblad P. Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria. BMC Res Notes 2015; 8:459. [PMID: 26387086 PMCID: PMC4575469 DOI: 10.1186/s13104-015-1425-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for strong and tightly regulated promoters to construct more reliable and predictable genetic modules for synthetic biology and metabolic engineering. For this reason we have previously constructed a TetR regulated L promoter library for the cyanobacterium Synechocystis PCC 6803. In addition to the L03 promoter showing wide dynamic range of transcriptional regulation, we observed the L09 promoter as unique in high leaky gene expression under repressed conditions. In the present study, we attempted to identify the cause of L09 promoter leakage. TetR binding to the promoter was studied by theoretical simulations of DNA breathing dynamics and by surface plasmon resonance (SPR) biosensor technology to analyze the kinetics of the DNA-protein interactions. RESULTS DNA breathing dynamics of a promoter was computed with the extended nonlinear Peyrard-Bishop-Dauxois mesoscopic model to yield a DNA opening probability profile at a single nucleotide resolution. The L09 promoter was compared to the L10, L11, and L12 promoters that were point-mutated and different in repressed promoter strength. The difference between DNA opening probability profiles is trivial on the TetR binding site. Furthermore, the kinetic rate constants of TetR binding, as measured by SPR biosensor technology, to the respective promoters are practically identical. This suggests that a trivial difference in probability as low as 1 × 10(-4) cannot lead to detectable variations in the DNA-protein interactions. Higher probability at the downstream region of transcription start site of the L09 promoter compared to the L10, L11, and L12 promoters was observed. Having practically the same kinetics of binding to TetR, the leakage problem of the L09 promoter might be due to enhanced RNA Polymerase (RNAP)-promoter interactions in the downstream region. CONCLUSIONS Both theoretical and experimental analyses of the L09 promoter's leakage problem exclude a mechanism of reduced TetR binding but instead suggest enhanced RNAP binding. These results assist in creating more tightly regulated promoters for realizing synthetic biology and metabolic engineering in biotechnological applications.
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Affiliation(s)
- Hsin-Ho Huang
- Department of Chemistry - Ångström, Science for Life Laboratory, Microbial Chemistry, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden.
| | - Christian Seeger
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, 751 23, Uppsala, Sweden.
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, 751 23, Uppsala, Sweden.
| | - Peter Lindblad
- Department of Chemistry - Ångström, Science for Life Laboratory, Microbial Chemistry, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden.
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25
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Zrimec J, Lapanje A. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1137-1145. [PMID: 26451825 DOI: 10.1109/tcbb.2015.2396057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.
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Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1. J Virol 2015; 89:6453-61. [PMID: 25878101 DOI: 10.1128/jvi.00363-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/03/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Sulfolobus spindle-shaped virus 1 represents a model for studying virus-host interaction in harsh environments, and it is so far the only member of the family Fuselloviridae that shows a UV-inducible life cycle. Although the virus has been extensively studied, mechanisms underpinning the maintenance of lysogeny as well as those regulating the UV induction have received little attention. Recently, a novel SSV1 transcription factor, F55, was identified. This factor was able to bind in vitro to several sequences derived from the early and UV-inducible promoters of the SSV1 genome. The location of these binding sites together with the differential affinity of F55 for these sequences led to the hypothesis that this protein might be involved in the maintenance of the SSV1 lysogeny. Here, we report an in vivo survey of the molecular events occurring at the UV-inducible region of the SSV1 genome, with a focus on the binding profile of F55 before and after the UV irradiation. The binding of F55 to the target promoters correlates with transcription repression, whereas its dissociation is paralleled by transcription activation. Therefore, we propose that F55 acts as a molecular switch for the transcriptional regulation of the early viral genes. IMPORTANCE Functional genomic studies of SSV1 proteins have been hindered by the lack of similarity with other characterized proteins. As a result, few insights into their in vivo roles have been gained throughout the last 3 decades. Here, we report the first in vivo investigation of an SSV1 transcription regulator, F55, that plays a key role in the transition from the lysogenic to the induced state of SSV1. We show that F55 regulates the expression of the UV-inducible as well as the early genes. Moreover, the differential affinity of this transcription factor for these targets allows a fine-tuned and temporal coordinated regulation of transcription of viral genes.
