1
|
Mao H, Han G, Xu L, Zhu D, Lin H, Cao X, Yu Y, Chen CD. Cis-existence of H3K27me3 and H3K36me2 in mouse embryonic stem cells revealed by specific ions of isobaric modification chromatogram. Stem Cell Res Ther 2015. [PMID: 26194893 PMCID: PMC4533945 DOI: 10.1186/s13287-015-0131-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Introduction Histone H3 lysine 27 trimethylation (H3K27me3) and H3 lysine 36 trimethylation (H3K36me3) are important epigenetic modifications correlated with transcription repression and activation, respectively. These two opposing modifications rarely co-exist in the same H3 polypeptide. However, a small but significant amount of H3 tails are modified with 5 methyl groups on K27 and K36 in mouse embryonic stem cells (mESCs) and it is unclear how the trimethylation is distributed on K27 or K36. Methods A label-free, bottom-up mass spectrum method, named specific ions of isobaric modification chromatogram (SIMC), was established to quantify the relative abundance of K27me2-K36me3 and K27me3-K36me2 in the same histone H3 tail. Results By using this method, we demonstrated that the H3K27me3-K36me2 comprises about 85 % of the penta-methylated H3 tails at K27 and K36 in mESCs. Upon mESC differentiation, the abundance of H3K27me3-K36me2 significantly decreased, while the level of H3K27me2-K36me3 remains unchanged. Conclusion Our study not only revealed the cis-existence of H3K27me3-K36me2 in mESCs, but also suggested that this combinatorial histone modification may assume a specific regulatory function during differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s13287-015-0131-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hailei Mao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China. .,State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Gang Han
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Longyong Xu
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Duming Zhu
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Hanqing Lin
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Xiongwen Cao
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Yi Yu
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, and Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| |
Collapse
|
2
|
Wang T, Zhou Q, Li F, Yu Y, Yin X, Wang J. Genetic Incorporation ofNε-Formyllysine, a New Histone Post-translational Modification. Chembiochem 2015; 16:1440-2. [DOI: 10.1002/cbic.201500170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 01/10/2023]
|
3
|
Abstract
Post-translational modifications of histones comprise an important part of epigenetic gene regulation. Mass spectrometry and immunochemical techniques are currently the methods of choice for identification and quantitation of known and novel histone modifications. While peptide-centric mass spectrometry is a well-established tool for identification and quantification of histone modifications, recent technological advances have allowed discrete modification patterns to be assessed on intact histones. Chromatin immunoprecipitation assays (ChIP and ChIP-on-chip) are currently gaining tremendous popularity and are used to explore gene-specific patterns of histone modifications on a genomic scale. In this review, we introduce the basic concepts and recent developments of mass spectrometry, as well as immunochemical techniques and their applications in the analysis of histone modifications.
Collapse
Affiliation(s)
- Morten Beck Trelle
- University of Southern Denmark, Center for Epigenetics & Department of Molecular Biology & Biochemistry, Odense M, Denmark.
| | | |
Collapse
|
4
|
Bilgraer R, Gillet S, Gil S, Evain-Brion D, Laprévote O. A new approach combining LC-MS and multivariate statistical analysis for revealing changes in histone modification levels. ACTA ACUST UNITED AC 2014; 10:2974-83. [DOI: 10.1039/c4mb00395k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new global histonomic approach for deciphering histone code disruption in human cells after xenobiotic exposure.
Collapse
Affiliation(s)
- Raphaël Bilgraer
- UMR CNRS 8638
- Faculté des Sciences Pharmaceutiques et Biologiques de Paris
- Université Paris Descartes
- Sorbonne Paris Cité
- 75006 Paris, France
| | - Sylvie Gillet
- UMR CNRS 8638
- Faculté des Sciences Pharmaceutiques et Biologiques de Paris
- Université Paris Descartes
- Sorbonne Paris Cité
- 75006 Paris, France
| | - Sophie Gil
- INSERM U1139
- Faculté des Sciences Pharmaceutiques et Biologiques de Paris
- Université Paris Descartes
- Sorbonne Paris Cité
- 75006 Paris, France
| | - Danièle Evain-Brion
- INSERM U1139
- Faculté des Sciences Pharmaceutiques et Biologiques de Paris
- Université Paris Descartes
- Sorbonne Paris Cité
- 75006 Paris, France
| | - Olivier Laprévote
- UMR CNRS 8638
- Faculté des Sciences Pharmaceutiques et Biologiques de Paris
- Université Paris Descartes
- Sorbonne Paris Cité
- 75006 Paris, France
| |
Collapse
|
5
|
Li KK, Luo C, Wang D, Jiang H, Zheng YG. Chemical and biochemical approaches in the study of histone methylation and demethylation. Med Res Rev 2012; 32:815-67. [PMID: 22777714 DOI: 10.1002/mrr.20228] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and offer information otherwise difficult to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation, chemical ligation, mass spectrometry, biochemical methylation and demethylation assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes, or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic applications in the clinic.
