1
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Frisbie VS, Hashimoto H, Xie Y, De Luna Vitorino FN, Baeza J, Nguyen T, Yuan Z, Kiselar J, Garcia BA, Debler EW. Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids. Nat Commun 2024; 15:2467. [PMID: 38503750 PMCID: PMC10951340 DOI: 10.1038/s41467-024-46637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx6K) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.
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Affiliation(s)
- Victoria S Frisbie
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hideharu Hashimoto
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Francisca N De Luna Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Josue Baeza
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tam Nguyen
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhangerjiao Yuan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Janna Kiselar
- Case Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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2
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Deák G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson J, Tuijtel M, Webb S, Wilson M. Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Nucleic Acids Res 2023; 51:7882-7899. [PMID: 37427792 PMCID: PMC10450195 DOI: 10.1093/nar/gkad577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
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Affiliation(s)
- Gauri Deák
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Gorka Sandoval
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Ruofan Chen
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Mark R D Taylor
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hayden Burdett
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - James A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Maarten W Tuijtel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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3
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A DOT1B/Ribonuclease H2 Protein Complex Is Involved in R-Loop Processing, Genomic Integrity, and Antigenic Variation in Trypanosoma brucei. mBio 2021; 12:e0135221. [PMID: 34749530 PMCID: PMC8576533 DOI: 10.1128/mbio.01352-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The parasite Trypanosoma brucei periodically changes the expression of protective variant surface glycoproteins (VSGs) to evade its host’s immune system in a process known as antigenic variation. One route to change VSG expression is the transcriptional activation of a previously silent VSG expression site (ES), a subtelomeric region containing the VSG genes. Homologous recombination of a different VSG from a large reservoir into the active ES represents another route. The conserved histone methyltransferase DOT1B is involved in transcriptional silencing of inactive ES and influences ES switching kinetics. The molecular machinery that enables DOT1B to execute these regulatory functions remains elusive, however. To better understand DOT1B-mediated regulatory processes, we purified DOT1B-associated proteins using complementary biochemical approaches. We identified several novel DOT1B interactors. One of these was the RNase H2 complex, previously shown to resolve RNA-DNA hybrids, maintain genome integrity, and play a role in antigenic variation. Our study revealed that DOT1B depletion results in an increase in RNA-DNA hybrids, accumulation of DNA damage, and ES switching events. Surprisingly, a similar pattern of VSG deregulation was observed in RNase H2 mutants. We propose that both proteins act together in resolving R-loops to ensure genome integrity and contribute to the tightly regulated process of antigenic variation.
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4
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Nunes VS, Moretti NS, da Silva MS, Elias MC, Janzen CJ, Schenkman S. Trimethylation of histone H3K76 by Dot1B enhances cell cycle progression after mitosis in Trypanosoma cruzi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118694. [PMID: 32151656 DOI: 10.1016/j.bbamcr.2020.118694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
Dot1 enzymes are histone methyltransferases that mono-, di- and trimethylate lysine 79 of histone H3 to affect several nuclear processes. The functions of these different methylation states are still largely unknown. Trypanosomes, which are flagellated protozoa that cause several parasitic diseases, have two Dot1 homologues. Dot1A catalyzes the mono- and dimethylation of lysine 76 during late G2 and mitosis, and Dot1B catalyzes trimethylation, which is a modification found in all stages of the cell cycle. Here, we generated Trypanosoma cruzi lines lacking Dot1B. Deletion of one allele resulted in parasites with increased levels of mono- and dimethylation and a reduction in H3K76me3. In the full knockout (DKO), no trimethylation was observed. Both the DKO and the single knockout (SKO) showed aberrant morphology and decreased growth due to cell cycle arrest after G2. This phenotype could be rescued by caffeine in the DKO, as caffeine is a checkpoint inhibitor of the cell cycle. The knockouts also phosphorylated γH2A without producing extensive DNA breaks, and Dot1B-depleted cells were more susceptible to general checkpoint kinase inhibitors, suggesting that a lack of H3K76 trimethylation prevents the initiation and/or completion of cytokinesis.