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Duan J, Shi J, Fiorentino A, Leites C, Chen X, Moy W, Chen J, Alexandrov BS, Usheva A, He D, Freda J, O'Brien NL, McQuillin A, Sanders AR, Gershon ES, DeLisi LE, Bishop AR, Gurling HMD, Pato MT, Levinson DF, Kendler KS, Pato CN, Gejman PV. A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder. Am J Hum Genet 2014; 95:744-53. [PMID: 25434007 PMCID: PMC4259974 DOI: 10.1016/j.ajhg.2014.11.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/03/2014] [Indexed: 12/17/2022] Open
Abstract
Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression.
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Affiliation(s)
- Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA.
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alessia Fiorentino
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Catherine Leites
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Xiangning Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Winton Moy
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jingchun Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Boian S Alexandrov
- Harvard Medical School, Boston, MA 02115, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Anny Usheva
- Harvard Medical School, Boston, MA 02115, USA
| | - Deli He
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jessica Freda
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Niamh L O'Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Alan R Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Lynn E DeLisi
- VA Boston Healthcare System, Harvard Medical School, Brockton, MA 02301, USA
| | - Alan R Bishop
- Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Hugh M D Gurling
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Douglas F Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Pablo V Gejman
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
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Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters. PLoS Comput Biol 2014; 10:e1003835. [PMID: 25275384 PMCID: PMC4183373 DOI: 10.1371/journal.pcbi.1003835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/26/2014] [Indexed: 01/23/2023] Open
Abstract
The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy), with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences. Binding of specific proteins to particular sites in the DNA sequence is a fundamental issue for gene regulation in molecular biology and genetic engineering. A deep understanding of cell physiology requires the analysis of a plethora of genes involving characterization of their promoter architectures that determine their regulation and gene transcription. In order to locate the promoter elements of a given gene, experimental determination of its transcription start site (TSS) is required. This is an expensive, time-consuming task that, depending on our requirements, could be simplified using computational analysis as a first approach. Nevertheless, most computational methods lack a physical basis on the protein-DNA interaction mechanism. We adopt here this strategy, by using a simple model for protein-DNA interaction to find TSS in a bunch of cyanobacteria promoters. We make use of physical tools to characterize these TSS and to relate them with biological properties as the relative strength of the promoter. Our study shows how a model based on a coarse-grained description of a biomolecule can give valuable insight on its biological function.
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Meyer S, Beslon G. Torsion-mediated interaction between adjacent genes. PLoS Comput Biol 2014; 10:e1003785. [PMID: 25188032 PMCID: PMC4154641 DOI: 10.1371/journal.pcbi.1003785] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/26/2014] [Indexed: 11/17/2022] Open
Abstract
DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of stress propagates over several kilobases. If another promoter is located in this range, this stress may strongly modify its opening properties, and hence facilitate or hinder its transcription. This mechanism implies that transcribed genes distant of a few kilobases are not independent, but coupled by torsional stress, an effect for which we propose the first quantitative and systematic model. In contrast to previously proposed mechanisms of transcriptional interference, the suggested coupling is not mediated by the transcription machineries, but results from the universal mechanical features of the double-helix. The model shows that the effect likely affects prokaryotes as well as eukaryotes, but with different consequences owing to their different basal levels of torsion. It also depends crucially on the relative orientation of the genes, enhancing the expression of eukaryotic divergent pairs while reducing that of prokaryotic convergent ones. To test the in vivo influence of the torsional coupling, we analyze the expression of isolated gene pairs in the Drosophila melanogaster genome. Their orientation and distance dependence is fully consistent with the model, suggesting that torsional gene coupling may constitute a widespread mechanism of (co)regulation in eukaryotes.