Collapse
Affiliation(s)
- Keqin Kathy Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | | |
Collapse
|
6
|
Hersman E, Nelson DM, Griffith WP, Jelinek C, Cotter RJ. Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 312:5-16. [PMID: 22389584 PMCID: PMC3289288 DOI: 10.1016/j.ijms.2011.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The in vitro deuteroacetylation of histones obtained from biological sources has been used previously in bottom-up mass spectrometry analyses to quantitate the percent of endogenous acetylation of specific lysine sites and/or peptides. In this report, derivatization of unmodified lysine residues on histones is used in combination with high performance mass spectrometry, including combined HPLC MS/MS, to distinguish and quantitate endogenously acetylated isoforms occurring within the same tryptic peptide sequence and to extend this derivatization strategy to other post-translational modifications, specifically methylation, dimethylation and trimethylation. The in vitro deuteroacetylation of monomethylated lysine residues is observed, though dimethylated or trimethylated residues are not derivatised. Comparison of the relative intensities ascribed to the deuteroacetylated and monomethylated species with the deuteroacetylated but unmethylated analog, provides an opportunity to estimate the percent of methylation at that site. In addition to the observed fragmentation patterns, the very high mass accuracy available on the Orbitrap mass spectrometer can be used to confirm the structural isoforms, and in particular to distinguish between trimethylated and acetylated species.
Collapse
Affiliation(s)
- Elisabeth Hersman
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | | |
Collapse
|
7
|
Balakrishnan L, Milavetz B. Decoding the histone H4 lysine 20 methylation mark. Crit Rev Biochem Mol Biol 2011; 45:440-52. [PMID: 20735237 DOI: 10.3109/10409238.2010.504700] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular biology of histone H4 lysine 20 (H4K20) methylation, like many other post-translational modifications of histones, has been the subject of intensive interest in recent years. While there is an emerging consensus linking H4K20me1, H4K20me2, and H4K20me3 to transcription, repair, and constitutive heterochromatin, respectively, the specific details of these associations and the biological mechanisms by which the methylated histones are introduced and function are now the subject of active investigation. Although a large number of methylases capable of methylating H4K20 have been identified and characterized; there is no known demethylase of H4K20, though the search is ongoing. Additionally, many recent studies have been directed at understanding the role of methylated H4K20 and other histone modifications associated with different biological processes in the context of a combinatorial histone code. It seems likely that continued study of the methylation of H4K20 will yield extremely valuable insights concerning the regulation of histone modifications before and during cell division and the impact of these modifications on subsequent gene expression.
Collapse
Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
| | | |
Collapse
|
8
|
Li KK, Luo C, Wang D, Jiang H, Zheng YG. Chemical and biochemical approaches in the study of histone methylation and demethylation. Med Res Rev 2010. [DOI: 10.1002/med.20228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Bradshaw RA, Medzihradszky KF, Chalkley RJ. Protein PTMs: post-translational modifications or pesky trouble makers? JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1095-1097. [PMID: 20635432 PMCID: PMC3133960 DOI: 10.1002/jms.1786] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Analysis of protein post-translational modifications using mass spectrometry is an intensive area of proteomic research. This perspective discusses the current state of the field with respect to what can be achieved, the challenges encountered, most notably with modification site assignment, the reliability of the published results, consequences of unreliable data and what is needed to be done to improve the situation.
