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Angerilli A, Tait J, Berges J, Shcherbakova I, Pokrovsky D, Schauer T, Smialowski P, Hsam O, Mentele E, Nicetto D, Rupp RA. The histone H4K20 methyltransferase SUV4-20H1/KMT5B is required for multiciliated cell differentiation in Xenopus. Life Sci Alliance 2023; 6:e202302023. [PMID: 37116939 PMCID: PMC10147948 DOI: 10.26508/lsa.202302023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
H4 lysine 20 dimethylation (H4K20me2) is the most abundant histone modification in vertebrate chromatin. It arises from sequential methylation of unmodified histone H4 proteins by the mono-methylating enzyme PR-SET7/KMT5A, followed by conversion to the dimethylated state by SUV4-20H (KMT5B/C) enzymes. We have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases. In the larval epidermis, this results in a severe loss of cilia in multiciliated cells (MCC), a key component of mucociliary epithelia. MCC precursor cells are correctly specified, amplify centrioles, but ultimately fail in ciliogenesis because of the perturbation of cytoplasmic processes. Genome-wide transcriptome profiling reveals that SUV4-20H1/H2-depleted ectodermal explants preferentially down-regulate the expression of several hundred ciliogenic genes. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that its catalytic activity is needed for axoneme formation. Overexpression of the H4K20me1-specific histone demethylase PHF8/KDM7B also rescues the ciliogenic defect in a significant manner. Taken together, this indicates that the conversion of H4K20me1 to H4K20me2 by SUV4-20H1 is critical for the formation of cilia tufts.
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Affiliation(s)
- Alessandro Angerilli
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janet Tait
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Julian Berges
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Sektion Pädiatrische Pneumologie und Allergologie und Mukoviszidose-Zentrum, Universitäts-Klinikum Heidelberg, Heidelberg, Germany
| | - Irina Shcherbakova
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Daniil Pokrovsky
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tamas Schauer
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Pawel Smialowski
- Institute for Stem Cell Research, Helmholtz Centre Munich, Neuherberg, Germany
- Department of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ohnmar Hsam
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Klinik und Poliklinik für Neurologie der Universität Regensburg, Regensburg, Germany
| | - Edith Mentele
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Nicetto
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Ambys Medicines, South San Francisco, CA, USA
| | - Ralph Aw Rupp
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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Pokrovsky D, Forné I, Straub T, Imhof A, Rupp RAW. A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis. PLoS Biol 2021; 19:e3001377. [PMID: 34491983 PMCID: PMC8535184 DOI: 10.1371/journal.pbio.3001377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/22/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On the one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harness developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here, we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle-arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles (HMPs), in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted toward normality on morphological, molecular, and epigenetic levels. These results suggest that the cell cycle block by HUA alters stage-specific HMPs. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.
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Affiliation(s)
- Daniil Pokrovsky
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ignasi Forné
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Straub
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ralph A. W. Rupp
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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Schuh L, Loos C, Pokrovsky D, Imhof A, Rupp RAW, Marr C. H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos. Cell Syst 2020; 11:653-662.e8. [PMID: 33296683 DOI: 10.1016/j.cels.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 11/26/2022]
Abstract
DNA replication during cell division leads to dilution of histone modifications and can thus affect chromatin-mediated gene regulation, raising the question of how the cell-cycle shapes the histone modification landscape, particularly during embryogenesis. We tackled this problem by manipulating the cell cycle during early Xenopus laevis embryogenesis and analyzing in vivo histone H4K20 methylation kinetics. The global distribution of un-, mono-, di-, and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle-arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific biological methylation rate constants were required to explain the measured H4K20 methylation state kinetics. While demethylation is essential for regulating H4K20 methylation kinetics in non-cycling cells, demethylation is very likely dispensable in rapidly dividing cells of early embryos, suggesting that cell-cycle-mediated dilution of H4K20 methylation is an essential regulatory component for shaping its epigenetic landscape during early development. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Lea Schuh
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniil Pokrovsky
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Axel Imhof
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Ralph A W Rupp
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.
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Schnatbaum K, Solis‐Mezarino V, Pokrovsky D, Schäfer F, Nagl D, Hornberger L, Zerweck J, Knaute T, Avramova‐Nehmer J, Schutkowski M, Hornung V, Wenschuh H, Völker‐Albert MC, Imhof A, Reimer U. Front Cover: New Approaches for Absolute Quantification of Stable‐Isotope‐Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag. Proteomics 2020. [DOI: 10.1002/pmic.202070081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Schnatbaum K, Solis-Mezarino V, Pokrovsky D, Schäfer F, Nagl D, Hornberger L, Zerweck J, Knaute T, Avramova-Nehmer J, Schutkowski M, Hornung V, Wenschuh H, Völker-Albert MC, Imhof A, Reimer U. New Approaches for Absolute Quantification of Stable-Isotope-Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag. Proteomics 2020; 20:e2000007. [PMID: 32267065 DOI: 10.1002/pmic.202000007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Indexed: 01/16/2023]
Abstract
Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re-quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.
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Affiliation(s)
| | | | - Daniil Pokrovsky
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Großhadernerstrasse 9, Planegg-Martinsried, 82152, Germany
| | - Frederike Schäfer
- EpiQMAx GmbH, Großhaderner Str. 9, Planegg-Martinsried, 82152, Germany
| | - Dennis Nagl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Lars Hornberger
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | - Johannes Zerweck
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | - Tobias Knaute
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | | | - Mike Schutkowski
- Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Holger Wenschuh
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | | | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Großhadernerstrasse 9, Planegg-Martinsried, 82152, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
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Bonnet J, Lindeboom RGH, Pokrovsky D, Stricker G, Çelik MH, Rupp RAW, Gagneur J, Vermeulen M, Imhof A, Müller J. Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation. Dev Cell 2019; 51:632-644.e6. [PMID: 31630981 DOI: 10.1016/j.devcel.2019.09.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/09/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Gene transcription in eukaryotes is regulated through dynamic interactions of a variety of different proteins with DNA in the context of chromatin. Here, we used mass spectrometry for absolute quantification of the nuclear proteome and methyl marks on selected lysine residues in histone H3 during two stages of Drosophila embryogenesis. These analyses provide comprehensive information about the absolute copy number of several thousand proteins and reveal unexpected relationships between the abundance of histone-modifying and -binding proteins and the chromatin landscape that they generate and interact with. For some histone modifications, the levels in Drosophila embryos are substantially different from those previously reported in tissue culture cells. Genome-wide profiling of H3K27 methylation during developmental progression and in animals with reduced PRC2 levels illustrates how mass spectrometry can be used for quantitatively describing and comparing chromatin states. Together, these data provide a foundation toward a quantitative understanding of gene regulation in Drosophila.
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Affiliation(s)
- Jacques Bonnet
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rik G H Lindeboom
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Department of Molecular Biology, Radboud University, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
| | - Daniil Pokrovsky
- Institute for Molecular Biology, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany; Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Georg Stricker
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Muhammed Hasan Çelik
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Ralph A W Rupp
- Institute for Molecular Biology, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Department of Molecular Biology, Radboud University, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands.
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany.
| | - Jürg Müller
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
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