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Affiliation(s)
- Sam Meyer
- Université de Lyon, INSA Lyon, INRIA, LIRIS, CNRS UMR5205, Lyon, France
| | - Guillaume Beslon
- Université de Lyon, INSA Lyon, INRIA, LIRIS, CNRS UMR5205, Lyon, France
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30
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Variation and constraints in species-specific promoter sequences. J Theor Biol 2014; 363:357-66. [PMID: 25149367 DOI: 10.1016/j.jtbi.2014.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 08/04/2014] [Indexed: 11/24/2022]
Abstract
A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes. In particular, we have analyzed base composition, periodicity and information content in sets of aligned promoters clustered according to functional information in order to obtain an insight on the main structural differences between promoters regulating genes with different functions. Our results show that when we select promoters according to some biological information, in a single species, at least in vertebrates, we observe structurally different classes of sequences. The highly variable and differentiated gene expression patterns may explain the great extent of structural differentiation observed in complex organisms. In fact, despite our analysis is focused on Homo sapiens, we provide also a comparison with other species, selected at different positions in the phylogenetic tree.
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31
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Gelev V, Zabolotny JM, Lange M, Hiromura M, Yoo SW, Orlando JS, Kushnir A, Horikoshi N, Paquet E, Bachvarov D, Schaffer PA, Usheva A. A new paradigm for transcription factor TFIIB functionality. Sci Rep 2014; 4:3664. [PMID: 24441171 PMCID: PMC3895905 DOI: 10.1038/srep03664] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/12/2013] [Indexed: 12/23/2022] Open
Abstract
Experimental and bioinformatic studies of transcription initiation by RNA polymerase II (RNAP2) have revealed a mechanism of RNAP2 transcription initiation less uniform across gene promoters than initially thought. However, the general transcription factor TFIIB is presumed to be universally required for RNAP2 transcription initiation. Based on bioinformatic analysis of data and effects of TFIIB knockdown in primary and transformed cell lines on cellular functionality and global gene expression, we report that TFIIB is dispensable for transcription of many human promoters, but is essential for herpes simplex virus-1 (HSV-1) gene transcription and replication. We report a novel cell cycle TFIIB regulation and localization of the acetylated TFIIB variant on the transcriptionally silent mitotic chromatids. Taken together, these results establish a new paradigm for TFIIB functionality in human gene expression, which when downregulated has potent anti-viral effects.
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Affiliation(s)
- Vladimir Gelev
- 1] Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA [2]
| | - Janice M Zabolotny
- 1] Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA [2]
| | - Martin Lange
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Makoto Hiromura
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Sang Wook Yoo
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joseph S Orlando
- Department of Microbiology and Molecular Genetics, Program in Virology, Harvard Medical School at Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Anna Kushnir
- Department of Microbiology and Molecular Genetics, Program in Virology, Harvard Medical School at Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Nobuo Horikoshi
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Eric Paquet
- Centre Hospitalier Universitaire de Québec (CHUQ)-Centre de Recherche, Hopital L'Hôtel-Dieu de Québec et Université Laval, Québec G1R 2J6, Canada
| | - Dimcho Bachvarov
- Centre Hospitalier Universitaire de Québec (CHUQ)-Centre de Recherche, Hopital L'Hôtel-Dieu de Québec et Université Laval, Québec G1R 2J6, Canada
| | - Priscilla A Schaffer
- Department of Microbiology and Molecular Genetics, Program in Virology, Harvard Medical School at Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Anny Usheva
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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32
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Oberstrass FC, Fernandes LE, Lebel P, Bryant Z. Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics. PHYSICAL REVIEW LETTERS 2013; 110:178103. [PMID: 23679785 PMCID: PMC3696636 DOI: 10.1103/physrevlett.110.178103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 05/16/2023]
Abstract
Changes in global DNA linking number can be accommodated by localized changes in helical structure. We have used single-molecule torque measurements to investigate sequence-specific strand separation and Z-DNA formation. By controlling the boundary conditions at the edges of sequences of interest, we have confirmed theoretical predictions of distinctive boundary-dependent backbending patterns in torque-twist relationships. Abrupt torque jumps are associated with the formation and collapse of DNA bubbles, permitting direct observations of DNA breathing dynamics.