Collapse
Affiliation(s)
| | | | - Robert J. Chalkley
- Correspondence to: Robert J. Chalkley, Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, N-472, San Francisco, CA 94158-2517, USA.,
| |
Collapse
|
10
|
Cuomo A, Moretti S, Minucci S, Bonaldi T. SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells. Amino Acids 2010; 41:387-99. [PMID: 20617350 DOI: 10.1007/s00726-010-0668-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/16/2010] [Indexed: 01/22/2023]
Abstract
In living cells, the N-terminal tails of core histones, the proteinaceous component of nucleosomes, are subjected to a range of covalent post-translational modifications (PTMs), which have specific roles in modulating chromatin structure and function. A growing body of evidence suggests that deregulation of histone modification patterns, upstream or downstream of DNA methylation, is a critical event in cancer initiation and progression. However, a comprehensive description of how histone modifications, singly or in combination, is disrupted in transformed cells is missing; consequently the issue whether and how specific changes in histone PTMs patterns correlate to particular tumor features is still elusive. In the present study, we focused on human breast cancer and comprehensively analyzed PTMs on histone H3 and H4 from four cancer cell lines (MCF7, MDA-MB231, MDA-MB453 and T-47D), in comparison with normal epithelial breast cells. We performed high-resolution mass spectrometry analysis of histones, in combination with stable isotope labeling with amino acids in cell culture (SILAC), to quantitatively track the modification changes in cancer cells, as compared to their normal counterpart. Our investigation focuses on lysine acetylation and methylation on fourteen distinct sites in H3 and H4. We observed significant changes for several modifications in cancer cells: while in a few cases those modifications had been previously described as a hallmark of human tumors, we could identify novel modifications, whose abundance is significantly altered in breast cancer cells. Overall, these modifications may represent part of a "breast cancer-specific epigenetic signature", with implications in the characterization of histone-related biomarkers. This work demonstrates that SILAC-based proteomics is a powerful tool to study qualitatively and quantitatively histone PTMs patterns, contributing significantly to the comprehension of epigenetic phenomena in cancer biology.
Collapse
Affiliation(s)
- Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), IFOM-IEO Campus, Via Adamello 16, 20139, Milan, Italy
| | | | | | | |
Collapse
|
11
|
Dal Piaz F, Tosco A, Eletto D, Piccinelli AL, Moltedo O, Franceschelli S, Sbardella G, Remondelli P, Rastrelli L, Vesci L, Pisano C, De Tommasi N. The identification of a novel natural activator of p300 histone acetyltranferase provides new insights into the modulation mechanism of this enzyme. Chembiochem 2010; 11:818-27. [PMID: 20373302 DOI: 10.1002/cbic.200900721] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many severe human pathologies are related to alterations of the fine balance between histone acetylation and deacetylation; because not all such diseases involve hypoacetylation, but also hyperacetylation, compounds able to enhance or repress the activities of histone acetyltransferases (HATs) could be promising therapeutic agents. We evaluated in vitro and in cell the ability of eleven natural polyisoprenylated benzophenone derivatives to modulate the HAT activity of p300/CBP, an enzyme that plays a pivotal role in a variety of cellular processes. Some of the tested compounds bound efficiently to the p300/CBP protein: in particular, guttiferone A, guttiferone E and clusianone inhibit its HAT activity, whereas nemorosone showed a surprising ability to activate the enzyme. The ability of nemorosone to penetrate cell membranes and modulate histone acetylation into the cell together with its high affinity for the p300/CBP enzyme made this compound a suitable lead for the design of optimized anticancer drugs. Besides, the studies performed at a cellular and molecular level on both the inhibitors and the activator provided new insights into the modulation mechanism of p300/CBP by small molecules.
Collapse
Affiliation(s)
- Fabrizio Dal Piaz
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Salerno, Via Ponte Don Melillo 1, 84084 Fisciano, SA, Italy.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Eliuk SM, Maltby D, Panning B, Burlingame AL. High resolution electron transfer dissociation studies of unfractionated intact histones from murine embryonic stem cells using on-line capillary LC separation: determination of abundant histone isoforms and post-translational modifications. Mol Cell Proteomics 2010; 9:824-37. [PMID: 20133344 DOI: 10.1074/mcp.m900569-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Epigenetic regulation of chromatin is dependent on both the histone protein isoforms and state of their post-translational modifications. The assignment of all post-translational modification sites for each individual intact protein isoform remains an experimental challenge. We present an on-line reversed phase LC tandem mass spectrometry approach for the separation of intact, unfractionated histones and a high resolution mass analyzer, the Orbitrap, with electron transfer dissociation capabilities to detect and record accurate mass values for the molecular and fragment ions observed. From a single LC-electron transfer dissociation run, this strategy permits the identification of the most abundant intact proteins, determination of the isoforms present, and the localization of post-translational modifications.
Collapse
Affiliation(s)
- Shannon M Eliuk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | | | | | | |
Collapse
|
13
|
Abstract
Analysis of intact proteins by tandem mass spectrometry has mostly been confined to high-end mass spectrometry platforms. This protocol describes the application of routine HPLC to separate proteins, MALDI-ToF mass spectrometry to interrogate intact protein species and electron transfer dissociation/proton transfer reaction within a quadrupole ion trap to perform tandem mass spectrometry.
