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Zappacosta F, Wagner CD, Della Pietra A, Gerhart SV, Keenan K, Korenchuck S, Quinn CJ, Barbash O, McCabe MT, Annan RS. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Mol Cell Proteomics 2021; 20:100067. [PMID: 33775892 PMCID: PMC8138768 DOI: 10.1016/j.mcpro.2021.100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Histones are highly posttranslationally modified proteins that regulate gene expression by modulating chromatin structure and function. Acetylation and methylation are the most abundant histone modifications, with methylation occurring on lysine (mono-, di-, and trimethylation) and arginine (mono- and dimethylation) predominately on histones H3 and H4. In addition, arginine dimethylation can occur either symmetrically (SDMA) or asymmetrically (ADMA) conferring different biological functions. Despite the importance of histone methylation on gene regulation, characterization and quantitation of this modification have proven to be quite challenging. Great advances have been made in the analysis of histone modification using both bottom-up and top-down mass spectrometry (MS). However, MS-based analysis of histone posttranslational modifications (PTMs) is still problematic, due both to the basic nature of the histone N-terminal tails and to the combinatorial complexity of the histone PTMs. In this report, we describe a simplified MS-based platform for histone methylation analysis. The strategy uses chemical acetylation with d0-acetic anhydride to collapse all the differently acetylated histone forms into one form, greatly reducing the complexity of the peptide mixture and improving sensitivity for the detection of methylation via summation of all the differently acetylated forms. We have used this strategy for the robust identification and relative quantitation of H4R3 methylation, for which stoichiometry and symmetry status were determined, providing an antibody-independent evidence that H4R3 is a substrate for both Type I and Type II PRMTs. Additionally, this approach permitted the robust detection of H4K5 monomethylation, a very low stoichiometry methylation event (0.02% methylation). In an independent example, we developed an in vitro assay to profile H3K27 methylation and applied it to an EZH2 mutant xenograft model following small-molecule inhibition of the EZH2 methyltransferase. These specific examples highlight the utility of this simplified MS-based approach to quantify histone methylation profiles. Simplification of histone complexity for analysis of lysine and arginine methylation. Improved sensitivity for the analysis of dimethylarginine symmetry. Accurate ratio of symmetric and asymmetric H4R3 dimethylarginine in cancer cells. Catalog of accessible histone methyl marks to facilitate assay development.
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Affiliation(s)
- Francesca Zappacosta
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Craig D Wagner
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Sarah V Gerhart
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Kathryn Keenan
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Chad J Quinn
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Roland S Annan
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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Kraus AJ, Vanselow JT, Lamer S, Brink BG, Schlosser A, Siegel TN. Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes. Nat Commun 2020; 11:1498. [PMID: 32198348 PMCID: PMC7083915 DOI: 10.1038/s41467-020-15274-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/01/2020] [Indexed: 12/29/2022] Open
Abstract
Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histones or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in Trypanosoma brucei, we identified 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we found TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription. Histone modification and deposition are key regulators of transcription. Here, Kraus et al. provide a quantitative histone acetylome for Trypanosoma brucei, identify histone modifications enriched at transcription start sites, and show how H4 and H2A.Z acetylation affect histone deposition and transcription in trypanosomes.
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Affiliation(s)
- Amelie J Kraus
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.,Institute for Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany.,German Federal Institute for Risk Assessment, Unit Safety of Chemicals, Department Chemicals and Product Safety, Berlin, Germany
| | - Stephanie Lamer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Benedikt G Brink
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - T Nicolai Siegel
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany. .,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany. .,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.
