1
|
Application of modified histone peptide arrays in chromatin research. Arch Biochem Biophys 2019; 661:31-38. [DOI: 10.1016/j.abb.2018.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 01/15/2023]
|
2
|
Treindl F, Ruprecht B, Beiter Y, Schultz S, Döttinger A, Staebler A, Joos TO, Kling S, Poetz O, Fehm T, Neubauer H, Kuster B, Templin MF. A bead-based western for high-throughput cellular signal transduction analyses. Nat Commun 2016; 7:12852. [PMID: 27659302 PMCID: PMC5036152 DOI: 10.1038/ncomms12852] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/08/2016] [Indexed: 12/28/2022] Open
Abstract
Dissecting cellular signalling requires the analysis of large number of proteins. The DigiWest approach we describe here transfers the western blot to a bead-based microarray platform. By combining gel-based protein separation with immobilization on microspheres, hundreds of replicas of the initial blot are created, thus enabling the comprehensive analysis of limited material, such as cells collected by laser capture microdissection, and extending traditional western blotting to reach proteomic scales. The combination of molecular weight resolution, sensitivity and signal linearity on an automated platform enables the rapid quantification of hundreds of specific proteins and protein modifications in complex samples. This high-throughput western blot approach allowed us to identify and characterize alterations in cellular signal transduction that occur during the development of resistance to the kinase inhibitor Lapatinib, revealing major changes in the activation state of Ephrin-mediated signalling and a central role for p53-controlled processes. Dissecting cellular signalling requires the analysis of large numbers of proteins. Here the authors describe DigiWest, a high-throughput protein detection method that combines the concept of western and widely-used bead array systems that allows rapid quantification of hundreds of specific proteins.
Collapse
Affiliation(s)
- Fridolin Treindl
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
| | - Benjamin Ruprecht
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.,Center for Integrated Protein Science Munich, 85354 Freising, Germany
| | - Yvonne Beiter
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
| | - Silke Schultz
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Anette Döttinger
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Annette Staebler
- Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Simon Kling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Tanja Fehm
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Hans Neubauer
- Department of Obstetrics and Gynecology, Medical Faculty and University Hospital of the Heinrich-Heine University Duesseldorf, 40225 Düsseldorf, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.,Center for Integrated Protein Science Munich, 85354 Freising, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technische Universität München, 85354 Freising, Germany
| | - Markus F Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard-Karls-Universität Tübingen, Tübingen, 72770 Reutlingen, Germany
| |
Collapse
|
3
|
Abstract
Histones are subject to frequent combinatorial post-translational modifications (PTMs), forming a complex chemical "language" that is interpreted by PTM-specific histone-interacting protein modules (reader domains). These specific interactions are thought to instruct gene expression and downstream biological functions. While the majority of studies have focused on individual modifications, our current understanding of the combinatorial PTM patterns on histones is starting to emerge, benefiting from the convergence of multiple technologies. Here, we review the key technical advances and progress on discovery and characterization of combinatorial histone PTM patterns. We focus on the interactions between reader domains and combinatorial PTMs, which is essential for understanding the mechanism and biological meaning of establishing and interpreting information embedded in histone PTM patterns.
Collapse
Affiliation(s)
- Zhangli Su
- Department
of Biomolecular
Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department
of Biomolecular
Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, Wisconsin 53715, United States
| |
Collapse
|
4
|
Oriented Peptide Immobilization on Microspheres. Methods Mol Biol 2015; 1352:183-97. [PMID: 26490476 DOI: 10.1007/978-1-4939-3037-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Reproducible immobilization of peptides and proteins on microsphere surfaces is a critical factor for optimal sensitivity and selectivity in bead-based assays. However, peptides with unusually large numbers of lysine residues-whose amines are targeted in the most common microsphere immobilization chemistries-may be particularly challenging to use in bead-based arrays, as they may lose activity through multipoint attachments and incorrect presentation. For this reason, it is imperative to achieve site-directed attachment chemistry, such that a single site of attachment provides reproducibly oriented peptides on the microsphere surface. This can be achieved by inserting a unique targetable residue, such as a cysteine. Here, we present methods for attaching cysteine-containing peptides to standard carboxy-functionalized microsphere surfaces using thiol- rather than amine-directed chemistries. We show that the presence of a cationic detergent (CTAB) and a "passivating" agent such as β-mercaptoethanol facilitates improved bead recovery after peptide immobilization and may enhance functionality of the attached peptides.
