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Wang H, Liao Z, Yang Z, Xiao W, Yang Z, He J, Zhang X, Yan X, Tang C. Histone derived antimicrobial peptides identified from Mytilus coruscus serum by peptidomics. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109546. [PMID: 38614412 DOI: 10.1016/j.fsi.2024.109546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
Histones and their N-terminal or C-terminal derived peptides have been studied in vertebrates and presented as potential antimicrobial agents playing important roles in the innate immune defenses. Although histones and their derived peptides had been reported as components of innate immunity in invertebrates, the knowledge about the histone derived antimicrobial peptides (HDAPs) in invertebrates are still limited. Using a peptidomic technique, a set of peptide fragments derived from the histones was identified in this study from the serum of microbes challenged Mytilus coruscus. Among the 85 identified histone-derived-peptides with high confidence, 5 HDAPs were chemically synthesized and the antimicrobial activities were verified, showing strong growth inhibition against Gram-positive bacteria, Gram-negative bacteria, and fungus. The gene expression level of the precursor histones matched by representative HDAPs were further tested using q-PCR, and the results showed a significant upregulation of the histone gene expression levels in hemocytes, gill, and mantle of the mussel after immune stress. In addition, three identified HDAPs were selected for preparation of specific antibodies, and the corresponding histones and their derived C-terminal fragments were detected by Western blotting in the blood cell and serum of immune challenged mussel, respectively, indicating the existence of HDAPs in M. coruscus. Our findings revealed the immune function of histones in Mytilus, and confirmed the existence of HDAPs in the mussel. The identified Mytilus HDAPs represent a new source of immune effector with antimicrobial function in the innate immune system, and thus provide promising candidates for the treatment of microbial infections in aquaculture and medicine.
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Affiliation(s)
- Haodong Wang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Zongxin Yang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Wenhui Xiao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Zilin Yang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Jianyu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Xiaojun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Changsheng Tang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China.
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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3
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Lui KW, Ngai SM. PrSM-Level Side-by-Side Comparison of Online LC-MS Methods with Intact Histone H3 and H4 Proteoforms. J Proteome Res 2021; 20:4331-4345. [PMID: 34327993 DOI: 10.1021/acs.jproteome.1c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heterogeneity of histone H3 proteoforms makes histone H3 top-down analysis challenging. To enhance the detection coverage of the proteoforms, performing liquid chromatography (LC) front-end to mass spectrometry (MS) detection is recommended. Here, using optimized electron-transfer/high-energy collision dissociation (EThcD) parameters, we have conducted a proteoform-spectrum match (PrSM)-level side-by-side comparison of reversed-phase LC-MS (RPLC-MS), "dual-gradient" weak cation-exchange/hydrophilic interaction LC-MS (dual-gradient WCX/HILIC-MS), and "organic-rich" WCX/HILIC-MS on the top-down analyses of H3.1, H3.2, and H4 proteins extracted from a HeLa cell culture. While both dual-gradient WCX/HILIC and organic-rich WCX/HILIC could resolve intact H3 and H4 proteoforms by the number of acetylations, the organic-rich method could enhance the separations of different trimethyl/acetyl near-isobaric H3 proteoforms. In comparison with RPLC-MS, both of the WCX/HILIC-MS methods enhanced the qualities of the H3 PrSMs and remarkably improved the range, reproducibility, and confidence in the identifications of H3 proteoforms.