Collapse
Affiliation(s)
- Sarah R Hart
- Michael Barber Centre for Mass Spectrometry, University of Manchester, Manchester, UK
| |
Collapse
|
14
|
Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA. High throughput characterization of combinatorial histone codes. Mol Cell Proteomics 2009; 8:2266-84. [PMID: 19654425 DOI: 10.1074/mcp.m900238-mcp200] [Citation(s) in RCA: 247] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present a novel method utilizing "saltless" pH gradient weak cation exchange-hydrophilic interaction liquid chromatography directly coupled to electron transfer dissociation (ETD) mass spectrometry for the automated on-line high throughput characterization of hypermodified combinatorial histone codes. This technique, performed on a low resolution mass spectrometer, displays an improvement over existing methods with an approximately 100-fold reduction in sample requirements and analysis time. The scheme presented is capable of identifying all of the major combinatorial histone codes present in a sample in a 2-h analysis. The large N-terminal histone peptides are eluted by the pH and organic solvent weak cation exchange-hydrophilic interaction liquid chromatography gradient and directly introduced via nanoelectrospray ionization into a benchtop linear quadrupole ion trap mass spectrometer equipped with ETD. Each polypeptide is sequenced, and the modification sites are identified by ETD fragmentation. The isobaric trimethyl and acetyl modifications are resolved chromatographically and confidently distinguished by the synthesis of mass spectrometric and chromatographic information. We demonstrate the utility of the method by complete characterization of human histone H3.2 and histone H4 from butyrate-treated cells, but it is generally applicable to the analysis of highly modified peptides. We find this methodology very useful for chromatographic separation of isomeric species that cannot be separated well by any other chromatographic means, leading to less complicated tandem mass spectra. The improved separation and increased sensitivity generated novel information about much less abundant forms. In this method demonstration we report over 200 H3.2 forms and 70 H4 forms, including forms not yet detected in human cells, such as the remarkably highly modified histone H3.2 K4me3K9acK14acK18acK23acK27acK36me3. Such detail provided by our proteomics platform will be essential for determining how histone modifications occur and act in combination to propagate the histone code during transcriptional events and could greatly enable sequencing of the histone component of human epigenomes.
Collapse
Affiliation(s)
- Nicolas L Young
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | | | | | | | | | | |
Collapse
|
15
|
Wang CM, Tsai SN, Yew TW, Kwan YW, Ngai SM. Identification of histone methylation multiplicities patterns in the brain of senescence-accelerated prone mouse 8. Biogerontology 2009; 11:87-102. [PMID: 19434510 DOI: 10.1007/s10522-009-9231-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 04/27/2009] [Indexed: 12/31/2022]
Abstract
Histone post-translational modifications (PTMs) are involved in diverse biological processes and methylation was regarded as a long-term epigenetic mark. Though aging represented one of the major risk factors for neurodegenerative diseases, no systematic investigations had correlated the patterns of histone PTMs in the brain with aging and the roles of such concerted histone PTMs in brain aging are still unknown. In this study, enzyme digestion, nano-LC, MALDI-TOF/TOF MS analysis and Western blotting were combined to investigate the defined methylation of core histones (H2A, H2B, H3 and H4) in the brain of 12-month-old senescence accelerated mouse prone 8 (SAMP8). The expression of several modified histones in the brain of 3-, and 12-month-old SAMP8 mice as well as that of the age-matched control senescence accelerated-resistant mouse (SAMR1) was compared. In the brain of 12-month-old SAMP8 mice, seven methylation sites (H3K24, H3K27, H3K36, H3K79, H3R128, H4K20 and H2A R89) were detected and most PTMs sites were located on histone H3. Mono-methylated H4K20 decreased significantly in the brain of 12-month-old SAMP8 mice. Methylated H3K27 and H3K36 coexisted in the aged brain with different methylation multiplicities. Di-methylated H3K79 expressed in the neurons of cerebral cortex and hippocampus. This study showed histone methylation patterns in the aged SAMP8 mice brain and provided the experimental evidences for further research on histone PTMs in the aged brain. We hope these results could initiate a platform for the exchange of comprehensive information concerning aging or neurodegenerative disease and help us interpret the change of gene expression and DNA repair ability at epigenetic level.
Collapse
Affiliation(s)
- Chun Mei Wang
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | | | | | | | | |
Collapse
|
16
|
Narayanan A, Jacobson MP. Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol 2009; 19:156-63. [DOI: 10.1016/j.sbi.2009.02.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 02/20/2009] [Accepted: 02/24/2009] [Indexed: 02/08/2023]
|
17
|
Garcia BA, Thomas CE, Kelleher NL, Mizzen CA. Tissue-specific expression and post-translational modification of histone H3 variants. J Proteome Res 2008; 7:4225-36. [PMID: 18700791 DOI: 10.1021/pr800044q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analyses of histone H3 from 10 rat tissues using a Middle Down proteomics platform revealed tissue-specific differences in their expression and global PTM abundance. ESI/FTMS with electron capture dissociation showed that, in general, these proteins were hypomodified in heart, liver and testes. H3.3 was hypermodified compared to H3.2 in some, but not all tissues. In addition, a novel rat testes-specific H3 protein was identified with this approach.