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Affiliation(s)
| | | | - Paul Lebel
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA 94305, USA
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Bergues-Pupo AE, Bergues JM, Falo F. Modeling the interaction of DNA with alternating fields. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022703. [PMID: 23496544 DOI: 10.1103/physreve.87.022703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Indexed: 05/22/2023]
Abstract
We study the influence of a terahertz field on thermal properties of DNA molecules. A Peyrard-Bishop-Dauxois model with the inclusion of a solvent interaction term is considered. The terahertz field is included as a sinusoidal driven force in the equation of motion. We show how under certain field and system parameters, the melting transition and bubble formation are modified.
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Affiliation(s)
- A E Bergues-Pupo
- Departamento de Física, Universidad de Oriente, 90500 Santiago de Cuba, Cuba
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Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells. Sci Rep 2013; 3:1184. [PMID: 23378916 PMCID: PMC3560359 DOI: 10.1038/srep01184] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/14/2013] [Indexed: 12/13/2022] Open
Abstract
We report that terahertz (THz) irradiation of mouse mesenchymal stem cells (mMSCs) with a single-frequency (SF) 2.52 THz laser or pulsed broadband (centered at 10 THz) source results in irradiation specific heterogenic changes in gene expression. The THz effect depends on irradiation parameters such as the duration and type of THz source, and on the degree of stem cell differentiation. Our microarray survey and RT-PCR experiments demonstrate that prolonged broadband THz irradiation drives mMSCs toward differentiation, while 2-hour irradiation (regardless of THz sources) affects genes transcriptionally active in pluripotent stem cells. The strictly controlled experimental environment indicates minimal temperature changes and the absence of any discernable response to heat shock and cellular stress genes imply a non-thermal response. Computer simulations of the core promoters of two pluripotency markers reveal association between gene upregulation and propensity for DNA breathing. We propose that THz radiation has potential for non-contact control of cellular gene expression.
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Nowak-Lovato K, Alexandrov LB, Banisadr A, Bauer AL, Bishop AR, Usheva A, Mu F, Hong-Geller E, Rasmussen KØ, Hlavacek WS, Alexandrov BS. Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics. PLoS Comput Biol 2013; 9:e1002881. [PMID: 23341768 PMCID: PMC3547798 DOI: 10.1371/journal.pcbi.1002881] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/29/2012] [Indexed: 12/23/2022] Open
Abstract
Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications. Cellular transcription factors (TFs) are proteins that regulate gene expression, and thereby cellular activity and fate, by binding to specific DNA segments. The physicochemical determinants of protein-DNA binding specificity are not completely understood. Here, we report that the propensity of transient opening and re-closing of the double helix, resulting from thermal fluctuations, aka “DNA breathing” or “DNA bubbles,” can be associated with binding affinity in the case of Fis, a well-studied nucleoid-associated protein in Escherichia coli. We found that a particular breathing profile is characteristic of high-affinity Fis binding sites and that DNA fragments known to bind Fis in vivo are statistically enriched for this profile. Furthermore, we used simulations of DNA breathing dynamics to guide design of gel-shift experiments aimed at testing the idea that local breathing influences Fis binding. As a result, we show that via nucleotide modifications but without modifying nucleotides that directly contact Fis, we were able to transform a low-affinity Fis binding site into a high-affinity site and vice versa. The nucleotide modifications were designed only based on DNA breathing simulations. Our study suggests that strong Fis-DNA binding depends on DNA breathing - a novel physicochemical characteristic that could be used for prediction and rational design of TF binding sites.