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Affiliation(s)
- Kin-Wing Lui
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong 999077, P. R. China
| | - Sai-Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong 999077, P. R. China.,State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, P. R. China
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4
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Völker-Albert MC, Schmidt A, Forne I, Imhof A. Analysis of Histone Modifications by Mass Spectrometry. ACTA ACUST UNITED AC 2019; 92:e54. [PMID: 30040183 DOI: 10.1002/cpps.54] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Histone N termini undergo diverse post-translational modifications that significantly extend the information potential of the genetic code. Moreover, these modifications mark specific chromatin regions, modulating epigenetic control, lineage commitment, and overall function of chromosomes. It is widely accepted that histone modifications affect chromatin function, but the exact mechanisms by which modifications on histone tails and specific combinations of modifications are generated, and how they cross-talk with one another, are still enigmatic. Mass spectrometry is the gold-standard method for analyzing histone modifications, as it allows the quantification of modifications and combinations. This unit describes how high-resolution mass spectrometry can be used to study histone post-translational modifications. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Moritz Carl Völker-Albert
- Protein Analysis Unit, Biomedical Center of the Ludwig Maximilian University Munich, Munich, Germany
| | - Andreas Schmidt
- Protein Analysis Unit, Biomedical Center of the Ludwig Maximilian University Munich, Munich, Germany
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center of the Ludwig Maximilian University Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center of the Ludwig Maximilian University Munich, Munich, Germany
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Gargano AFG, Shaw JB, Zhou M, Wilkins CS, Fillmore TL, Moore RJ, Somsen GW, Paša-Tolić L. Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS. J Proteome Res 2018; 17:3791-3800. [PMID: 30226781 PMCID: PMC6220366 DOI: 10.1021/acs.jproteome.8b00458] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Top-down proteomics is an emerging
analytical strategy to characterize
combinatorial protein post-translational modifications (PTMs). However,
sample complexity and small mass differences between chemically closely
related proteoforms often limit the resolution attainable by separations
employing a single liquid chromatographic (LC) principle. In particular,
for ultramodified proteins like histones, extensive and time-consuming
fractionation is needed to achieve deep proteoform coverage. Herein,
we present the first online nanoflow comprehensive two-dimensional
liquid chromatography (nLC×LC) platform top-down mass spectrometry
analysis of histone proteoforms. The described two-dimensional LC
system combines weak cation exchange chromatography under hydrophilic
interaction LC conditions (i.e., charge- and hydrophilicity-based
separation) with reversed phase liquid chromatography (i.e., hydrophobicity-based
separation). The two independent chemical selectivities were run at
nanoflows (300 nL/min) and coupled online with high-resolution mass
spectrometry employing ultraviolet photodissociation (UVPD-HRMS).
The nLC×LC workflow increased the number of intact protein masses
observable relative to one-dimensional approaches and allowed characterization
of hundreds of proteoforms starting from limited sample quantities
(∼1.5 μg).
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Affiliation(s)
- Andrea F G Gargano
- Center for Analytical Sciences Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands.,Vrije Universiteit Amsterdam , Department of Bioanalytical Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , de Boelelaan 1085 , 1081HV Amsterdam , The Netherlands
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Christopher S Wilkins
- Biological Sciences Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Thomas L Fillmore
- Biological Sciences Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
| | - Govert W Somsen
- Center for Analytical Sciences Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands.,Vrije Universiteit Amsterdam , Department of Bioanalytical Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , de Boelelaan 1085 , 1081HV Amsterdam , The Netherlands
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , P.O. Box 999, Richland , Washington 99352 , United States
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Catuogno S, Esposito CL, Ungaro P, de Franciscis V. Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option. Pharmaceuticals (Basel) 2018; 11:ph11030079. [PMID: 30149585 PMCID: PMC6161095 DOI: 10.3390/ph11030079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms include DNA methylation, posttranslational modifications of histones, chromatin remodeling factors, and post transcriptional gene regulation by noncoding RNAs. All together, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Targeting enzymatic regulators responsible for DNA and chromatin modifications hold promise for modulating the transcriptional regulation of genes that are involved in cancer, as well as in chronic noncommunicable metabolic diseases like obesity, diabetes, and cardiovascular diseases. Increasingly studies are emerging, leading to the identification of specific and effective molecules targeting epigenetic pathways involved in disease onset. In this regard, RNA interference, which uses small RNAs to reduce gene expression and nucleic acid aptamers are arising as very promising candidates in therapeutic approach. Common to all these strategies is the imperative challenge of specificity. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules due to their ability to bind with high affinity to specific ligands, their high chemical flexibility as well as tissue penetration capability. In this review, we will focus on the recent progress in the field of aptamers used as targeting moieties able to recognize and revert epigenetics marks involved in diseases onset.