Collapse
Affiliation(s)
- Benjamin A Garcia
- Institute for Genomic Biology, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | | | | | | |
Collapse
|
18
|
An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 2008; 3:1018-25. [DOI: 10.1038/nprot.2008.66] [Citation(s) in RCA: 421] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
19
|
Abstract
Two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE) systems employing combinations of acetic acid/urea (AU), acetic acid/urea/Triton X-100 (AUT) and sodium dodecyl sulfate (SDS) gel formulations are uniquely effective for resolution of histone variants and their modified derivatives. Coupled with Western transfer methods using modification-specific antibodies and recent advances in mass spectrometry, 2D PAGE emerges as a versatile tool for histone purification and analysis. This chapter describes 2D PAGE gel systems appropriate for histone proteins, including detailed procedures for designing, running, and staining gels. Methods for electrophoretic transfer of histones from AUTxSDS and AUTxAU 2D gels are described and evaluated. Alternatively, methods are provided for obtaining highly purified protein samples from fixed and stained gels via electroelution of proteins from specific gel spots.
Collapse
Affiliation(s)
- George R Green
- Department of Pharmaceutical Sciences, Mercer University College of Pharmacy and Health Sciences, Atlanta, GA, USA
| | | |
Collapse
|
20
|
Abstract
Chromatin structure plays a vital role in the transmission of heritable gene expression patterns. The recent application of mass spectrometry to histone biology provides several striking insights into chromatin regulation. The continuing identification of new histone post-translational modifications is revolutionizing the ways in which we think about how access to genomic DNA is controlled. While post-translational modifications of the flexible histone tails continue to be an active area of investigation, the recent discovery of multiple modifications in the structured globular domains of histones provides new insights into how the nucleosome works. Recent experiments underscore the importance of a subgroup of these modifications: those that regulate histone-DNA interactions on the lateral surface of the nucleosome. This information highlights an emerging new paradigm in chromatin control, that of the epigenetic regulation of nucleosome mobility.
Collapse
Affiliation(s)
- Michael S Cosgrove
- Syracuse University, Department of Biology, Syracuse, New York, NY 13244, USA.
| |
Collapse
|
21
|
Bergmüller E, Gehrig PM, Gruissem W. Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana. J Proteome Res 2007; 6:3655-68. [PMID: 17691833 DOI: 10.1021/pr0702159] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic DNA is structurally packed into chromatin by the basic histone proteins H2A, H2B, H3, and H4. There is increasing evidence that incorporation and post-translational modifications of histone variants have a fundamental role in gene regulation. While modifications of H3 and H4 histones are now well-established, considerably less is known about H2B modifications. Here, we present the first detailed characterization of H2B-variants isolated from the model plant Arabidopsis thaliana. We combined reversed-phase chromatography with tandem mass spectrometry to identify post-translational modifications of the H2B-variants HTB1, HTB2, HTB4, HTB9, and HTB11, isolated from total chromatin and euchromatin-enriched fractions. The HTB9-variant has acetylation sites at lysines 6, 11, 27, 32, 38, and 39, while Lys-145 can be ubiquitinated. Analogous modifications and an additional methylation of Lys-3 were identified for HTB11. HTB2 shows similar acetylation and ubiquitination sites and an additional methylation at Lys-11. Furthermore, the N-terminal alanine residues of HTB9 and HTB11 were found to be mono-, di-, or trimethylated or unmodified. No methylation of arginine residues was detected. The data suggest that most of these modification sites are only partially occupied. Our study significantly expands the map of covalent Arabidopsis histone modifications and is the first step to unraveling the histone code in higher plants.
Collapse
Affiliation(s)
- Eveline Bergmüller
- Institute of Plant Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | | |
Collapse
|
22
|
Su X, Ren C, Freitas MA. Mass spectrometry-based strategies for characterization of histones and their post-translational modifications. Expert Rev Proteomics 2007; 4:211-25. [PMID: 17425457 PMCID: PMC2572816 DOI: 10.1586/14789450.4.2.211] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Due to the intimate interactions between histones and DNA, the characterization of histones has become the focus of great attention. A series of mass spectrometry-based technologies have been dedicated to the characterization and quantitation of different histone forms. This review focuses on the discussion of mass spectrometry-based strategies used for the characterization of histones and their post-translational modifications.