Collapse
|
5
|
Bead-Based Peptide Arrays for Profiling the Specificity of Modification State-Specific Antibodies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2015; 1348:251-65. [PMID: 26424278 DOI: 10.1007/978-1-4939-2999-3_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Modification state-specific antibodies are powerful tools for investigating posttranslational modifications in proteins. The majority of these antibodies have been generated against peptide-antigen conjugates. They are useful in a plethora of methods, such as Western blotting, immunohistochemistry, sandwich immunoassay, immunoprecipitation, and immunoprecipitation coupled with mass spectrometry. Phosphorylation, acetylation, methylation, sulfation, nitrosylation, ubiquitination, and sumoylation are some of the modifications that can be studied using such antibodies. However, investigating the on- and off-target binding of antibodies is crucial to the interpretation of experimental data. Peptide arrays are excellent tools for such in-depth studies of off-target and on-target binding of antibodies. Dozens or even hundreds of modified peptides can be integrated into a single experimental setup to analyze the antibody's binding behavior. Here, we propose three different protocols for peptide bead array generation and describe their suitability for such types of assay.
Collapse
|
6
|
Kungulovski G, Mauser R, Jeltsch A. Affinity reagents for studying histone modifications & guidelines for their quality control. Epigenomics 2015; 7:1185-96. [DOI: 10.2217/epi.15.59] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Histone post-translational modifications (PTMs) have pivotal functions in many chromatin processes, which makes their detection and characterization an imperative in chromatin biology. The established approaches for histone PTM characterization are generally based on affinity reagents specific for modified histone tails such as antibodies and, most recently, recombinant reading domains. Hence, the proper performance of these reagents is a critical precondition for the validity of the generated experimental data. In this review, we evaluate and update the quality criteria for assessment of the binding specificity of histone PTM affinity reagents. In addition, we discuss in detail the advantages and pitfalls of using antibodies and recombinant reading domains in chromatin biology research. Reading domains provide key advantages, such as consistent quality and recombinant production, but the future will tell if this emerging technology keeps its promises.
Collapse
Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Rebekka Mauser
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| |
Collapse
|
7
|
Su Z, Denu JM. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications. ACTA ACUST UNITED AC 2015; 111:21.32.1-21.32.21. [PMID: 26131849 DOI: 10.1002/0471142727.mb2132s111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications.
Collapse
Affiliation(s)
- Zhangli Su
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin.,Wisconsin Institutes for Discovery, University of Wisconsin, Madison, Wisconsin
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin.,Wisconsin Institutes for Discovery, University of Wisconsin, Madison, Wisconsin
| |
Collapse
|
8
|
Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
9
|
Kungulovski G, Kycia I, Mauser R, Jeltsch A. Specificity Analysis of Histone Modification-Specific Antibodies or Reading Domains on Histone Peptide Arrays. Methods Mol Biol 2015; 1348:275-284. [PMID: 26424280 DOI: 10.1007/978-1-4939-2999-3_24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Histone posttranslational modifications (PTMs) have a crucial role in chromatin regulation and dynamics. They are specifically bound by so-called reading domains, which mediate the biological effects of histone PTMs. On a similar note, antibodies are invaluable reagents in chromatin biology for the detection, characterization, and mapping of histone PTMs. Despite these central roles in chromatin research and biology, the specificity of many antibodies and reading domains has been insufficiently characterized and documented. Here we describe in detail the application of the MODified™ Histone Peptide Array for the investigation of the binding specificity of histone binding antibodies or domains. The array contains 384 histone tail peptides carrying 59 posttranslational modifications in different combinations which can be used to study the primary binding specificity, but at the same time also allow to determine the combinatorial effect of secondary marks on antibody or reading domain binding.
Collapse
Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Ina Kycia
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rebekka Mauser
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany.
| |
Collapse
|
10
|
Kungulovski G, Kycia I, Tamas R, Jurkowska RZ, Kudithipudi S, Henry C, Reinhardt R, Labhart P, Jeltsch A. Application of histone modification-specific interaction domains as an alternative to antibodies. Genome Res 2014; 24:1842-53. [PMID: 25301795 PMCID: PMC4216925 DOI: 10.1101/gr.170985.113] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we successfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies.
