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Li C, Huang Z, Gu L. SETD2 reduction adversely affects the development of mouse early embryos. J Cell Biochem 2019; 121:797-803. [PMID: 31407364 DOI: 10.1002/jcb.29325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/15/2019] [Indexed: 01/03/2023]
Abstract
SET domain-containing protein 2 (SETD2), the protein of regulating trimethylation status of histone H3 at lysine 36 (H3K36), participates in the maintenance of chromatin architecture, transcription elongation, genome stability, and other biological events. However, its function in preimplantation embryos is still obscure. In this study, specific small interfering RNA was employed to investigate the functions of SETD2. We find that deletion of SETD2 results in the developmental delay of mouse early embryos, indicative of the compromised developmental potential. Remarkably, SETD2 knockdown induces the accumulation of the DNA lesions and apoptotic blastomeres in early embryos. In addition, the methylation level of H3K36 is significantly reduced in two-cell embryos depleted of SETD2. In summary, our data indicate that SETD2 maintains genome stability perhaps via regulating trimethylation status of H3K36, consequently controlling the embryo quality. These findings pave the avenue for understanding the cross-talk between epigenome and SETD2 during early embryo development.
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Affiliation(s)
- Chunling Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhenyue Huang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ling Gu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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2
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ElBashir R, Vanselow JT, Kraus A, Janzen CJ, Siegel TN, Schlosser A. Fragment ion patchwork quantification for measuring site-specific acetylation degrees. Anal Chem 2016; 87:9939-45. [PMID: 26335048 DOI: 10.1021/acs.analchem.5b02517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce fragment ion patchwork quantification as a new mass spectrometry-based approach for the highly accurate quantification of site-specific acetylation degrees. This method combines (13)C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Acetylation degrees are determined from the isotope patterns of acetylated b and y ions. We show that this approach allows to determine site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei. In addition, we demonstrate how this approach can be used to identify substrate sites of histone acetyltransferases.
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Affiliation(s)
| | | | | | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter University of Wuerzburg , Am Hubland, 97074 Wuerzburg, Germany
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3
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Richardson SL, Hanjra P, Zhang G, Mackie BD, Peterson DL, Huang R. A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases. Anal Biochem 2015; 478:59-64. [PMID: 25778392 DOI: 10.1016/j.ab.2015.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 03/04/2015] [Indexed: 01/22/2023]
Abstract
Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI-MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH4H2PO4 to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.
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Affiliation(s)
- Stacie L Richardson
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Pahul Hanjra
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Gang Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Brianna D Mackie
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Darrell L Peterson
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA.
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4
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Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD. The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3. Mol Cell Proteomics 2014; 13:2896-910. [PMID: 25106422 DOI: 10.1074/mcp.m114.038174] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to form the catalytic module of the ADA and SAGA transcriptional coactivator complexes. Gcn5 also contains an acetyl-lysine binding bromodomain that has been implicated in regulating nucleosomal acetylation in vitro, as well as at gene promoters in cells. However, the contribution of the Gcn5 bromodomain in regulating site specificity of HAT activity remains unclear. Here, we used a combined acid-urea gel and quantitative mass spectrometry approach to compare the HAT activity of wild-type and Gcn5 bromodomain-mutant ADA subcomplexes (Gcn5-Ada2-Ada3). Wild-type ADA subcomplex acetylated H3 lysines with the following specificity; H3K14 > H3K23 > H3K9 ≈ H3K18 > H3K27 > H3K36. However, when the Gcn5 bromodomain was defective in acetyl-lysine binding, the ADA subcomplex demonstrated altered site-specific acetylation on free and nucleosomal H3, with H3K18ac being the most severely diminished. H3K18ac was also severely diminished on H3K14R, but not H3K23R, substrates in wild-type HAT reactions, further suggesting that Gcn5-catalyzed acetylation of H3K14 and bromodomain binding to H3K14ac are important steps preceding H3K18ac. In sum, this work details a previously uncharacterized cross-talk between the Gcn5 bromodomain "reader" function and enzymatic HAT activity that might ultimately affect gene expression. Future studies of how mutations in bromodomains or other histone post-translational modification readers can affect chromatin-templated enzymatic activities will yield unprecedented insight into a potential "histone/epigenetic code." MS data are available via ProteomeXchange with identifier PXD001167.
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Affiliation(s)
- Anne M Cieniewicz
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Linley Moreland
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Alison E Ringel
- ‖Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; **Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Samuel G Mackintosh
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Ana Raman
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Tonya M Gilbert
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Cynthia Wolberger
- §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ‖Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; **Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Alan J Tackett
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205;
| | - Sean D Taverna
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
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5
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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.
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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
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