Collapse
Affiliation(s)
- Xiaodan Su
- The Ohio State Unviersity, Department of Molecular Virology Immunology & Medical Genetics, Human Cancer Genetics, Columbus, OH, USA
| | | | | |
Collapse
|
23
|
Knapp AR, Ren C, Su X, Lucas DM, Byrd JC, Freitas MA, Parthun MR. Quantitative profiling of histone post-translational modifications by stable isotope labeling. Methods 2007; 41:312-9. [PMID: 17309842 PMCID: PMC2572810 DOI: 10.1016/j.ymeth.2006.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 08/19/2006] [Indexed: 11/28/2022] Open
Abstract
Methods for accurately quantitating changes in histone post-translational modifications are necessary for developing an understanding of how their dynamic nature influences nuclear events involving access to genomic DNA. This article describes methods for the use of in vivo stable isotope label incorporation for quantitating the levels of modification at specific residues in histone proteins. These methods are applicable to a wide variety of model systems and examples of their use in both mammalian cells and Saccharomyces cerevisiae are presented.
Collapse
Affiliation(s)
- Amy R Knapp
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF, Allis CD. Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci U S A 2007; 104:2086-91. [PMID: 17284592 PMCID: PMC1892956 DOI: 10.1073/pnas.0610993104] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Indexed: 11/18/2022] Open
Abstract
Individual posttranslational modifications (PTMs) on histones have well established roles in certain biological processes, notably transcriptional programming. Recent genomewide studies describe patterns of covalent modifications, such as H3 methylation and acetylation at promoters of specific target genes, or "bivalent domains," in stem cells, suggestive of a possible combinatorial interplay between PTMs on the same histone. However, detection of long-range PTM associations is often problematic in antibody-based or traditional mass spectrometric-based analyses. Here, histone H3 from a ciliate model was analyzed as an enriched source of transcriptionally active chromatin. Using a recently developed mass spectrometric approach, combinatorial modification states on single, long N-terminal H3 fragments (residues 1-50) were determined. The entire modification status of intact N termini was obtained and indicated correlations between K4 methylation and H3 acetylation. In addition, K4 and K27 methylation were identified concurrently on one H3 species. This methodology is applicable to other histones and larger polypeptides and will likely be a valuable tool in understanding the roles of combinatorial patterns of PTMs.
Collapse
Affiliation(s)
| | | | - Yifan Liu
- Laboratories of *Chromatin Biology and
| | - Alan J. Tackett
- Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10021
| | | | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904; and
| | - Brian T. Chait
- Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10021
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904; and
- Department of Pathology, Health Sciences Center, University of Virginia, Charlottesville, VA 22908
| | | |
Collapse
|
25
|
Garcia BA, Shabanowitz J, Hunt DF. Characterization of histones and their post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2007; 11:66-73. [PMID: 17157550 DOI: 10.1016/j.cbpa.2006.11.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Accepted: 11/16/2006] [Indexed: 10/23/2022]
Abstract
Histone proteins and their accompanying post-translational modifications have received much attention for their ability to affect chromatin structure and, hence, regulate gene expression. Recently, mass spectrometry has become an important complementary tool for the analysis of histone variants and modification sites, for determining the degree of occupancy of these modifications and for quantifying differential expression of these modifications from various samples. Additionally, as advancements in mass spectrometry technologies continue, the ability to read entire 'histone codes' across large regions of histone polypeptides or intact protein is possible. As chromatin biology demands, mass spectrometry has adapted and continues as a key technology for the analysis of gene regulation networks involving histone modifications.
Collapse
Affiliation(s)
- Benjamin A Garcia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | |
Collapse
|
26
|
Su X, Jacob NK, Amunugama R, Lucas DM, Knapp AR, Ren C, Davis ME, Marcucci G, Parthun MR, Byrd JC, Fishel RA, Freitas MA. Liquid chromatography mass spectrometry profiling of histones. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 850:440-54. [PMID: 17254850 PMCID: PMC2694509 DOI: 10.1016/j.jchromb.2006.12.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 12/08/2006] [Accepted: 12/17/2006] [Indexed: 11/25/2022]
Abstract
Here we describe the use of reverse-phase liquid chromatography mass spectrometry (RPLC-MS) to simultaneously characterize variants and post-translationally modified isoforms for each histone. The analysis of intact proteins significantly reduces the time of sample preparation and simplifies data interpretation. LC-MS analysis and peptide mass mapping have previously been applied to identify histone proteins and to characterize their post-translational modifications. However, these studies provided limited characterization of both linker histones and core histones. The current LC-MS analysis allows for the simultaneous observation of all histone PTMs and variants (both replacement and bulk histones) without further enrichment, which will be valuable in comparative studies. Protein identities were verified by the analysis of histone H2A species using RPLC fractionation, AU-PAGE separation and nano-LC-MS/MS.