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Affiliation(s)
- Silvia Catuogno
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Carla Lucia Esposito
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Paola Ungaro
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Vittorio de Franciscis
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
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7
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Harauz G. And Yet it is Modified-Holding a Candle to the Dark Matter of White Matter. Proteomics 2017; 17. [PMID: 28851044 DOI: 10.1002/pmic.201700299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Indexed: 11/08/2022]
Abstract
The multilamellar membrane myelin sheath of the CNS, that enwraps axons to facilitate saltatory conduction in higher vertebrates, is held together by myelin basic protein (MBP). Yet this generalization masks how enigmatic MBP is, much like cosmological "dark matter." First, the casual use of the singular form for "protein" distracts that there are multiple, developmentally regulated "classic" splice isoforms ranging from 14 to 21.5 kDa, each with extensive PTMs. Second, the static image of MBP adhering two cytoplasmic leaflets of the oligodendrocyte membrane together in close apposition, suggests it to be inaccessible to modifying enzymes. And yet it is modified (to paraphrase Galileo's phrase on the earth's motion). In this issue of Proteomics, Sarg et al. apply an integrated CE-MS approach to investigate the PTMs of 18.5 kDa MBP from mouse brains of different ages. They identify new sites and types of modification, as well as confirming previously known PTMs. Innovative tools for unraveling the intricacies of the myelin basic proteome and how it organizes CNS myelin (much like basic histones organize chromatin), will help us understand white matter development and plasticity in health, during ageing, and in demyelinating diseases such as multiple sclerosis.
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Affiliation(s)
- George Harauz
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
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Siviero F, Rezende-Teixeira P, Andrade AD, Santelli RV, Machado-Santelli GM. The histone genes cluster in Rhynchosciara americana and its transcription profile in salivary glands during larval development. Genet Mol Biol 2016; 39:580-588. [PMID: 27727361 PMCID: PMC5127150 DOI: 10.1590/1678-4685-gmb-2015-0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/16/2016] [Indexed: 11/22/2022] Open
Abstract
In this work we report the characterization of the Rhynchosciara americana histone genes cluster nucleotide sequence. It spans 5,131 bp and contains the four core histones and the linker histone H1. Putative control elements were detected. We also determined the copy number of the tandem repeat unit through quantitative PCR, as well as the unequivocal chromosome location of this unique locus in chromosome A band 13. The data were compared with histone clusters from the genus Drosophila, which are the closest known homologues.
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Affiliation(s)
- Fábio Siviero
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Paula Rezende-Teixeira
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alexandre de Andrade
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Roberto Vicente Santelli
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Glaucia Maria Machado-Santelli
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
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9
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Faserl K, Kremser L, Müller M, Teis D, Lindner HH. Quantitative proteomics using ultralow flow capillary electrophoresis-mass spectrometry. Anal Chem 2015; 87:4633-40. [PMID: 25839223 PMCID: PMC4423236 DOI: 10.1021/acs.analchem.5b00312] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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In this work, we evaluate the incorporation
of an ultralow flow
interface for coupling capillary electrophoresis (CE) and mass spectrometry
(MS), in combination with reversed-phase high-pressure liquid chromatography
(HPLC) fractionation as an alternate workflow for quantitative proteomics.
Proteins, extracted from a SILAC (stable isotope labeling by amino
acids in cell culture) labeled and an unlabeled yeast strain were
mixed and digested enzymatically in solution. The resulting peptides
were fractionated using RP-HPLC and analyzed by CE–MS yielding
a total of 28 538 quantified peptides that correspond to 3 272
quantified proteins. CE–MS analysis was performed using a neutral
capillary coating, providing the highest separation efficiency at
ultralow flow conditions (<10 nL/min). Moreover, we were able to
demonstrate that CE–MS is a powerful method for the identification
of low-abundance modified peptides within the same sample. Without
any further enrichment strategies, we succeeded in quantifying 1 371
phosphopeptides present in the CE–MS data set and found 49
phosphopeptides to be differentially regulated in the two yeast strains.
Including acetylation, phosphorylation, deamidation, and oxidized
forms, a total of 8 106 modified peptides could be identified
in addition to 33 854 unique peptide sequences found. The work
presented here shows the first quantitative proteomics approach that
combines SILAC labeling with CE–MS analysis.