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Affiliation(s)
- Vinicius Santana Nunes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil; Centro de Ensino, Pesquisa e Inovação, Hospital Evangélico de Vila Velha, 29118-060 Vila Velha, ES, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil
| | | | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil.
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5
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Szöőr B, Silvester E, Matthews KR. A Leap Into the Unknown - Early Events in African Trypanosome Transmission. Trends Parasitol 2020; 36:266-278. [PMID: 32014419 DOI: 10.1016/j.pt.2019.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/19/2019] [Accepted: 12/25/2019] [Indexed: 01/09/2023]
Abstract
African trypanosomes are mainly transmitted by tsetse flies. In recent years there has been good progress in understanding how the parasites prepare for transmission, detect their changed environment through the perception of different environmental cues, and respond by changing their developmental gene expression. In this review, we discuss the different signals and signaling mechanisms used by the parasites to carry out the early events necessary for their establishment in the fly. We also compare Trypanosoma brucei and Trypanosoma congolense, parasites that share a common pathway in the early stages of fly colonization but apparently use different mechanisms to achieve this.
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Affiliation(s)
- Balázs Szöőr
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
| | - Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
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6
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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7
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Stiefler-Jensen D, Schwarz-Linnet T, de Lichtenberg C, Nguyen TTTN, Rand KD, Huang L, She Q, Teilum K. The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications. Protein Sci 2017; 26:1819-1827. [PMID: 28681456 DOI: 10.1002/pro.3220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
Abstract
Enzymes from thermophilic and hyper-thermophilic organisms have an intrinsic high stability. Understanding the mechanisms behind their high stability will be important knowledge for the engineering of novel enzymes with high stability. Lysine methylation of proteins is prevalent in Sulfolobus, a genus of hyperthermophilic and acidophilic archaea. Both unspecific and temperature dependent lysine methylations are seen, but the significance of this post-translational modification has not been investigated. Here, we test the effect of eliminating in vivo lysine methylation on the stability of an esterase (EstA). The enzyme was purified from the native host S. islandicus as well as expressed as a recombinant protein in E. coli, a mesophilic host that does not code for any machinery for in vivo lysine methylation. We find that lysine mono methylation indeed has a positive effect on the stability of EstA, but the effect is small. The effect of the lysine methylation on protein stability is secondary to that of protein expression in E. coli, as the E. coli recombinant enzyme is compromised both on stability and activity. We conclude that these differences are not attributed to any covalent difference between the protein expressed in hyperthermophilic versus mesophilic hosts.
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Affiliation(s)
| | - Troels Schwarz-Linnet
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Casper de Lichtenberg
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Kasper D Rand
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, København, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
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8
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Zimmermann H, Subota I, Batram C, Kramer S, Janzen CJ, Jones NG, Engstler M. A quorum sensing-independent path to stumpy development in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006324. [PMID: 28394929 PMCID: PMC5398725 DOI: 10.1371/journal.ppat.1006324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/20/2017] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
Abstract
For persistent infections of the mammalian host, African trypanosomes limit their population size by quorum sensing of the parasite-excreted stumpy induction factor (SIF), which induces development to the tsetse-infective stumpy stage. We found that besides this cell density-dependent mechanism, there exists a second path to the stumpy stage that is linked to antigenic variation, the main instrument of parasite virulence. The expression of a second variant surface glycoprotein (VSG) leads to transcriptional attenuation of the VSG expression site (ES) and immediate development to tsetse fly infective stumpy parasites. This path is independent of SIF and solely controlled by the transcriptional status of the ES. In pleomorphic trypanosomes varying degrees of ES-attenuation result in phenotypic plasticity. While full ES-attenuation causes irreversible stumpy development, milder attenuation may open a time window for rescuing an unsuccessful antigenic switch, a scenario that so far has not been considered as important for parasite survival.
