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  1. AU="Pokrovsky, Daniil"
  2. AU="Kotansky, Brian"
  3. AU="Kumaravel, Arthi"
  4. AU="Lordkipanize, David"
  5. AU="Kurzawinski, Tom R"
  6. AU="Wu, Xinwu"
  7. AU="Grijalva, Marcelo"
  8. AU="van Zuylen, Wendy J"
  9. AU="Asarnow, L D"
  10. AU="So, Ronald"
  11. AU="deSouza, Ashwin L"
  12. AU="Härtlova, Anetta"
  13. AU="Ghanem, Ahmed I"
  14. AU="Yue Lu"
  15. AU="Pincus, Laura B"
  16. AU="Ibrahim, Nashwan"
  17. AU=Bray Molly S AU=Bray Molly S
  18. AU="Bregy, Amadé"
  19. AU=Kaper J B
  20. AU="León-Ramón, Susana"
  21. AU="Simpson, Andrew"
  22. AU="Peters, Wibke"
  23. AU="Malik, Sajid Ali"
  24. AU="V, Gomathi"

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  1. Artikel ; Online: A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis.

    Pokrovsky, Daniil / Forné, Ignasi / Straub, Tobias / Imhof, Axel / Rupp, Ralph A W

    PLoS biology

    2021  Band 19, Heft 9, Seite(n) e3001377

    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 ... ...

    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.
    Mesh-Begriff(e) Animals ; Aphidicolin/pharmacology ; Cell Cycle ; Cell Proliferation/drug effects ; Embryo, Nonmammalian/embryology ; Enzyme Inhibitors/pharmacology ; Epigenesis, Genetic ; Histone Code ; Hydroxyurea/pharmacology ; Xenopus laevis/embryology
    Chemische Substanzen Enzyme Inhibitors ; Aphidicolin (38966-21-1) ; Hydroxyurea (X6Q56QN5QC)
    Sprache Englisch
    Erscheinungsdatum 2021-09-07
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3001377
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos.

    Schuh, Lea / Loos, Carolin / Pokrovsky, Daniil / Imhof, Axel / Rupp, Ralph A W / Marr, Carsten

    Cell systems

    2020  Band 11, Heft 6, Seite(n) 653–662.e8

    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 ... ...

    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.
    Mesh-Begriff(e) Animals ; Cell Cycle Checkpoints/genetics ; Cell Proliferation ; Demethylation ; Methylation ; Xenopus laevis/embryology
    Sprache Englisch
    Erscheinungsdatum 2020-12-08
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2020.11.003
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: The histone H4K20 methyltransferase SUV4-20H1/KMT5B is required for multiciliated cell differentiation in Xenopus.

    Angerilli, Alessandro / Tait, Janet / Berges, Julian / Shcherbakova, Irina / Pokrovsky, Daniil / Schauer, Tamas / Smialowski, Pawel / Hsam, Ohnmar / Mentele, Edith / Nicetto, Dario / Rupp, Ralph Aw

    Life science alliance

    2023  Band 6, Heft 7

    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 ... ...

    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.
    Mesh-Begriff(e) Animals ; Cell Differentiation/genetics ; Chromatin ; Histone Methyltransferases/genetics ; Histone Methyltransferases/metabolism ; Histones/metabolism ; Xenopus laevis/genetics
    Chemische Substanzen Chromatin ; Histone Methyltransferases (EC 2.1.1.-) ; Histones ; KMT5B protein, Xenopus (EC 2.1.1.43)
    Sprache Englisch
    Erscheinungsdatum 2023-04-28
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2575-1077
    ISSN (online) 2575-1077
    DOI 10.26508/lsa.202302023
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation.

    Bonnet, Jacques / Lindeboom, Rik G H / Pokrovsky, Daniil / Stricker, Georg / Çelik, Muhammed Hasan / Rupp, Ralph A W / Gagneur, Julien / Vermeulen, Michiel / Imhof, Axel / Müller, Jürg

    Developmental cell

    2019  Band 51, Heft 5, Seite(n) 632–644.e6

    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 ... ...