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Affiliation(s)
- Klaus Faserl
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Leopold Kremser
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Martin Müller
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - David Teis
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Herbert H Lindner
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
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Lopez R, Sarg B, Lindner H, Bartolomé S, Ponte I, Suau P, Roque A. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation. Nucleic Acids Res 2015; 43:4463-76. [PMID: 25870416 PMCID: PMC4482070 DOI: 10.1093/nar/gkv304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/27/2015] [Indexed: 11/29/2022] Open
Abstract
Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation.
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Affiliation(s)
- Rita Lopez
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Bettina Sarg
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, A-6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, A-6020, Innsbruck, Austria
| | - Salvador Bartolomé
- Laboratorio de Luminiscencia y Espectroscopia de Biomoléculas, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Nehmé H, Nehmé R, Lafite P, Routier S, Morin P. Human protein kinase inhibitor screening by capillary electrophoresis using transverse diffusion of laminar flow profiles for reactant mixing. J Chromatogr A 2013; 1314:298-305. [PMID: 24075461 DOI: 10.1016/j.chroma.2013.08.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/10/2013] [Accepted: 08/12/2013] [Indexed: 12/24/2022]
Abstract
A capillary electrophoresis (CE)-based enzyme assay method has been developed to screen protein kinase inhibitors. Four human kinases GSK3β, DYRK1A, CDK5/p25 and CDK1/cyclin B were chosen to test this novel method. These enzymes have been identified as very promising targets to develop treatments against cancer and neurodegenerative diseases. The efficiency of drugs against these relevant biological targets has never been carried out by CE. For this proposal, the capillary was used as a nanoreactor in which four reactants (the enzyme, its two substrates and its potential inhibitor) were successively injected, mixed by using transverse diffusion of laminar flow profiles and incubated. The adenosine 5'-diphosphate (ADP) formed during the enzymatic reaction was detected by UV and quantified. The efficiency of the developed CE method was validated by determining the IC50 values of a wide variety of inhibitors covering a large domain of affinity toward kinases and containing representative and chemically divergent skeletons. Excellent agreement was found between the results obtained by CE and those reported in the literature when using conventional radiometric enzyme assays. Moreover, CE was successfully used to determine the inhibitory effect of several potential inhibitors that was not yet assessed by conventional methods and is crucial for structure activity relation studies. This novel CE method is simple, rapid, very economic (few tens of nanoliters per IC50) and eco-friendly since no radioactivity was required. It could be extended to high-throughput screening of kinase inhibitors, which is of great interest for biomedical and pharmaceutical research fields.
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Affiliation(s)
- Hala Nehmé
- Institut de Chimie Organique et Analytique, Université d'Orléans, CNRS FR 2708, UMR 7311, Orléans, France
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Sarg B, Faserl K, Kremser L, Halfinger B, Sebastiano R, Lindner HH. Comparing and combining capillary electrophoresis electrospray ionization mass spectrometry and nano-liquid chromatography electrospray ionization mass spectrometry for the characterization of post-translationally modified histones. Mol Cell Proteomics 2013; 12:2640-56. [PMID: 23720761 DOI: 10.1074/mcp.m112.024109] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We present the first comprehensive capillary electrophoresis electrospray ionization mass spectrometry (CESI-MS) analysis of post-translational modifications derived from H1 and core histones. Using a capillary electrophoresis system equipped with a sheathless high-sensitivity porous sprayer and nano-liquid chromatography electrospray ionization mass spectrometry (nano-LC-ESI-MS) as two complementary techniques, we characterized H1 histones isolated from rat testis. Without any pre-separation of the perchloric acid extraction, a total of 70 different modified peptides, including 50 phosphopeptides, were identified in the rat linker histones H1.0, H1a-H1e, and H1t. Out of the 70 modified H1 histone peptides, 27 peptides could be identified with CESI-MS only, and 11 solely with LC-ESI-MS. Immobilized metal-affinity chromatography enrichment prior to MS analysis yielded a total of 55 phosphopeptides; 22 of these peptides could be identified only by CESI-MS, and 19 only by LC-ESI-MS, showing the complementarity of the two techniques. We mapped 42 H1 modification sites, including 31 phosphorylation sites, of which 8 were novel sites. For the analysis of core histones, we chose a different strategy. In a first step, the sulfuric-acid-extracted core histones were pre-separated using reverse-phase high-performance liquid chromatography. Individual rat testis core histone fractions obtained in this way were digested and analyzed via bottom-up CESI-MS. This approach yielded the identification of 42 different modification sites including acetylation (lysine and N(α)-terminal); mono-, di-, and trimethylation; and phosphorylation. When we applied CESI-MS for the analysis of intact core histone subtypes from butyrate-treated mouse tumor cells, we were able to rapidly detect their degree of modification, and we found this method very useful for the separation of isobaric trimethyl and acetyl modifications. Taken together, our results highlight the need for additional techniques for the comprehensive analysis of post-translational modifications. CESI-MS is a promising new proteomics tool as demonstrated by this, the first comprehensive analysis of histone modifications, using rat testis as an example.