Collapse
Affiliation(s)
- Xiaodan Su
- Department of Chemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Naduparambil K. Jacob
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Ravindra Amunugama
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - David M. Lucas
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Amy R. Knapp
- Department of Molecular and Cellular Biochemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Chen Ren
- Department of Chemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Melanie E. Davis
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Guido Marcucci
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Mark R. Parthun
- Department of Molecular and Cellular Biochemistry, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - John C. Byrd
- Department of Internal Medicine, Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Richard A. Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| | - Michael A. Freitas
- Department of Molecular Virology, Immunology, and Medical Genetics; Human Cancer Genetics, College of Medicine and Public Health The Ohio State University Columbus, OH
| |
Collapse
|
27
|
Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
Collapse
Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
| | | |
Collapse
|
28
|
Roe MR, Griffin TJ. Gel-free mass spectrometry-based high throughput proteomics: Tools for studying biological response of proteins and proteomes. Proteomics 2006; 6:4678-87. [PMID: 16888762 DOI: 10.1002/pmic.200500876] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Revolutionary advances in biological mass spectrometry (MS) have provided a basic tool to make possible comprehensive proteomic analysis. Traditionally, two-dimensional gel electrophoresis has been used as a separation method coupled with MS to facilitate analysis of complex protein mixtures. Despite the utility of this method, the many challenges of comprehensive proteomic analysis has motivated the development of gel-free MS-based strategies to obtain information not accessible using two-dimensional gel separations. These advanced strategies have enabled researchers to dig deeper into complex proteomes, gaining insights into the composition, quantitative response, covalent modifications and macromolecular interactions of proteins that collectively drive cellular function. This review describes the current state of gel-free, high throughput proteomic strategies using MS, including (i) the separation approaches commonly used for complex mixture analysis; (ii) strategies for large-scale quantitative analysis; (iii) analysis of post-translational modifications; and (iv) recent advances and future directions. The use of these strategies to make new discoveries at the proteome level into the effects of disease or other cellular perturbations is discussed in a variety of contexts, providing information on the potential of these tools in electromagnetic field research.
Collapse
Affiliation(s)
- Mikel R Roe
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | | |
Collapse
|
29
|
Naldi M, Andrisano V, Fiori J, Calonghi N, Pagnotta E, Parolin C, Pieraccini G, Masotti L. Histone proteins determined in a human colon cancer by high-performance liquid chromatography and mass spectrometry. J Chromatogr A 2006; 1129:73-81. [PMID: 16887128 DOI: 10.1016/j.chroma.2006.06.100] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 06/27/2006] [Accepted: 06/28/2006] [Indexed: 11/22/2022]
Abstract
The application of reversed-phase high-pressure liquid chromatography under gradient conditions and electrospray ion trap mass spectrometry (LC-ESI-MS) to the analysis of global modification levels of core histones is described. The optimised LC-ESI-MS method was applied for the first time to the characterisation of histones extracted from HT29, a human colon cancer cell line. Eight histones (H1-1, H1-2, H2A-1, H2A-2, H2B, H3-1, H3-2, H4) were separated on a C4 stationary phase with complete resolution, never reached in previous HPLC-MS methods, by using a gradient elution with the combined presence of heptafluorobutyric acid and formic acid as acidic modifiers in the mobile phase. Heptafluorobutyric acid was found to improve selectivity, whereas the presence of formic acid decreased ion suppression. Histones eluted from the column were detected with an ion trap mass spectrometer with an electrospray source. The peak averaged mass spectra were reconstructed by Mag Tran 1.0 software and the mass of the various isoforms of histones were derived. Method validation was conducted by performing the same sample analysis by coupling LC-ESI to a quadrupole-time-of-flight mass spectrometer (Q-TOF). The number of histone forms and their mass were found to differ not significantly from those obtained by ion trap mass spectrometer. Also the relative modifications abundance within the same histone type was found following the same trend as the two mass analysers. This method was then applied to the characterisation of changes in histone modification in HT29, never analysed by LC-MS before, treated with histone deacetylase inhibitors such as valproate and sodium butyrate, also used in preclinical trials as anticancer drugs. In particular, both the inhibitors produced a significant increase in H4 histone acetylated forms: 89% increase of the diacetyl dimethyl H4 form was observed with 1mM valproate supplementation, whereas 5 mM butyrate led to a 68% increase of the same form. Triacetyl monomethyl H4 (11,377 Da) and triacetyl dimethyl H4 (11,390 Da) were found only in cells treated with butyrate. Selective changes of H3 histone were detected with butyrate, in agreement with recently reported western blotting studies. Modifications in the H2A histone degree of acetylation were revealed by treatment of the cells with butyrate (H2A-1, H2A-2) and valproate (H2A-2). The results of the proposed methodology confirmed that inhibition of histone deacetylases caused histone hyperacetylation, responsible for decondensation and reorganization of interphase dynamic chromatin. This method resulted in selective and sensitive method to monitor variations in the acetylation and methylation state of histones after treatment of HT29 with inhibitors, and is therefore suitable for further application in new drug discovery for tumour therapy.
