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Yu B, Iwahara J. Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation. Biopolymers 2024; 115:e23553. [PMID: 37254885 PMCID: PMC10687310 DOI: 10.1002/bip.23553] [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: 12/06/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of DNA-scanning by proteins are nontrivial due to the simultaneous presence of multiple translocation mechanisms and many sites for the protein to nonspecifically bind to DNA. Nuclear magnetic resonance (NMR) spectroscopy can provide information about the target DNA search processes at an atomic level. Paramagnetic relaxation enhancement (PRE) is particularly useful to study how the proteins scan DNA in the search process. Previously, relatively simple two-state or three-state exchange models were used to explain PRE data reflecting the target search process. In this work, using more realistic discrete-state stochastic kinetics models embedded into an NMR master equation, we analyzed the PRE data for the HoxD9 homeodomain interacting with DNA. The kinetic models that incorporate sliding, dissociation, association, and intersegment transfer can reproduce the PRE profiles observed at some different ionic strengths. The analysis confirms the previous interpretation of the PRE data and shows that the protein's probability distribution among nonspecific sites is nonuniform during the target DNA search process.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068
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2
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Wang X, Bigman LS, Greenblatt HM, Yu B, Levy Y, Iwahara J. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res 2023; 51:4701-4712. [PMID: 36774964 PMCID: PMC10250230 DOI: 10.1093/nar/gkad045] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/14/2023] Open
Abstract
In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions (IDRs) with large negative charge, some of which involve a consecutive sequence of aspartate (D) or glutamate (E) residues. We refer to them as D/E repeats. The functional role of D/E repeats is not well understood, though some of them are known to cause autoinhibition through intramolecular electrostatic interaction with functional domains. In this work, we investigated the impacts of D/E repeats on the target DNA search kinetics for the high-mobility group box 1 (HMGB1) protein and the artificial protein constructs of the Antp homeodomain fused with D/E repeats of varied lengths. Our experimental data showed that D/E repeats of particular lengths can accelerate the target association in the overwhelming presence of non-functional high-affinity ligands ('decoys'). Our coarse-grained molecular dynamics (CGMD) simulations showed that the autoinhibited proteins can bind to DNA and transition into the uninhibited complex with DNA through an electrostatically driven induced-fit process. In conjunction with the CGMD simulations, our kinetic model can explain how D/E repeats can accelerate the target association process in the presence of decoys. This study illuminates an unprecedented role of the negatively charged IDRs in the target search process.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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3
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Vo TD, Schneider AL, Wilson WD, Poon GMK. Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6. Phys Chem Chem Phys 2021; 23:13490-13502. [PMID: 34120158 PMCID: PMC8233815 DOI: 10.1039/d1cp01568k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic protein/DNA interactions arise from the neutralization of the DNA phosphodiester backbone as well as coupled exchanges by charged protein residues as salt bridges or with mobile ions. Much focus has been and continues to be paid to interfacial ion pairs with DNA. The role of extra-interfacial ionic interactions, particularly as dynamic drivers of DNA sequence selectivity, remain poorly known. The ETS family of transcription factors represents an attractive model for addressing this knowledge gap given their diverse ionic composition in primary structures that fold to a tightly conserved DNA-binding motif. To probe the importance of extra-interfacial salt bridges in DNA recognition, we compared the salt-dependent binding by Elk1 with ETV6, two ETS homologs differing markedly in ionic composition. While both proteins exhibit salt-dependent binding with cognate DNA that corresponds to interfacial phosphate contacts, their nonspecific binding diverges from cognate binding as well as each other. Molecular dynamics simulations in explicit solvent, which generated ionic interactions in agreement with the experimental binding data, revealed distinct salt-bridge dynamics in the nonspecific complexes formed by the two proteins. Impaired DNA contact by ETV6 resulted in fewer backbone contacts in the nonspecific complex, while Elk1 exhibited a redistribution of extra-interfacial salt bridges via residues that are non-conserved between the two ETS relatives. Thus, primary structure variation in ionic residues can encode highly differentiated specificity mechanisms in a highly conserved DNA-binding motif.
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Affiliation(s)
- Tam D Vo
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA. and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
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4
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Huang K, Xhani S, Albrecht AV, Ha VLT, Esaki S, Poon GMK. Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1. J Biol Chem 2019; 294:9666-9678. [PMID: 31048376 DOI: 10.1074/jbc.ra119.007866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/01/2019] [Indexed: 12/19/2022] Open
Abstract
Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.
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Affiliation(s)
| | | | | | | | | | - Gregory M K Poon
- From the Department of Chemistry and .,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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5
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Perez-Borrajero C, Lin CSH, Okon M, Scheu K, Graves BJ, Murphy ME, McIntosh LP. The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor. J Mol Biol 2019; 431:593-614. [DOI: 10.1016/j.jmb.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
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6
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Raccaud M, Friman ET, Alber AB, Agarwal H, Deluz C, Kuhn T, Gebhardt JCM, Suter DM. Mitotic chromosome binding predicts transcription factor properties in interphase. Nat Commun 2019; 10:487. [PMID: 30700703 PMCID: PMC6353955 DOI: 10.1038/s41467-019-08417-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after photobleaching, single molecule imaging of DNA binding, and mapping of TF binding and chromatin accessibility. TFs associating to mitotic chromosomes are enriched in DNA-rich compartments in interphase and display slower mobility in interphase and mitosis. Remarkably, MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times. This suggests that non-specific DNA binding properties of TFs regulate their search efficiency and occupancy of specific genomic sites.