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Affiliation(s)
- Henriette Zimmermann
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ines Subota
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
- * E-mail:
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9
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Dejung M, Subota I, Bucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F, Janzen CJ. Quantitative Proteomics Uncovers Novel Factors Involved in Developmental Differentiation of Trypanosoma brucei. PLoS Pathog 2016; 12:e1005439. [PMID: 26910529 PMCID: PMC4765897 DOI: 10.1371/journal.ppat.1005439] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/15/2016] [Indexed: 11/18/2022] Open
Abstract
Developmental differentiation is a universal biological process that allows cells to adapt to different environments to perform specific functions. African trypanosomes progress through a tightly regulated life cycle in order to survive in different host environments when they shuttle between an insect vector and a vertebrate host. Transcriptomics has been useful to gain insight into RNA changes during stage transitions; however, RNA levels are only a moderate proxy for protein abundance in trypanosomes. We quantified 4270 protein groups during stage differentiation from the mammalian-infective to the insect form and provide classification for their expression profiles during development. Our label-free quantitative proteomics study revealed previously unknown components of the differentiation machinery that are involved in essential biological processes such as signaling, posttranslational protein modifications, trafficking and nuclear transport. Furthermore, guided by our proteomic survey, we identified the cause of the previously observed differentiation impairment in the histone methyltransferase DOT1B knock-out strain as it is required for accurate karyokinesis in the first cell division during differentiation. This epigenetic regulator is likely involved in essential chromatin restructuring during developmental differentiation, which might also be important for differentiation in higher eukaryotic cells. Our proteome dataset will serve as a resource for detailed investigations of cell differentiation to shed more light on the molecular mechanisms of this process in trypanosomes and other eukaryotes.
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Affiliation(s)
- Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Ines Subota
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Ferdinand Bucerius
- Department Biology I, Genetics, University of Munich (LMU), Großhaderner, Martinsried, Germany
| | - Gülcin Dindar
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Michael Boshart
- Department Biology I, Genetics, University of Munich (LMU), Großhaderner, Martinsried, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
- * E-mail: (FB); (CJJ)
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University Wuerzburg, Am Hubland, Wuerzburg, Germany
- * E-mail: (FB); (CJJ)
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10
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Stulemeijer IJE, De Vos D, van Harten K, Joshi OK, Blomberg O, van Welsem T, Terweij M, Vlaming H, de Graaf EL, Altelaar AFM, Bakker BM, van Leeuwen F. Dot1 histone methyltransferases share a distributive mechanism but have highly diverged catalytic properties. Sci Rep 2015; 5:9824. [PMID: 25965993 PMCID: PMC4650758 DOI: 10.1038/srep09824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/19/2015] [Indexed: 11/17/2022] Open
Abstract
The conserved histone methyltransferase Dot1 establishes an H3K79 methylation pattern
consisting of mono-, di- and trimethylation states on histone H3 via a distributive
mechanism. This mechanism has been shown to be important for the regulation of the
different H3K79 methylation states in yeast. Dot1 enzymes in yeast, Trypanosoma
brucei (TbDot1A and TbDot1B, which methylate H3K76) and human (hDot1L)
generate very divergent methylation patterns. To understand how these
species-specific methylation patterns are generated, the methylation output of the
Dot1 enzymes was compared by expressing them in yeast at various expression levels.
Computational simulations based on these data showed that the Dot1 enzymes have
highly distinct catalytic properties, but share a distributive mechanism. The
mechanism of methylation and the distinct rate constants have implications for the
regulation of H3K79/K76 methylation. A mathematical model of H3K76 methylation
during the trypanosome cell cycle suggests that temporally-regulated consecutive
action of TbDot1A and TbDot1B is required for the observed regulation of H3K76
methylation states.
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Affiliation(s)
- Iris J E Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Dirk De Vos
- Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Kirsten van Harten
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Onkar K Joshi
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Olga Blomberg
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Marit Terweij
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Erik L de Graaf
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Barbara M Bakker
- Department of Pediatrics, Systems Biology Centre for Energy Metabolism and Ageing, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, 9713 GZ, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
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