Collapse
Affiliation(s)
- M Naldi
- Department of Biochemistry G. Moruzzi, Via Irnerio 48, University of Bologna, 40126 Bologna, Italy
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Boyne MT, Pesavento JJ, Mizzen CA, Kelleher NL. Precise Characterization of Human Histones in the H2A Gene Family by Top Down Mass Spectrometry. J Proteome Res 2006; 5:248-53. [PMID: 16457589 DOI: 10.1021/pr050269n] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Top Down analysis revealed that at least fourteen genes encoding histone H2A are coexpressed in HeLa cells. Characterization of these species revealed that all except H2A.Z and H2A.F/Z were alpha-N-acetylated, H2A.O and H2A.C,D,I,N,P were the most abundant, and those exceeding approximately 10% abundance lacked post-translational modifications. This unequivocal identification of H2A forms illustrates the advantages of Top Down Mass Spectrometry and provides a global perspective of H2A regulation through the cell cycle.
Collapse
Affiliation(s)
- Michael T Boyne
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | |
Collapse
|
31
|
Simons BL, Wang G, Shen RF, Knepper MA. In vacuo isotope coded alkylation technique (IVICAT); an N-terminal stable isotopic label for quantitative liquid chromatography/mass spectrometry proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:2463-77. [PMID: 16862635 DOI: 10.1002/rcm.2615] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present a new isotopic labeling strategy to modify the N-terminal amino group of peptides in a quantifiable reaction without the use of expensive reagents or solvents. The In Vacuo Isotope Coded Alkylation Technique (IVICAT) is a methylation reaction, carried out at low pressure (<100 mTorr), that results in a stable quaternary trimethylammonium group, thus adding a permanent positive charge at the N-terminus of peptides without modifying the epsilon-amino groups of lysine. The methylation reaction increases the signal intensity of modified peptides in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and liquid chromatography (LC)/MS and the isotopic peak pair differs by 9 mass units which can be easily resolved by either instrument. N-terminally trimethylated peptides exhibit collision-induced dissociation (CID) mass spectra that differ from their unmodified analogues by an enhanced b-ion series in MS2 spectra due to the fixed positive charge. Using LC/MS/MS with an LTQ mass analyzer for quantification, the experimentally determined ratios of H9- to D9-trimethyl-labeled peptides of beta-casein provided accurate estimates of the actual ratios with low % error. IVICAT labeling also accurately quantified proteins in rat kidney inner medullary collecting duct cell types, as judged by comparison with relative quantification by subsequent immunoblotting experiments. IVICAT labeling, when used in conjunction with the new proteomics software QUIL, can accurately report relative protein abundances and increase the sequence coverage of proteins of tissue proteomes.
Collapse
Affiliation(s)
- Brigitte L Simons
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | | | | | | |
Collapse
|
32
|
Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics 2005; 5:194-203. [PMID: 16210244 DOI: 10.1074/mcp.m500285-mcp200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Post-translational histone modifications modulate chromatin-templated processes and therefore affect cellular proliferation, growth, and development. Although post-translational modifications on the core histones have been under intense investigation for several years, the modifications on variant histones are poorly understood. We used tandem mass spectrometry to identify covalent modifications on a histone H2A variant, macroH2A1.2. MacroH2A1.2 can be monoubiquitinated; however, the site of monoubiquitination has not been documented. In this study we used green fluorescent protein-tagged macroH2A1.2 to determine that Lys(115) is a site of ubiquitination. In addition, we found that this variant H2A is methylated on the epsilon amino group of lysine residues Lys(17), Lys(122), and Lys(238) and phosphorylated on Thr(128). Three of these modifications were also found to be present in the endogenous protein by mass spectrometric analysis. These results provide the first direct evidence that multiple post-translational modifications are imposed on macroH2A1.2, suggesting that, like canonical H2A, this variant H2A is subject to regulation by combinatorial use of covalent modifications.
Collapse
Affiliation(s)
- Feixia Chu
- Mass Spectrometry Facility and Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA
| | | | | | | | | | | |
Collapse
|