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Affiliation(s)
- Mahé Raccaud
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Elias T Friman
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Andrea B Alber
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Harsha Agarwal
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Timo Kuhn
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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7
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Iwahara J, Zandarashvili L, Kemme CA, Esadze A. NMR-based investigations into target DNA search processes of proteins. Methods 2018; 148:57-66. [PMID: 29753002 DOI: 10.1016/j.ymeth.2018.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022] Open
Abstract
To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental means. In this review, we provide an introductory overview on the NMR methods for the structural, dynamic, and kinetic investigations of target DNA search by proteins. We also discuss advantages and disadvantages of these NMR methods over other methods such as single-molecule techniques and biochemical approaches.
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Affiliation(s)
- Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States.
| | - Levani Zandarashvili
- Department of Biochemistry and Biophysics, University of Pennsylvania, United States
| | - Catherine A Kemme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States
| | - Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, United States
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8
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Sahu D, Iwahara J. Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium. J Phys Chem B 2017; 121:9548-9556. [PMID: 28922916 DOI: 10.1021/acs.jpcb.7b07779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the target DNA search process, sequence-specific DNA-binding proteins first nonspecifically bind to DNA and stochastically move from one site to another before reaching their targets. To rigorously assess how the translocation process influences NMR signals from proteins interacting with nonspecific DNA, we incorporated a discrete-state kinetic model for protein translocation on DNA into the McConnell equation. Using this equation, we simulated line shapes of NMR signals from proteins undergoing translocations on DNA through sliding, dissociation/reassociation, and intersegment transfer. Through this analysis, we validated an existing NMR approach for kinetic investigations of protein translocation on DNA, which utilizes NMR line shapes of two nonspecific DNA-protein complexes and their mixture. We found that, despite its use of simplistic two-state approximation neglecting the presence of many microscopic states, the previously proposed NMR approach provides accurate kinetic information on the intermolecular translocations of proteins between two DNA molecules. Interestingly, our results suggest that the same NMR approach can also provide qualitative information about the one-dimensional diffusion coefficient for proteins sliding on DNA.
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Affiliation(s)
- Debashish Sahu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555-1068, United States
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9
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Currie SL, Lau DKW, Doane JJ, Whitby FG, Okon M, McIntosh LP, Graves BJ. Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5. Nucleic Acids Res 2017; 45:2223-2241. [PMID: 28161714 PMCID: PMC5389675 DOI: 10.1093/nar/gkx068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/29/2017] [Indexed: 12/21/2022] Open
Abstract
Autoinhibition enables spatial and temporal regulation of cellular processes by coupling protein activity to surrounding conditions, often via protein partnerships or signaling pathways. We report the molecular basis of DNA-binding autoinhibition of ETS transcription factors ETV1, ETV4 and ETV5, which are often overexpressed in prostate cancer. Inhibitory elements that cooperate to repress DNA binding were identified in regions N- and C-terminal of the ETS domain. Crystal structures of these three factors revealed an α-helix in the C-terminal inhibitory domain that packs against the ETS domain and perturbs the conformation of its DNA-recognition helix. Nuclear magnetic resonance spectroscopy demonstrated that the N-terminal inhibitory domain (NID) is intrinsically disordered, yet utilizes transient intramolecular interactions with the DNA-recognition helix of the ETS domain to mediate autoinhibition. Acetylation of selected lysines within the NID activates DNA binding. This investigation revealed a distinctive mechanism for DNA-binding autoinhibition in the ETV1/4/5 subfamily involving a network of intramolecular interactions not present in other ETS factors. These distinguishing inhibitory elements provide a platform through which cellular triggers, such as protein–protein interactions or post-translational modifications, may specifically regulate the function of these oncogenic proteins.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Desmond K W Lau
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
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10
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In-depth study of DNA binding of Cys2His2 finger domains in testis zinc-finger protein. PLoS One 2017; 12:e0175051. [PMID: 28384299 PMCID: PMC5383199 DOI: 10.1371/journal.pone.0175051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 11/26/2022] Open
Abstract
Previously, we identified that both fingers 1 and 2 in the three Cys2His2 zinc-finger domains (TZD) of testis zinc-finger protein specifically bind to its cognate DNA; however, finger 3 is non-sequence–specific. To gain insights into the interaction mechanism, here we further investigated the DNA-binding characteristics of TZD bound to non-specific DNAs and its finger segments bound to cognate DNA. TZD in non-specific DNA binding showed smaller chemical shift perturbations, as expected. However, the direction of shift perturbation, change of DNA imino-proton NMR signal, and dynamics on the 15N backbone atom significantly differed between specific and non-specific binding. Using these unique characteristics, we confirmed that the three single-finger segments (TZD1, TZD2 and TZD3) and the two-finger segment (TZD23) non-specifically bind to the cognate DNA. In comparison, the other two-finger segment (TZD12) binding to the cognate DNA features simultaneous non-specific and semi-specific binding, both slowly exchanged in terms of NMR timescale. The process of TZD binding to the cognate DNA is likely stepwise: initially TZD non-specifically binds to DNA, then fingers 1 and 2 insert cooperatively into the major groove of DNA by semi-specific binding, and finally finger 3 non-specifically binds to DNA, which promotes the specific binding on fingers 1 and 2 and stabilizes the formation of a specific TZD–DNA complex.
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11
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Abstract
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.
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Affiliation(s)
- Gregory M K Poon
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA.,b Center for Diagnostics and Therapeutics, Georgia State University , Atlanta , GA , USA
| | - Hye Mi Kim
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA
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