    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.
    Mesh-Begriff(e) Animals ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Histone Code ; Histone-Lysine N-Methyltransferase/genetics ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/genetics ; Histones/metabolism ; Proteome/genetics ; Proteome/metabolism
    Chemische Substanzen Chromatin ; Drosophila Proteins ; Histones ; Proteome ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; PRC2 protein, Drosophila (EC 2.1.1.43)
    Sprache Englisch
    Erscheinungsdatum 2019-10-17
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2019.09.011
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: New Approaches for Absolute Quantification of Stable-Isotope-Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag.

    Schnatbaum, Karsten / Solis-Mezarino, Victor / Pokrovsky, Daniil / Schäfer, Frederike / Nagl, Dennis / Hornberger, Lars / Zerweck, Johannes / Knaute, Tobias / Avramova-Nehmer, Julia / Schutkowski, Mike / Hornung, Veit / Wenschuh, Holger / Völker-Albert, Moritz Carl / Imhof, Axel / Reimer, Ulf

    Proteomics

    2020  Band 20, Heft 10, Seite(n) e2000007

    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 ... ...

    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.
    Mesh-Begriff(e) Amino Acids/genetics ; Humans ; Isotope Labeling/standards ; Mass Spectrometry ; Peptides/chemistry ; Peptides/genetics ; Peptides/isolation & purification ; Proteins/chemistry ; Proteins/genetics ; Proteomics/standards ; Ultraviolet Rays
    Chemische Substanzen Amino Acids ; Peptides ; Proteins
    Sprache Englisch
    Erscheinungsdatum 2020-05-20
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.202000007
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Identification and characterization of ToRC, a novel ISWI-containing ATP-dependent chromatin assembly complex.

    Emelyanov, Alexander V / Vershilova, Elena / Ignatyeva, Maria A / Pokrovsky, Daniil K / Lu, Xingwu / Konev, Alexander Y / Fyodorov, Dmitry V

    Genes & development

    2012  Band 26, Heft 6, Seite(n) 603–614

    Abstract: SNF2-like motor proteins, such as ISWI, cooperate with histone chaperones in the assembly and remodeling of chromatin. Here we describe a novel, evolutionarily conserved, ISWI-containing complex termed ToRC (Toutatis-containing chromatin remodeling ... ...

    Abstract SNF2-like motor proteins, such as ISWI, cooperate with histone chaperones in the assembly and remodeling of chromatin. Here we describe a novel, evolutionarily conserved, ISWI-containing complex termed ToRC (Toutatis-containing chromatin remodeling complex). ToRC comprises ISWI, Toutatis/TIP5 (TTF-I-interacting protein 5), and the transcriptional corepressor CtBP (C-terminal-binding protein). ToRC facilitates ATP-dependent nucleosome assembly in vitro. All three subunits are required for its maximal biochemical activity. The toutatis gene exhibits strong synthetic lethal interactions with CtBP. Thus, ToRC mediates, at least in part, biological activities of CtBP and Toutatis. ToRC subunits colocalize in euchromatic arms of polytene chromosomes. Furthermore, nuclear localization and precise distribution of ToRC in chromosomes are dependent on CtBP. ToRC is involved in CtBP-mediated regulation of transcription by RNA polymerase II in vivo. For instance, both Toutatis and CtBP are required for repression of genes of a proneural gene cluster, achaete-scute complex (AS-C), in Drosophila larvae. Intriguingly, native C-terminally truncated Toutatis isoforms do not associate with CtBP and localize predominantly to the nucleolus. Thus, Toutatis forms two alternative complexes that have differential distribution and can participate in distinct aspects of nuclear DNA metabolism.
    Mesh-Begriff(e) Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Alcohol Oxidoreductases/genetics ; Alcohol Oxidoreductases/metabolism ; Animals ; Cell Nucleus/metabolism ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; DNA/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemische Substanzen Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Drosophila Proteins ; ISWI protein ; Tou protein, Drosophila ; Transcription Factors ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Alcohol Oxidoreductases (EC 1.1.-) ; C-terminal binding protein (EC 1.1.1.-) ; Adenosine Triphosphatases (EC 3.6.1.-)
    Sprache Englisch
    Erscheinungsdatum 2012-03-16
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.180604.111
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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