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Zolotarjova NI, Wynn R. Binding Assays for Bromodomain Proteins: Their Utility in Drug Discovery in Oncology and Inflammatory Disease. ACTA ACUST UNITED AC 2019; 80:3.16.1-3.16.14. [PMID: 30040205 DOI: 10.1002/cpph.35] [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] [Indexed: 11/12/2022]
Abstract
Bromodomains are protein domains that recognize acetylated lysine residues and are important for recruiting a large number of protein and multiprotein complexes to sites of lysine acetylation. They play an important role in chromatin biology and are popular targets for drug discovery. Compound screening in this area requires the use of biochemical assays to assess the binding potency of potential drug candidates. Foremost among the efforts to target bromodomains are those aimed at identifying compounds that interact with the bromodomain and extra-terminal domain (BET) family of bromodomain-containing proteins (BRD2, BRD3, BRD4, and BRDT). Inhibitors of these proteins are under clinical development for a large variety of oncologic indications. Described in this unit are several assays to assess the binding potency and selectivity within the BET protein family. Included are AlphaScreen, fluorescence polarization, and thermal shift assays. The strengths and weaknesses of each assay are discussed. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Richard Wynn
- Applied Technology Department, Incyte Corporation, Wilmington, Delaware
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Sanchez OF, Mendonca A, Carneiro AD, Yuan C. Engineering Recombinant Protein Sensors for Quantifying Histone Acetylation. ACS Sens 2017; 2:426-435. [PMID: 28723212 DOI: 10.1021/acssensors.7b00026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
H3K14ac (acetylation of lysine 14 of histone H3) is one of the most important epigentic modifications. Aberrant changes in H3K14ac have been associated with various diseases, including cancers and neurological disorders. Tools that enable detection and quantification of H3K14ac levels in cell extracts and in situ are thus of critical importance to reveal its role in various biological processes. Current detection techniques of specific histone modifications, however, are constrained by tedious sample pretreatments, lack of quantitative accuracy, and reliance on high quality antibodies. To address this issue, we engineered recombinant sensors that are suitable for probing histone acetylation levels using various biological samples. The protein sensor contains recongition domain(s) with sequences derived from the bromodomain of human polybromo-1 (PB1), a natural H3K14ac reader domain. Various sensor designs were tested using nuclear extracts and live cells. The sensor containing dimeric repeats of bromodomain was found most effective in quantifying H3K14ac level in both in vitro and in situ assays. The sensor has a linear detection range of 0.5-50 nM when mixed with nuclear extracts. The sensor colocalizes with H3K14ac antibodies in situ when transfected into human embryonic kidney 293T (HEK293T) cells and is thus capable of providing spatial details of histone modification within the nucleus. Corrected nuclear fluorescence intensity was used to quantify the modification level in situ and found to correlate well with our in vitro assays. Our sensor offers a novel tool to characterize the histone modification level using nuclear extracts and probe histone modification change in live cells.
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Affiliation(s)
- Oscar F. Sanchez
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Agnes Mendonca
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Ana D. Carneiro
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chongli Yuan
- School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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Sanchez OF, Williamson D, Cai L, Yuan C. A sensitive protein-based sensor for quantifying histone acetylation levels. Talanta 2015; 140:212-218. [DOI: 10.1016/j.talanta.2015.03.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/19/2015] [Accepted: 03/21/2015] [Indexed: 01/05/2023]
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Qian K, Pietilä T, Rönty M, Michon F, Frilander MJ, Ritari J, Tarkkanen J, Paulín L, Auvinen P, Auvinen E. Identification and validation of human papillomavirus encoded microRNAs. PLoS One 2013; 8:e70202. [PMID: 23936163 PMCID: PMC3728184 DOI: 10.1371/journal.pone.0070202] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/17/2013] [Indexed: 01/28/2023] Open
Abstract
We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.
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Affiliation(s)
- Kui Qian
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Tuuli Pietilä
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Haartman Institute, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital Laboratory, Helsinki, Finland
| | - Mikko Rönty
- Department of Pathology, Helsinki University Hospital Laboratory, Helsinki, Finland
| | - Frederic Michon
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Jarmo Ritari
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Tarkkanen
- Department of Pathology, Helsinki University Hospital Laboratory, Helsinki, Finland
| | - Lars Paulín
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eeva Auvinen
- Haartman Institute, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Virology and Immunology, Helsinki University Hospital Laboratory, Helsinki, Finland
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Chung CW, Witherington J. Progress in the discovery of small-molecule inhibitors of bromodomain--histone interactions. ACTA ACUST UNITED AC 2011; 16:1170-85. [PMID: 21956175 DOI: 10.1177/1087057111421372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bromodomains are structurally conserved protein modules present in a large number of chromatin-associated proteins and in many nuclear histone acetyltransferases. The bromodomain functions as an acetyl-lysine binding domain and has been shown to be pivotal in regulating protein-protein interactions in chromatin-mediated cellular gene transcription, cell proliferation, and viral transcriptional activation. Structural analyses of these modules in complex with acetyl-lysine peptide ligands provide insights into the molecular basis for recognition and ligand selectivity within this epigenetic reader family. However, there are significant challenges in configuring assays to identify inhibitors of these proteins. This review focuses on the progress made in developing methods to identify peptidic and small-molecule ligands using biophysical label-free and biochemical approaches. The advantage of each technique and the results reported are summarized, highlighting the potential applicably to other reader domains and the caveats in translation from simple in vitro systems to a biological context.