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Affiliation(s)
- Bettina Sarg
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, A-6020 Innsbruck, Austria
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Zhang K, Tian S, Fan E. Protein lysine acetylation analysis: current MS-based proteomic technologies. Analyst 2013; 138:1628-36. [DOI: 10.1039/c3an36837h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Separation and purification of multiply acetylated proteins using cation-exchange chromatography. Methods Mol Biol 2013; 981:103-13. [PMID: 23381856 PMCID: PMC3779653 DOI: 10.1007/978-1-62703-305-3_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
High-performance liquid chromatography (HPLC) is extremely useful for the study of proteins and the characterization of their posttranslational modifications. Here we describe a method that utilizes cation-exchange HPLC to separate multiply acetylated histone H3 species on the basis of their charge and hydrophilicity. This high-resolution method allows for the separation of histone H3 species that differ by as few as one acetyl group, and is compatible with subsequent analysis by a variety of techniques, including mass spectrometry and western blotting.
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15
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Yonamine Y, Hoshino Y, Shea KJ. ELISA-mimic screen for synthetic polymer nanoparticles with high affinity to target proteins. Biomacromolecules 2012; 13:2952-7. [PMID: 22813352 DOI: 10.1021/bm300986j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic polymer nanoparticles (NPs) that display high affinity to protein targets have significant potential for medical and biotechnological applications as protein capture agents or functional replacements of antibodies ("plastic antibodies"). In this study, we modified an immunological assay (enzyme-linked immunosorbent assay: ELISA) into a high-throughput screening method to select nanoparticles with high affinity to target proteins. Histone and fibrinogen were chosen as target proteins to demonstrate this concept. The selection process utilized a biotinylated NP library constructed with combinations of functional monomers. The screen identified NPs with distinctive functional group compositions that exhibited high affinity to either histone or fibrinogen. The variation of protein affinity with changes in the nature and amount of functional groups in the NP provided chemical insight into the principle determinants of protein-NP binding. The NP affinity was semiquantified using the ELISA-mimic assay by varying the NP concentrations. The screening results were found to correlate with solution-based assay results. This screening system utilizing a biotinylated NP is a general approach to optimize functional monomer compositions and can be used to rapidly search for synthetic polymers with high (or low) affinity for target biological macromolecules.
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Affiliation(s)
- Yusuke Yonamine
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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16
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Guo SW. The endometrial epigenome and its response to steroid hormones. Mol Cell Endocrinol 2012; 358:185-96. [PMID: 22067514 DOI: 10.1016/j.mce.2011.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 10/21/2011] [Accepted: 10/21/2011] [Indexed: 01/21/2023]
Abstract
The human endometrium undergoes cyclic morphological and functional changes during the menstrual cycle. These changes are driven mainly by steroid hormones and orchestrated by a myriad of genes - many of which have been identified recently as being epigenetically regulated. Epigenetic modifications, including DNA methylation and histone acetylations, are shown recently to be involved in functional changes in endometrium and endometrial diseases. Since epigenetics itself is a rapidly evolving field, this review starts with an overview of epigenetics and its intrinsic connections with endometrial response to steroid hormones, highlighting its various levels of complexities. This is followed by a review of published and unpublished work on "writers", "erasers", and other players of endometrial epigenome. In the end, areas in need for future research in this area will be exposed.