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Affiliation(s)
- Kristy Nowak-Lovato
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Afsheen Banisadr
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amy L. Bauer
- X-Theoretical Design Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anny Usheva
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Fangping Mu
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Elizabeth Hong-Geller
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail: (WSH); (BSA)
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail: (WSH); (BSA)
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Alexandrov BS, Rasmussen KØ, Bishop AR, Usheva A. 76 Protein–DNA binding and breathing dynamics of DNA. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. Mol Psychiatry 2012; 17:1328-39. [PMID: 21968932 DOI: 10.1038/mp.2011.129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.
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Alexandrov BS, Fukuyo Y, Lange M, Horikoshi N, Gelev V, Rasmussen KØ, Bishop AR, Usheva A. DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells. Nucleic Acids Res 2012; 40:10116-23. [PMID: 22904068 PMCID: PMC3488223 DOI: 10.1093/nar/gks758] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein–DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.
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Affiliation(s)
- Boian S Alexandrov
- Harvard Medical School, Department of Medicine, Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
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Tapia-Rojo R, Prada-Gracia D, Mazo JJ, Falo F. Mesoscopic model for free-energy-landscape analysis of DNA sequences. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:021908. [PMID: 23005786 DOI: 10.1103/physreve.86.021908] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 07/21/2012] [Indexed: 06/01/2023]
Abstract
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.
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Affiliation(s)
- R Tapia-Rojo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
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40
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Zeida A, Machado MR, Dans PD, Pantano S. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:021903. [PMID: 23005781 DOI: 10.1103/physreve.86.021903] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 06/01/2012] [Indexed: 06/01/2023]
Abstract
Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ~80% of the DNA curvature present in experimentally solved structures.
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Affiliation(s)
- Ari Zeida
- Institut Pasteur de Montevideo, Calle Mataojo 2020, Montevideo, Codigo Postal 11400, Uruguay
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41
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Vanitha M, Daniel M. Internal nonlinear dynamics of a short lattice DNA model in terms of propagating kink-antikink solitons. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:041911. [PMID: 22680502 DOI: 10.1103/physreve.85.041911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 03/09/2012] [Indexed: 06/01/2023]
Abstract
We study the internal nonlinear dynamics of an inhomogeneous short lattice DNA model by solving numerically the governing discrete perturbed sine-Gordon equations under the limits of a uniform and a nonuniform angular rotation of bases. The internal dynamics is expressed in terms of open-state configurations represented by kink and antikink solitons with fluctuations. The inhomogeneity in the strands and hydrogen bonds as well as nonuniformity in the rotation of bases introduce fluctuations in the profile of the solitons without affecting their robust nature and the propagation. These fluctuations spread into the tail regions of the soliton in the case of periodic inhomogeneity. However, the localized form of inhomogeneity generates amplified fluctuations in the profile of the soliton. The fluctuations are expected to enhance the denaturation process in the DNA molecule.
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Affiliation(s)
- M Vanitha
- Centre for Nonlinear Dynamics, School of Physics, Bharathidasan University, Tiruchirapalli 620 024, India
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42
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Kalosakas G. Charge transport in DNA: dependence of diffusion coefficient on temperature and electron-phonon coupling constant. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:051905. [PMID: 22181442 DOI: 10.1103/physreve.84.051905] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/14/2011] [Indexed: 05/31/2023]
Abstract
The diffusion coefficient is calculated for a charge propagating along a double-stranded DNA, while it interacts with the nonlinear fluctuational openings of base pairs. The latter structural dynamics of DNA is described by the Peyrard-Bishop-Dauxois model [T. Dauxois, M. Peyrard, and A. R. Bishop, Phys Rev. E 47 R44 (1993)], which represents essential anharmonicities of base-pair stretchings. The dependence of the diffusion coefficient on the temperature and the electron-phonon coupling constant is presented. The diffusion coefficient decreases when either the temperature or the electron-phonon coupling increases. Analytical expressions are provided that describe the temperature dependence of the diffusion coefficient. The variation of the parameters of these expressions with the electron-phonon coupling constant is also discussed. These results quantitatively demonstrate how DNA structural nonlinear dynamics affects macroscopic charge transport properties.