Collapse
Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Ina Kycia
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Raluca Tamas
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | | | | | | | | | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany;
| |
Collapse
|
11
|
Venne AS, Zahedi RP. The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
12
|
Su Z, Boersma MD, Lee JH, Oliver SS, Liu S, Garcia BA, Denu JM. ChIP-less analysis of chromatin states. Epigenetics Chromatin 2014; 7:7. [PMID: 24872844 PMCID: PMC4022240 DOI: 10.1186/1756-8935-7-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/09/2014] [Indexed: 11/26/2022] Open
Abstract
Background Histone post-translational modifications (PTMs) are key epigenetic regulators in chromatin-based processes. Increasing evidence suggests that vast combinations of PTMs exist within chromatin histones. These complex patterns, rather than individual PTMs, are thought to define functional chromatin states. However, the ability to interrogate combinatorial histone PTM patterns at the nucleosome level has been limited by the lack of direct molecular tools. Results Here we demonstrate an efficient, quantitative, antibody-free, chromatin immunoprecipitation-less (ChIP-less) method for interrogating diverse epigenetic states. At the heart of the workflow are recombinant chromatin reader domains, which target distinct chromatin states with combinatorial PTM patterns. Utilizing a newly designed combinatorial histone peptide microarray, we showed that three reader domains (ATRX-ADD, ING2-PHD and AIRE-PHD) displayed greater specificity towards combinatorial PTM patterns than corresponding commercial histone antibodies. Such specific recognitions were employed to develop a chromatin reader-based affinity enrichment platform (matrix-assisted reader chromatin capture, or MARCC). We successfully applied the reader-based platform to capture unique chromatin states, which were quantitatively profiled by mass spectrometry to reveal interconnections between nucleosomal histone PTMs. Specifically, a highly enriched signature that harbored H3K4me0, H3K9me2/3, H3K79me0 and H4K20me2/3 within the same nucleosome was identified from chromatin enriched by ATRX-ADD. This newly reported PTM combination was enriched in heterochromatin, as revealed by the associated DNA. Conclusions Our results suggest the broad utility of recombinant reader domains as an enrichment tool specific to combinatorial PTM patterns, which are difficult to probe directly by antibody-based approaches. The reader affinity platform is compatible with several downstream analyses to investigate the physical coexistence of nucleosomal PTM states associated with specific genomic loci. Collectively, the reader-based workflow will greatly facilitate our understanding of how distinct chromatin states and reader domains function in gene regulatory mechanisms.
Collapse
Affiliation(s)
- Zhangli Su
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA ; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Melissa D Boersma
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA ; Biotechnology Center, University of Wisconsin, Madison, WI 53706, USA
| | - Jin-Hee Lee
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA ; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Samuel S Oliver
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA ; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Shichong Liu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA ; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| |
Collapse
|
13
|
Venne AS, Kollipara L, Zahedi RP. The next level of complexity: Crosstalk of posttranslational modifications. Proteomics 2014; 14:513-24. [DOI: 10.1002/pmic.201300344] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/06/2013] [Accepted: 11/21/2013] [Indexed: 12/22/2022]
Affiliation(s)
- A. Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
| | | | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
| |
Collapse
|
14
|
Catch and measure-mass spectrometry-based immunoassays in biomarker research. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:927-32. [PMID: 24060810 DOI: 10.1016/j.bbapap.2013.09.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/28/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022]
Abstract
Mass spectrometry-based (MS) methods are effective tools for discovering protein biomarker candidates that can differentiate between physiological and pathophysiological states. Promising candidates are validated in studies comprising large patient cohorts. Here, targeted protein analytics are used to increase sample throughput. Methods involving antibodies, such as sandwich immunoassays or Western blots, are commonly applied at this stage. Highly-specific and sensitive mass spectrometry-based immunoassays that have been established in recent years offer a suitable alternative to sandwich immunoassays for quantifying proteins. Mass Spectrometric ImmunoAssays (MSIA) and Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA/iMALDI) are two prominent types of MS-based immunoassays in which the capture is done either at the protein or the peptide level. We present an overview of these emerging types of immunoassays and discuss their suitability for the discovery and validation of protein biomarkers. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
Collapse
|