51
|
Ahringer J, Gasser SM. Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function. Genetics 2018; 208:491-511. [PMID: 29378810 PMCID: PMC5788517 DOI: 10.1534/genetics.117.300386] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/18/2017] [Indexed: 01/08/2023] Open
Abstract
Chromatin is organized and compacted in the nucleus through the association of histones and other proteins, which together control genomic activity. Two broad types of chromatin can be distinguished: euchromatin, which is generally transcriptionally active, and heterochromatin, which is repressed. Here we examine the current state of our understanding of repressed chromatin in Caenorhabditis elegans, focusing on roles of histone modifications associated with repression, such as methylation of histone H3 lysine 9 (H3K9me2/3) or the Polycomb Repressive Complex 2 (MES-2/3/6)-deposited modification H3K27me3, and on proteins that recognize these modifications. Proteins involved in chromatin repression are important for development, and have demonstrated roles in nuclear organization, repetitive element silencing, genome integrity, and the regulation of euchromatin. Additionally, chromatin factors participate in repression with small RNA pathways. Recent findings shed light on heterochromatin function and regulation in C. elegans, and should inform our understanding of repressed chromatin in other animals.
Collapse
Affiliation(s)
- Julie Ahringer
- The Gurdon Institute, University of Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge CB2 1QN, United Kingdom
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland, and
- Faculty of Natural Sciences, University of Basel, 4056, Switzerland
| |
Collapse
|
52
|
Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA. Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Epigenetics Chromatin 2017; 10:34. [PMID: 28683815 PMCID: PMC5501349 DOI: 10.1186/s13072-017-0139-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/27/2017] [Indexed: 01/15/2023] Open
Abstract
Background Middle-down mass spectrometry (MS), i.e., analysis of long (~50–60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities. Here, we demonstrate that the middle-down MS strategy can be combined with metabolic labeling for enhanced quantification of histone proteins and their combinatorial PTMs in a dynamic manner. Methods We used a nanoHPLC-MS/MS system consisting of hybrid weak cation exchange–hydrophilic interaction chromatography combined with high resolution MS and MS/MS with ETD fragmentation. After spectra identification, we filtered confident hits and quantified polypeptides using our in-house software isoScale. Results We first verified that middle-down MS can discriminate and differentially quantify unlabeled from heavy labeled histone N-terminal tails (heavy lysine and arginine residues). Results revealed no bias toward identifying and quantifying unlabeled versus heavy labeled tails, even if the heavy labeled peptides presented the typical skewed isotopic pattern typical of long protein sequences that hardly get 100% labeling. Next, we plated epithelial cells into a media with heavy methionine-(methyl-13CD3), the precursor of the methyl donor S-adenosylmethionine and stimulated epithelial to mesenchymal transition (EMT). We assessed that results were reproducible across biological replicates and with data obtained using the more widely adopted bottom-up MS strategy, i.e., analysis of short tryptic peptides. We found remarkable differences in the incorporation rate of methylations in non-confluent cells versus confluent cells. Moreover, we showed that H3K27me3 was a critical player during the EMT process, as a consistent portion of histones modified as H3K27me2K36me2 in epithelial cells were converted into H3K27me3K36me2 in mesenchymal cells. Conclusions We demonstrate that middle-down MS, despite being a more scarcely exploited MS technique than bottom-up, is a robust quantitative method for histone PTM characterization. In particular, middle-down MS combined with metabolic labeling is currently the only methodology available for investigating turnover of combinatorial histone PTMs in dynamic systems. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0139-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA
| | - Congcong Lu
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA
| | - Xiaoshi Wang
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA
| | - Kelly R Karch
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA
| | | | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104, USA.
| |
Collapse
|
53
|
Abstract
INTRODUCTION Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac. The traditional bottom-up MS strategy identifies and quantifies short (aa 4-20) tryptic peptides, and it is thus not suitable for the characterization of combinatorial PTMs. Areas covered: Here, we review the advancement of the middle-down MS strategy applied to histones, which consists in the analysis of intact histone N-terminal tails (aa 50-60). Middle-down MS has reached sufficient robustness and reliability, and it is far less technically challenging than PTM quantification on intact histones (top-down). However, the very few chromatin biology studies applying middle-down MS resulting from PubMed searches indicate that it is still very scarcely exploited, potentially due to the apparent high complexity of method and analysis. Expert commentary: We will discuss the state-of-the-art workflow and examples of existing studies, aiming to highlight its potential and feasibility for studies of cell biologists interested in chromatin and epigenetics.
