1
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Engl W, Kunstar-Thomas A, Chen S, Ng WS, Sielaff H, Zhao ZW. Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics. Nat Commun 2024; 15:7646. [PMID: 39223123 PMCID: PMC11369179 DOI: 10.1038/s41467-024-52040-y] [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: 12/30/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Despite their prevalent cancer implications, the in vivo dynamics of SWI/SNF chromatin remodelers and how misregulation of such dynamics underpins cancer remain poorly understood. Using live-cell single-molecule tracking, we quantify the intranuclear diffusion and chromatin-binding of three key subunits common to all major human SWI/SNF remodeler complexes (BAF57, BAF155 and BRG1), and resolve two temporally distinct stable binding modes for the fully assembled complex. Super-resolved density mapping reveals heterogeneous, nanoscale remodeler binding "hotspots" across the nucleoplasm where multiple binding events (especially longer-lived ones) preferentially cluster. Importantly, we uncover distinct roles of the bromodomain in modulating chromatin binding/targeting in a DNA-accessibility-dependent manner, pointing to a model where successive longer-lived binding within "hotspots" leads to sustained productive remodeling. Finally, systematic comparison of six common BRG1 mutants implicated in various cancers unveils alterations in chromatin-binding dynamics unique to each mutant, shedding insight into a multi-modal landscape regulating the spatio-temporal organizational dynamics of SWI/SNF remodelers.
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Affiliation(s)
- Wilfried Engl
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Aliz Kunstar-Thomas
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Siyi Chen
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore.
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, 119077, Singapore.
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2
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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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3
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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4
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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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5
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De Silva SM, Dhiman A, Sood S, Mercedes KF, Simmons W, Henen M, Vögeli B, Dykhuizen E, Musselman C. PBRM1 bromodomains associate with RNA to facilitate chromatin association. Nucleic Acids Res 2023; 51:3631-3649. [PMID: 36808431 PMCID: PMC10164552 DOI: 10.1093/nar/gkad072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here, we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.
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Affiliation(s)
- Saumya M De Silva
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Kilsia F Mercedes
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - William J Simmons
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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6
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Lapa SA, Antipova OS, Chudinov AV. New Method for Evaluating the Substrate Efficiency of Modified Deoxynucleoside Triphosphates for Selex. Mol Biol 2022. [DOI: 10.1134/s0026893322030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Sharma T, Robinson DCL, Witwicka H, Dilworth FJ, Imbalzano AN. The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation. Nucleic Acids Res 2021; 49:8060-8077. [PMID: 34289068 PMCID: PMC8373147 DOI: 10.1093/nar/gkab617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.
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Affiliation(s)
- Tapan Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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8
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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9
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Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers. Curr Opin Struct Biol 2021; 71:1-6. [PMID: 33993059 DOI: 10.1016/j.sbi.2021.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 11/21/2022]
Abstract
The past two decades have witnessed rapid advances in the identification and characterization of epigenetic readers, capable of recognizing or reading post-translational modifications in histones. More recently, a new set of readers with the ability to interact with the nucleosome through concomitant binding to histones and DNA has emerged. In this review, we discuss mechanistic insights underlying bivalent histone and DNA recognition by newly characterized readers and highlight the importance of binding to DNA for their association with chromatin.
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10
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Lupo BE, Chu P, Harms MJ, Morrison EA, Musselman CA. Evolutionary Conservation of Structural and Functional Coupling between the BRM AT-Hook and Bromodomain. J Mol Biol 2021; 433:166845. [PMID: 33539881 PMCID: PMC8184587 DOI: 10.1016/j.jmb.2021.166845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/13/2023]
Abstract
The BAF chromatin remodeling complex is critical for genome regulation. The central ATPase of BAF is either BRM or BRG1, both of which contain a C-terminal bromodomain, known to associate with acetylated lysines. We have recently demonstrated that in addition to acetyl-lysine binding, the BRG1/BRM bromodomain can associate with DNA through a lysine/arginine rich patch that is adjacent to the acetyl-lysine binding pocket. Flanking the bromodomain is an AT-hook separated by a short, proline-rich linker. We previously found that the AT-hook and bromodomain can associate with DNA in a multivalent manner. Here, we investigate the conservation of this composite module and find that the AT-hook, linker, and lysine/arginine rich bromodomain patch are ancient, conserved over ~1 billion years. We utilize extensive mutagenesis, NMR spectroscopy, and fluorescence anisotropy to dissect the contribution of each of these conserved elements in association of this module with DNA. Our results reveal a structural and functional coupling of the AT-hook and bromodomain mediated by the linker. The lysine/arginine rich patch on the bromodomain and the conserved elements of the AT-hook are critical for robust affinity for DNA, while the conserved elements of the linker are dispensable for overall DNA affinity but critical for maintaining the relative conformation of the AT-hook and bromodomain in binding to DNA. This supports that the coupled action of the AT-hook and bromodomain are important for BAF activity.
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Affiliation(s)
- Brianna E Lupo
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States
| | - Peirou Chu
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States
| | - Michael J Harms
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States; Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, United States
| | - Emma A Morrison
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States; Medical College of Wisconsin, Department of Biochemistry, Milwaukee, WI 53226, United States.
| | - Catherine A Musselman
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States; University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, United States.
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11
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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