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43
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Alexandrov BS, Rasmussen KØ, Bishop AR, Usheva A, Alexandrov LB, Chong S, Dagon Y, Booshehri LG, Mielke CH, Phipps ML, Martinez JS, Chen HT, Rodriguez G. Non-thermal effects of terahertz radiation on gene expression in mouse stem cells. BIOMEDICAL OPTICS EXPRESS 2011; 2:2679-89. [PMID: 21991556 PMCID: PMC3184876 DOI: 10.1364/boe.2.002679] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/11/2011] [Accepted: 08/17/2011] [Indexed: 05/18/2023]
Abstract
In recent years, terahertz radiation sources are increasingly being exploited in military and civil applications. However, only a few studies have so far been conducted to examine the biological effects associated with terahertz radiation. In this study, we evaluated the cellular response of mesenchymal mouse stem cells exposed to THz radiation. We apply low-power radiation from both a pulsed broad-band (centered at 10 THz) source and from a CW laser (2.52 THz) source. Modeling, empirical characterization, and monitoring techniques were applied to minimize the impact of radiation-induced increases in temperature. qRT-PCR was used to evaluate changes in the transcriptional activity of selected hyperthermic genes. We found that temperature increases were minimal, and that the differential expression of the investigated heat shock proteins (HSP105, HSP90, and CPR) was unaffected, while the expression of certain other genes (Adiponectin, GLUT4, and PPARG) showed clear effects of the THz irradiation after prolonged, broad-band exposure.
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Affiliation(s)
- Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Anny Usheva
- Harvard Medical School, Beth Israel Deaconess Medical Center, Department of Medicine, Boston, MA 02215, USA
| | | | - Shou Chong
- Harvard Medical School, Beth Israel Deaconess Medical Center, Department of Medicine, Boston, MA 02215, USA
| | - Yossi Dagon
- Harvard Medical School, Beth Israel Deaconess Medical Center, Department of Medicine, Boston, MA 02215, USA
| | - Layla G. Booshehri
- Materials Physics and Applications Division - NHMFL, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Charles H. Mielke
- Materials Physics and Applications Division - NHMFL, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, NM 87545, USA
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, NM 87545, USA
| | - Hou-Tong Chen
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, NM 87545, USA
| | - George Rodriguez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, NM 87545, USA
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44
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Alexandrov BS, Valtchinov VI, Alexandrov LB, Gelev V, Dagon Y, Bock J, Kohane IS, Rasmussen KØ, Bishop AR, Usheva A. DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases. PLoS One 2011; 6:e19800. [PMID: 21625483 PMCID: PMC3098838 DOI: 10.1371/journal.pone.0019800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/15/2011] [Indexed: 11/23/2022] Open
Abstract
Trinucleotide repeats sequences (TRS) represent a common type of genomic DNA
motif whose expansion is associated with a large number of human diseases. The
driving molecular mechanisms of the TRS ongoing dynamic expansion across
generations and within tissues and its influence on genomic DNA functions are
not well understood. Here we report results for a novel and notable collective
breathing behavior of genomic DNA of tandem TRS, leading to propensity for large
local DNA transient openings at physiological temperature. Our Langevin
molecular dynamics (LMD) and Markov Chain Monte Carlo (MCMC) simulations
demonstrate that the patterns of openings of various TRSs depend specifically on
their length. The collective propensity for DNA strand separation of repeated
sequences serves as a precursor for outsized intermediate bubble states
independently of the G/C-content. We report that repeats have the potential to
interfere with the binding of transcription factors to their consensus sequence
by altered DNA breathing dynamics in proximity of the binding sites. These
observations might influence ongoing attempts to use LMD and MCMC simulations
for TRS–related modeling of genomic DNA functionality in elucidating the
common denominators of the dynamic TRS expansion mutation with potential
therapeutic applications.