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Thompson M. Polybromo-1: the chromatin targeting subunit of the PBAF complex. Biochimie 2008; 91:309-19. [PMID: 19084573 DOI: 10.1016/j.biochi.2008.10.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
The human Polybromo-1 protein (Pb1) was recently identified as a unique subunit of the PBAF (Polybromo, Brg1-Associated Factors) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. Pb1 coordinates key features common to all remodeling complexes, including chromatin localization, recruitment of protein subunits and alteration of chromatin architecture. A comprehensive analysis of individual domains composing Pb1 is used to propose new information regarding the function of Pb1 in the PBAF chromatin-remodeling complex. The newly identified regulatory role of this important protein is also examined to explain both native function and the emerging role of Pb1 as a tumor suppressor found to be mutated in breast cancer.
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Affiliation(s)
- Martin Thompson
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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Kinetic analysis of acetylation-dependent Pb1 bromodomain-histone interactions. Biophys Chem 2008; 136:7-12. [PMID: 18508185 DOI: 10.1016/j.bpc.2008.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2008] [Revised: 03/28/2008] [Accepted: 03/28/2008] [Indexed: 11/22/2022]
Abstract
Stopped-flow fluorescence anisotropy was used to determine the kinetic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains are acetyllysine binding motifs found in many chromatin associated proteins. Individual bromodomains were derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin-remodeling complex that has six tandem bromodomains in the amino-terminal region. The average k(on) and k(off) values for the formation of high-affinity complexes are 275 M(-1) s(-1) and 0.41 x 10(-3) s(-1), respectively. The average k(on) and k(off) values for the formation of low-affinity complexes are 119 M(-1) s(-1) and 1.42 x 10(-3) s(-1), respectively. Analysis of the on- and off-rates yields acetylation site-dependent equilibrium dissociation constants averaging 1.4 and 12.9 microM for high- and low-affinity complexes, respectively. This work represents the first examination of kinetic mechanisms of acetylation-dependent bromodomain-histone interactions.
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Thompson M, Chandrasekaran R. Thermodynamic analysis of acetylation-dependent Pb1 bromodomain-histone H3 interactions. Anal Biochem 2008; 374:304-12. [PMID: 18191465 PMCID: PMC2693409 DOI: 10.1016/j.ab.2007.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 12/23/2022]
Abstract
An acetyl-histone peptide library was used to determine the thermodynamic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains interact with histones by binding acetylated lysines. The bromodomain used in this study, BrD3, is derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin remodeling complex. Steady-state fluorescence anisotropy was used to examine the variations in specificity and affinity that drive molecular recognition. Temperature and salt concentration dependence studies demonstrate that the hydrophobic effect is the primary driving force, consistent with lysine acetylation being required for binding. An electrostatic effect was observed in only two complexes where the acetyl-lysine was adjacent to an arginine. The large change in heat capacity determined for the specific complex suggests that the dehydrated BrD3-histone interface forms a tightly bound, high-affinity complex with the target site. These explorations into the thermodynamic driving forces that confer acetylation site-dependent BrD3-histone interactions improve our understanding of how individual bromodomains work in isolation. Furthermore, this work will permit the development of hypotheses regarding how the native Pb1, and the broader class of bromodomain proteins, directs multisubunit chromatin remodeling complexes to specific acetyl-nucleosome sites in vivo.
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Affiliation(s)
- Martin Thompson
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA.
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Thompson M. Spectral Properties and DNA Targeting Features of a Thiazole Orange−Peptide Bioconjugate. Biomacromolecules 2007; 8:3628-33. [DOI: 10.1021/bm070334h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Thompson
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931
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Chandrasekaran R, Thompson M. Polybromo-1-bromodomains bind histone H3 at specific acetyl-lysine positions. Biochem Biophys Res Commun 2007; 355:661-6. [PMID: 17320048 DOI: 10.1016/j.bbrc.2007.01.193] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 01/31/2007] [Indexed: 11/16/2022]
Abstract
The human polybromo-1 protein is thought to localize the Polybromo, BRG1-associated factors chromatin-remodeling complex to kinetochores during mitosis via direct interaction of its six tandem bromodomains with acetylated nucleosomes. Bromodomains are acetyl-lysine binding modules roughly 100 amino acids in length originally found in chromatin associated proteins. Previous studies verified acetyl-histone binding by each bromodomain, but site-specificity, a central tenet of the histone code hypothesis, was not examined. Here, the acetylation site-dependence of bromodomain-histone interactions was examined using steady-state fluorescence anisotropy. Results indicate that single bromodomains bind specific acetyl-lysine sites within the histone tail with sub-micromolar affinity. Identification of duplicate target sites suggests that native Pb1 interacts with both copies of histone H3 upon nucleosome assembly. Quantitative analysis of single bromodomain-histone interactions can be used to develop hypotheses regarding the histone acetylation pattern that acts as the binding target of the native polybromo-1 protein.
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Affiliation(s)
- Renu Chandrasekaran
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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