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Vasquez JJ, Wedel C, Cosentino RO, Siegel TN. Exploiting CRISPR-Cas9 technology to investigate individual histone modifications. Nucleic Acids Res 2018; 46:e106. [PMID: 29912461 PMCID: PMC6182134 DOI: 10.1093/nar/gky517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/13/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination. By establishing an episome-based CRISPR-Cas9 system for T. brucei, we have edited wild type cells without inserting selectable markers, inserted a GFP tag between an ORF and its 3'UTR, deleted both alleles of a gene in a single transfection, and performed precise editing of genes that exist in multicopy arrays, replacing histone H4K4 with H4R4 in the absence of detectable off-target effects. The newly established genome editing toolbox allows for the generation of precise mutants without needing to change other regions of the genome, opening up opportunities to study the role of individual histone modifications, catalytic sites of enzymes or the regulatory potential of UTRs in their endogenous environments.
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Affiliation(s)
- Juan-José Vasquez
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Carolin Wedel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Raul O Cosentino
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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Limbeck E, Vanselow JT, Hofmann J, Schlosser A, Mally A. Linking site-specific loss of histone acetylation to repression of gene expression by the mycotoxin ochratoxin A. Arch Toxicol 2017; 92:995-1014. [PMID: 29098329 DOI: 10.1007/s00204-017-2107-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 11/30/2022]
Abstract
Ochratoxin A (OTA) is a potent renal carcinogen but its mechanism has not been fully resolved. In vitro and in vivo gene expression studies consistently revealed down-regulation of gene expression as the predominant transcriptional response to OTA. Based on the importance of specific histone acetylation marks in regulating gene transcription and our recent finding that OTA inhibits histone acetyltransferases (HATs), leading to loss of acetylation of histones and non-histone proteins, we hypothesized that OTA-mediated repression of gene expression may be causally linked to HAT inhibition and loss of histone acetylation. In this study, we used a novel mass spectrometry approach employing chemical 13C-acetylation of unmodified lysine residues for quantification of post-translational acetylation sites to identify site-specific alterations in histone acetylation in human kidney epithelial cells (HK-2) exposed to OTA. These results showed OTA-mediated hypoacetylation at almost all lysine residues of core histones, including loss of acetylation at H3K9 and H3K14, which are hallmarks of gene activation. ChIP-qPCR used to establish a possible link between H3K9 or H3K14 hypoacetylation and OTA-mediated down-regulation of selected genes (AMIGO2, CLASP2, CTNND1) confirmed OTA-mediated H3K9 hypoacetylation at promoter regions of these genes. Integrated analysis of OTA-mediated genome-wide changes in H3K9 acetylation identified by ChIP-Seq with published gene expression data further demonstrated that among OTA-responsive genes almost 80% of hypoacetylated genes were down-regulated, thus confirming an association between H3K9 acetylation status and gene expression of these genes. However, only 7% of OTA repressed genes showed loss of H3K9 acetylation within promoter regions. Interestingly, however, GO analysis and functional enrichment of down-regulated genes showing loss of H3K9 acetylation at their respective promoter regions revealed enrichment of genes involved in the regulation of transcription, including a number of transcription factors that are predicted to directly or indirectly regulate the expression of 98% of OTA repressed genes. Thus, it is possible that histone acetylation changes in a fairly small set of genes but with key function in transcriptional regulation may trigger a cascade of events that may lead to overall repression of gene expression. Taken together, our data provide evidence for a mechanistic link between loss of H3K9 acetylation as a consequence of OTA-mediated inhibition of HATs and repression of gene expression by OTA, thereby affecting cellular processes critical to tumorigenesis.
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Affiliation(s)
- Elisabeth Limbeck
- Department of Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97078, Würzburg, Germany
| | - Julian Hofmann
- Department of Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97078, Würzburg, Germany
| | - Angela Mally
- Department of Toxicology, University of Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany.