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Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetric and Gynecologic Hospital, and Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University Shanghai College of Medicine, 419 Fangxie Road, Shanghai 200011, China.
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17
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Shao N, Zhang K, Chen Y, He X, Zhang Y. Preparation and characterization of DNA aptamer based spin column for enrichment and separation of histones. Chem Commun (Camb) 2012; 48:6684-6. [PMID: 22644042 DOI: 10.1039/c2cc32376a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core histones play a critical role in the regulation of chromatin-templated biological process. Here we have developed a novel approach to enrich histone proteins based on the recognition of a specific aptamer. The method shows good selectivity toward histone proteins and is able to extract histones directly from complex whole cell lysates.
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Affiliation(s)
- Nan Shao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P. R. China
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18
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Faserl K, Sarg B, Kremser L, Lindner H. Optimization and Evaluation of a Sheathless Capillary Electrophoresis–Electrospray Ionization Mass Spectrometry Platform for Peptide Analysis: Comparison to Liquid Chromatography–Electrospray Ionization Mass Spectrometry. Anal Chem 2011; 83:7297-305. [DOI: 10.1021/ac2010372] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Klaus Faserl
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, A-6020 Innsbruck, Austria
| | - Bettina Sarg
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, A-6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, A-6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, A-6020 Innsbruck, Austria
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19
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Young NL, Plazas-Mayorca MD, Garcia BA. Systems-wide proteomic characterization of combinatorial post-translational modification patterns. Expert Rev Proteomics 2010; 7:79-92. [PMID: 20121478 DOI: 10.1586/epr.09.100] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein post-translational modifications (PTMs) have been widely shown to influence protein-protein interactions, direct subcellular location and transduce a variety of both internal and externally generated signals into cellular/phenotypic outcomes. Mass spectrometry has been a key tool for the elucidation of several types of PTMs in both qualitative and quantitative manners. As large datasets on the proteome-wide level are now being generated on a daily basis, the identification of combinatorial PTM patterns has become feasible. A survey of the recent literature in this area shows that many proteins undergo multiple modifications and that sequential or hierarchal patterns exist on many proteins; the biology of these modification patterns is only starting to be unraveled. This review will outline combinatorial PTM examples in biology, and the mass spectrometry-based techniques and applications utilized in the investigations of these combinatorial PTMs.
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Affiliation(s)
- Nicolas L Young
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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20
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Munro SK, Farquhar CM, Mitchell MD, Ponnampalam AP. Epigenetic regulation of endometrium during the menstrual cycle. Mol Hum Reprod 2010; 16:297-310. [PMID: 20139117 DOI: 10.1093/molehr/gaq010] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The endometrium undergoes morphological and functional changes during the menstrual cycle which are essential for uterine receptivity. These changes are driven by estrogen and progesterone and involve the fine control of many different genes-several of which have been identified as being epigenetically regulated. Epigenetic modification may therefore influence the functional changes in the endometrium required for successful implantation. There is, however, only limited information on epigenetic regulation in endometrium. We review the potential role of epigenetic regulation of key processes during the menstrual cycle and present our own findings following a preliminary study into global acetylation levels in the human endometrium. A changing epigenetic state is associated with the differentiation of stem cells into different lineages and thus may be involved in endometrial regeneration. Histone acetylation is implicated in the vascular endothelial growth factor pathway during angiogenesis, and studies using histone deacetylase inhibitors suggest an involvement in endometrial proliferation and differentiation. The processes of decidualization and implantation are also associated with epigenetic change and epigenetic modulators show variable expression across the menstrual cycle. Our own studies found that endometrial global histone acetylation, as determined by western blotting, changed throughout the menstrual cycle and correlated well with expected transcription activity during the different phases. This suggests that epigenetics may be involved in the regulation of endometrial gene expression during the menstrual cycle and that abnormal epigenetic modifications may therefore be associated with implantation failure and early pregnancy loss as well as with other endometrial pathologies.