Collapse
Affiliation(s)
- Simone Sidoli
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
54
|
Understanding Alzheimer's disease by global quantification of protein phosphorylation and sialylated N-linked glycosylation profiles: A chance for new biomarkers in neuroproteomics? J Proteomics 2017; 161:11-25. [DOI: 10.1016/j.jprot.2017.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/24/2017] [Accepted: 04/03/2017] [Indexed: 12/13/2022]
|
55
|
Schräder CU, Lee L, Rey M, Sarpe V, Man P, Sharma S, Zabrouskov V, Larsen B, Schriemer DC. Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping. Mol Cell Proteomics 2017; 16:1162-1171. [PMID: 28404794 DOI: 10.1074/mcp.m116.066803] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/07/2017] [Indexed: 01/10/2023] Open
Abstract
Trypsin dominates bottom-up proteomics, but there are reasons to consider alternative enzymes. Improving sequence coverage, exposing proteomic "dark matter," and clustering post-translational modifications in different ways and with higher-order drive the pursuit of reagents complementary to trypsin. Additionally, enzymes that are easy to use and generate larger peptides that capitalize upon newer fragmentation technologies should have a place in proteomics. We expressed and characterized recombinant neprosin, a novel prolyl endoprotease of the DUF239 family, which preferentially cleaves C-terminal to proline residues under highly acidic conditions. Cleavage also occurs C-terminal to alanine with some frequency, but with an intriguingly high "skipping rate." Digestion proceeds to a stable end point, resulting in an average peptide mass of 2521 units and a higher dependence upon electron-transfer dissociation for peptide-spectrum matches. In contrast to most proline-cleaving enzymes, neprosin effectively degrades proteins of any size. For 1251 HeLa cell proteins identified in common using trypsin, Lys-C, and neprosin, almost 50% of the neprosin sequence contribution is unique. The high average peptide mass coupled with cleavage at residues not usually modified provide new opportunities for profiling clusters of post-translational modifications. We show that neprosin is a useful reagent for reading epigenetic marks on histones. It generates peptide 1-38 of histone H3 and peptide 1-32 of histone H4 in a single digest, permitting the analysis of co-occurring post-translational modifications in these important N-terminal tails.
Collapse
Affiliation(s)
- Christoph U Schräder
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Linda Lee
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Martial Rey
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Vladimir Sarpe
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Petr Man
- §BioCev-Institute of Microbiology, Czech Academy of Sciences, Vestec, Czech Republic 117 20.,¶Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague, Czech Republic 116 36
| | - Seema Sharma
- ‖Thermo Fisher Scientific, San Jose, California 95134
| | | | - Brett Larsen
- **Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada M5G 1X5; and
| | - David C Schriemer
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada; .,‡‡Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| |
Collapse
|
56
|
Janssen KA, Sidoli S, Garcia BA. Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology. Methods Enzymol 2017; 586:359-378. [PMID: 28137571 DOI: 10.1016/bs.mie.2016.10.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets.
Collapse
Affiliation(s)
- K A Janssen
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - S Sidoli
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - B A Garcia
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
57
|
Castillo-Aguilera O, Depreux P, Halby L, Arimondo PB, Goossens L. DNA Methylation Targeting: The DNMT/HMT Crosstalk Challenge. Biomolecules 2017; 7:biom7010003. [PMID: 28067760 PMCID: PMC5372715 DOI: 10.3390/biom7010003] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022] Open
Abstract
Chromatin can adopt a decondensed state linked to gene transcription (euchromatin) and a condensed state linked to transcriptional repression (heterochromatin). These states are controlled by epigenetic modulators that are active on either the DNA or the histones and are tightly associated to each other. Methylation of both DNA and histones is involved in either the activation or silencing of genes and their crosstalk. Since DNA/histone methylation patterns are altered in cancers, molecules that target these modifications are interesting therapeutic tools. We present herein a vast panel of DNA methyltransferase inhibitors classified according to their mechanism, as well as selected histone methyltransferase inhibitors sharing a common mode of action.
Collapse
Affiliation(s)
- Omar Castillo-Aguilera
- Univ. Lille, ICPAL, EA 7365-GRITA-Groupe de Recherche sur les formes Injectables et les Technologies Associées, 3 rue du Pr. Laguesse, F-59000 Lille, France.
| | - Patrick Depreux
- Univ. Lille, ICPAL, EA 7365-GRITA-Groupe de Recherche sur les formes Injectables et les Technologies Associées, 3 rue du Pr. Laguesse, F-59000 Lille, France.
| | - Ludovic Halby
- FRE3600 Epigenetic Targeting of Cancer, CNRS, 31035 Toulouse, France.
| | - Paola B Arimondo
- FRE3600 Epigenetic Targeting of Cancer, CNRS, 31035 Toulouse, France.
- Churchill College, Cambridge CB3 0DS, UK.
| | - Laurence Goossens
- Univ. Lille, ICPAL, EA 7365-GRITA-Groupe de Recherche sur les formes Injectables et les Technologies Associées, 3 rue du Pr. Laguesse, F-59000 Lille, France.
| |
Collapse
|
58
|
Zahedi RP. Joining forces: studying multiple post-translational modifications to understand dynamic disease mechanisms. Expert Rev Proteomics 2016; 13:1055-1057. [PMID: 27584944 DOI: 10.1080/14789450.2016.1231577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- René P Zahedi
- a Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , Germany
| |
Collapse
|