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Jha PK, Khan MI, Mishra A, Das P, Sinha KK. HAT2 mediates histone H4K4 acetylation and affects micrococcal nuclease sensitivity of chromatin in Leishmania donovani. PLoS One 2017; 12:e0177372. [PMID: 28486547 PMCID: PMC5423686 DOI: 10.1371/journal.pone.0177372] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022] Open
Abstract
Histone post-translational modifications (PTMs) such as acetylation and methylation are known to affect chromatin higher order structures. Primary targets of these modifications include basic residues present at N-terminus tail region of core histones. Four histone acetyltransferase (HAT) genes have been identified in trypanosomatids. HAT1, HAT3 and HAT4 of Leishmania donovani have been partially characterized. However, there is no report about HAT2 of Leishmania donovani. Lysine residues present on the N-terminal tail of Leishmania donovani histone H4 are conserved in other trypanosomatids and humans. PTMs of lysines modulate various functions at chromatin level. The four histone acetyltransferases encoded in Leishmania genome were over-expressed to analyse their functional activity. All four HATs were found actively acetylating core histones H3/H4. Similar to L. donovani HAT3 and HAT4, HAT2 was found to be a member of MYST family protein and have SAS2 type domain. Over-expression of HAT2 significantly increases acetylation of H4K4. To analyse the effect of HAT2 over-expression on chromatin accessibility, micrococcal nuclease digestion assay was performed. MNase digestion resulted in a higher proportion of the mononucleosomes and dinucleosomes in HAT2 over-expressing cells as compared to WT L. donovani cells. Acetylation of lysine-4 neutralizes the amino terminal region of histone H4. This weakens its interaction with neighbouring nucleosomes and the linker DNA. HAT2 over-expression in L. donovani resulted in highly accessible chromatin suggesting chromatin decondensation. HAT2 may have an important role to play in global regulation of transcription in L. donovani. Better understanding of these epigenetic determinants of parasite would help in designing novel therapeutic strategies.
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Affiliation(s)
- Pravin K Jha
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Mohd Imran Khan
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Anshul Mishra
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Pradeep Das
- Molecular Biology Division, Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Kislay K Sinha
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
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Bienvenut WV, Scarpelli JP, Dumestier J, Meinnel T, Giglione C. EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. BMC Bioinformatics 2017; 18:182. [PMID: 28320318 PMCID: PMC5359831 DOI: 10.1186/s12859-017-1595-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 03/10/2017] [Indexed: 01/01/2023] Open
Abstract
Background Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles, such as mitochondria or chloroplast. Protein neo-N-termini can be located up to 100–150 amino acids downstream from the initiator methionine and are not easily predictable. Although some bioinformatics tools are available, they usually require extensive manual validation to identify the exact N-terminal position. The situation becomes even more complex when post-translational modifications take place at the neo-N-terminus. Although N-terminal acetylation occurs mostly in the cytosol, it is also observed in some organelles such as chloroplast. To date, no bioinformatics tool is available to define mature protein starting positions, the associated N-terminus acetylation status and/or yield for each proteoform. In this context, we have developed the EnCOUNTer tool (i) to score all characterized peptides using discriminating parameters to identify bona fide mature protein N-termini and (ii) to determine the N-terminus acetylation yield of the most reliable ones. Results Based on large scale proteomics analyses using the SILProNAQ methodology, tandem mass spectrometry favoured the characterization of thousands of peptides. Data processing using the EnCOUNTer tool provided an efficient and rapid way to extract the most reliable mature protein N-termini. Selected peptides were subjected to N-terminus acetylation yield determination. In an A. thaliana cell lysate, 1232 distinct proteotypic N-termini were characterized of which 648 were located at the predicted protein N-terminus (position 1/2) and 584 were located further downstream (starting at position > 2). A large number of these N-termini were associated with various well-defined maturation processes occurring on organelle-targeted proteins (mitochondria, chloroplast and peroxisome), secreted proteins or membrane-targeted proteins. It was also possible to highlight some protein alternative starts, splicing variants or erroneous protein sequence predictions. Conclusions The EnCOUNTer tool provides a unique way to extract accurately the most relevant mature proteins N-terminal peptides from large scale experimental datasets. Such data processing allows the identification of the exact N-terminus position and the associated acetylation yield. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1595-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Willy Vincent Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Jean-Pierre Scarpelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Johan Dumestier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
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