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Affiliation(s)
- S K Munro
- The Liggins Institute, The University of Auckland, Auckland 1142, New Zealand
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21
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Garcia BA. What does the future hold for Top Down mass spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:193-202. [PMID: 19942451 DOI: 10.1016/j.jasms.2009.10.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 10/14/2009] [Accepted: 10/21/2009] [Indexed: 05/28/2023]
Abstract
Mass spectrometry (MS) research has revolutionized modern biological and biomedical fields. At the heart of the majority of mass spectrometry experiments is the use of Bottom Up mass spectrometry methods where proteins are first proteolyzed into smaller fragments before MS interrogation. The advent of electron capture dissociation and, more recently, electron-transfer dissociation, however, has allowed Top Down (analysis of intact proteins) or middle down (analysis of large polypeptides) mass spectrometry to both experience large increases in development, growth, and overall usage. Nevertheless, for high-throughput large-scale proteomic studies, Bottom Up mass spectrometry has easily dominated the field. As Top Down mass spectrometry methodology and technology continue to develop, will it genuinely be able to compete with Bottom Up mass spectrometry for whole proteome analysis? Discussed here are the current approaches, applications, issues, and future view of high-throughput Top Down mass spectrometry.
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Affiliation(s)
- Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
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23
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Hoffmann MH, Trembleau S, Muller S, Steiner G. Nucleic acid-associated autoantigens: pathogenic involvement and therapeutic potential. J Autoimmun 2009; 34:J178-206. [PMID: 20031372 DOI: 10.1016/j.jaut.2009.11.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Autoimmunity to ubiquitously expressed macromolecular nucleic acid-protein complexes such as the nucleosome or the spliceosome is a characteristic feature of systemic autoimmune diseases. Disease-specificity and/or association with clinical features of some of these autoimmune responses suggest pathogenic involvement which, however, has been proven in only a few cases so far. Although the mechanisms leading to autoimmunity against nucleic acid-containing complexes are still far from being fully understood, there is increasing experimental evidence that the nucleic acid component may act as a co-stimulator or adjuvans via activation of nucleic acid-binding receptor systems such as Toll-like receptors in antigen-presenting cells. Dysregulated apoptosis and inappropriate stimulation of nucleic acid-sensing receptors may lead to loss of tolerance against the protein components of such complexes, activation of autoreactive T cells and formation of autoantibodies. This has been demonstrated to occur in systemic lupus erythematosus and seems to represent a general mechanism that may be crucial for the development of systemic autoimmune diseases. This review provides a comprehensive overview of the most thoroughly-characterized nucleic acid-associated autoantigens, describing their structure and biological function, as well as the nature and pathogenic importance of the reactivities directed against them. Furthermore, recent advances in immunotherapy such as antigen-specific approaches targeted at nucleic acid-binding antigens are discussed.
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Affiliation(s)
- Markus H Hoffmann
- Division of Rheumatology, Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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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.
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Affiliation(s)
- Nicolas L Young
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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Wood C, Snijders A, Williamson J, Reynolds C, Baldwin J, Dickman M. Post-translational modifications of the linker histone variants and their association with cell mechanisms. FEBS J 2009; 276:3685-97. [PMID: 19490123 DOI: 10.1111/j.1742-4658.2009.07079.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In recent years, a considerable amount of research has been focused on establishing the epigenetic mechanisms associated with DNA and the core histones. This effort is driven by the fact that epigenetics is intimately involved with genomics in a whole range of molecular processes. However, there is now a consensus that the epigenetics of the linker histones are just as important. The result of that consensus is that the post-translational modifications (PTMs) for most of the linker histone variants in human and mouse have now been established by a number of experimental techniques, foremost of which is mass spectrometry (MS). MS was also used by our group to establish the PTMs of the linker histone variants in chicken erythrocytes. Although it is now known which types of PTM occur at particular locations on the linker histone variants, there is still a large gap in the knowledge of how this data relates to function. The focus of this review is an analysis of the PTM data for the linker histones from several species, but with an emphasis on human, mouse, and chicken. Our analysis reveals that certain PTMs can be clearly correlated with specific functions of the linker histones in particular cell types, and that unique PTM patterns exist for different cell types.
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Affiliation(s)
- Christopher Wood
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK.
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