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Affiliation(s)
- Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Vlad I. Valtchinov
- National Center for Biomedical Computing, Informatics for Integrating
Biology and the Bedside, Boston, Massachusetts, United States of
America
| | - Ludmil B. Alexandrov
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Vladimir Gelev
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Yossi Dagon
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Jonathan Bock
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
| | - Isaac S. Kohane
- National Center for Biomedical Computing, Informatics for Integrating
Biology and the Bedside, Boston, Massachusetts, United States of
America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New
Mexico, United States of America
| | - Anny Usheva
- Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts, United States of America
- * E-mail:
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45
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Bandyopadhyay M, Gupta S, Segal D. DNA breathing dynamics: analytic results for distribution functions of relevant Brownian functionals. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:031905. [PMID: 21517523 DOI: 10.1103/physreve.83.031905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 05/30/2023]
Abstract
We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landscape. We suggest several probability distribution functions that characterize the breathing process, and adopt the recently studied backward Fokker-Planck method and the path decomposition method as elegant and flexible tools for deriving these distributions. In particular, for a bubble of an initial size x₀, we derive analytical expressions for (i) the distribution P(t{f}|x₀) of the first-passage time t{f}, characterizing the bubble lifetime, (ii) the distribution P(A|x₀) of the area A until the first-passage time, providing information about the effective reactivity of the bubble to processes within the DNA, (iii) the distribution P(M) of the maximum bubble size M attained before the first-passage time, and (iv) the joint probability distribution P(M,t{m}) of the maximum bubble size M and the time t{m} of its occurrence before the first-passage time. These distributions are analyzed in the limit of small and large bubble sizes. We supplement our analytical predictions with direct numericalsimulations of the related Langevin equation, and obtain a very good agreement in the appropriate limits. The nontrivial scaling behavior of the various quantities analyzed here can, in principle, be explored experimentally.
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Affiliation(s)
- Malay Bandyopadhyay
- Chemical Physics Theory Group, University of Toronto, 80 Saint George Street, Ontario M5S3H6, Canada
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46
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Apostolaki A, Kalosakas G. Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings. Phys Biol 2011; 8:026006. [DOI: 10.1088/1478-3975/8/2/026006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Maniadis P, Alexandrov BS, Bishop AR, Rasmussen KØ. Feigenbaum cascade of discrete breathers in a model of DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:011904. [PMID: 21405710 DOI: 10.1103/physreve.83.011904] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Indexed: 05/30/2023]
Abstract
We demonstrate that period-doubled discrete breathers appear from the anticontinuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between subharmonic solutions of the driven Morse oscillator. Subharmonic breathers exist whenever a stability overlap is present within the Feigenbaum cascade to chaos and therefore an entire cascade of such breathers exists. This phenomenon is present in any driven lattice where the on-site potential admits subharmonic solutions. In DNA these breathers may have ramifications for cellular gene expression.
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Affiliation(s)
- P Maniadis
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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48
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Bock J, Fukuyo Y, Kang S, Phipps ML, Alexandrov LB, Rasmussen KØ, Bishop AR, Rosen ED, Martinez JS, Chen HT, Rodriguez G, Alexandrov BS, Usheva A. Mammalian stem cells reprogramming in response to terahertz radiation. PLoS One 2010; 5:e15806. [PMID: 21209821 PMCID: PMC3013123 DOI: 10.1371/journal.pone.0015806] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 11/24/2010] [Indexed: 11/19/2022] Open
Abstract
We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.
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Affiliation(s)
- Jonathan Bock
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Yayoi Fukuyo
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Sona Kang
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ludmil B. Alexandrov
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Evan D. Rosen
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hou-Tong Chen
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - George Rodriguez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anny Usheva
- Department of Medicine, Endocrinology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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