DOCSLIB.ORG

Full Text (PDF)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Full Text (PDF) Int. J. Dev. Biol. 53: 335-354 (2009) DEVELOPMENTALTHE INTERNATIONAL JOURNAL OF doi: 10.1387/ijdb.082717ph BIOLOGY www.intjdevbiol.com Mechanisms of transcriptional repression by histone lysine methylation PHILIP HUBLITZ#, MAREIKE ALBERT## and ANTOINE H.F.M. PETERS* Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ABSTRACT During development, covalent modification of both, histones and DNA contribute to the specification and maintenance of cell identity. Repressive modifications are thought to stabilize cell type specific gene expression patterns, reducing the likelihood of reactivation of lineage-unrelated genes. In this report, we review the recent literature to deduce mechanisms underlying Polycomb and H3K9 methylation mediated repression, and describe the functional interplay with activating H3K4 methylation. We summarize recent data that indicate a close relationship between GC density of promoter sequences, transcription factor binding and the antagonizing activities of distinct epigenetic regulators such as histone methyltransferases (HMTs) and histone demethylases (HDMs). Subsequently, we compare chromatin signatures associated with different types of transcriptional outcomes from stable repression to highly dynamic regulated genes, strongly suggesting that the interplay of different epigenetic pathways is essential in defining specific types of heritable chromatin and associated transcriptional states. KEY WORDS: transcriptional control, histone lysine methylation, methyltransferase, demethylase, polycomb Genetic and epigenetic mechanisms ensure that complex devel- transcription factor occupancy in relation to transcriptional ON opmental programs are correctly executed. One important post- and OFF states. We mainly focus on the dynamics of activating translational modification that regulates transcriptional outcomes, H3K4 and repressive H3K27 methylation marks at promoter genome integrity and cellular identity is histone lysine methyla- sequences. The genomic data serve as a foundation to under- tion. Defined methylation patterns are related to distinct functional stand the interrelationship between transcription factor and chro- readouts of chromosomal DNA. The initial discoveries of histone matin based pathways. We in-depth review the responsible modifying enzymes lead to the postulation of the “histone code” classes of enzymes mediating those modifications and report on hypothesis, whereby defined histone modifications, acting in a their functional importance. In a second part, we review two combinatorial or sequential fashion on one or multiple histone scenarios of dynamically controlled transcriptional systems, termini, specify the transcriptional state of a gene by recruitment nuclear hormone receptor signaling, whose repression is largely of regulatory proteins. In this review, we discuss the indexing based on H3K9 methylation, and the regulation of the cell division potential of histone lysine methylation in the light of how histone cycle, where senescence and proliferation are controlled by H3K9 methyltransferases (HMTs) and histone demethylases (HDMs) and H3K27 methylation. Both systems are especially well charac- are targeted to given promoter contexts, how the GC content of terized in terms of recruitment of histone modifying enzymes and target promoters influences the regulatory response, and how the functional interplay between HMTs and HDMs ultimately defines Abbreviations used in this paper: AR, androgen receptor; CpG, cytosine- transcriptional states. For in-depth discussions of the develop- guanidine dinucleotide; ER, estrogen receptor; HDM, histone demethylase; mental functions of individual HMTs and HDMs, we refer the HMT, histone methyltransferase; NHR, nuclear hormone receptor; PcG, reader to recent reviews (Cloos et al., 2008; Martin and Zhang, polycomb group; PTM, post translational modification; RNAPII, DNA- 2005) (Fig. 1). We first summarize new insights gained by the dependent RNA-polymerase II; TrxG, trithorax group; TSS, transcriptional recent epigenomic profiling studies of histone methylation and start site. *Address correspondence to: Dr. Antoine H.F.M. Peters. Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland. Tel: +41-61-697-8761. Fax: +41-61-697-3976. e-mail: [email protected] # Note: Current address is EMBL Monterotondo, Mouse Biology Unit, Via E. Ramarini 32, 00015 Monterotondo, Italy. ## Note: This author is formerly known as Mareike Puschendorf. Current address is: Biotech Research and Innovation Centre. University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Published online: 28 April 2009. ISSN: Online 1696-3547, Print 0214-6282 © 2009 UBC Press Printed in Spain 336 P. Hublitz et al. in combining several epigenetic pathways to achieve the desired et al., 2006b) showed that core components of the Polycomb transcriptional outcome. Repressive Complex PRC1 (Rnf2, Phc1), PRC2 (Eed, Suz12) and H3K27me3 do not only colocalize to classical target genes Transcriptional repression by H3K27 methylation (such as the four Hox clusters) but also to many other loci. Particularly genes coding for developmental regulators including Bivalency of H3K4 and H3K27 methylation homeodomain (Dlx, Irx, Lhx, Pou, Pax, Six) and other transcrip- In mammals, recent genome-wide mapping studies of Polycomb tion factors (such as Fox, Sox, Gata and Tbx) were highly Group (PcG) and Trithorax Group (TrxG) proteins and their overrepresented among PcG target genes. These proteins serve marks, classically associated with repressed and active transcrip- master regulatory functions in organogenesis and morphogen- tional states, respectively, revealed many novel target genes. esis, pattern specification, cell differentiation, embryonic devel- These studies provide the framework to delineate mechanisms of opment and cell fate commitment (Boyer et al., 2006; Lee et al., targeting and gene regulation mediated by the different epige- 2006b). PcG targets are generally repressed in ES cells and are netic modifiers. Three initial ChIP-chip studies in human and preferentially activated during ES cell differentiation. In Eed and mouse ES cells (Bernstein et al., 2006a; Boyer et al., 2006; Lee Suz12 gene deficient ES cells that lack detectable amounts of PRC2 complexes and H3K27me3, tran- script levels of most PcG target genes were increased (Boyer et al., 2006; Lee et al., A Mll1-4 KMT2A-D 2006b). These data suggested that Set1a/b KMT2F/G Ash2L Nsd1 Polycomb complexes are required for main- me KMT2H (H3K4me2/3 only) me KMT3B Set7/9 KMT7 Nsd2/Whsc1 taining ES cell pluripotency and plasticity me me me me Meisetz Smyd2 KMT3C during embryonic development. me me me me me me Smyd1/Bop1 HypB While studying genomic regions that Smyd3 harbor highly conserved non-coding ele- Whistle ments, Bernstein and colleagues made a A remarkable observation. They noticed that ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVS KKP H3 4 36 extended regions marked by H3K27me3 me me were also marked by H3K4me3, a histone Lsd1 KDM1* me modification normally associated with tran- scriptional activity (Bernstein et al., 2006a). me me me Jhdm1a/b KDM2A/B* me me me Jhdm1a/b KDM2A/B* Sequential ChIP experiments confirmed that me me Jarid1a/Rbp2 KDM5A me me Jmjd2a KDM4A* identical alleles were labeled by both “re- me Jarid1b/c/d KDM5B/C/D pressive” and “activating” chromatin modi- fications, resulting in the term “bivalent do- mains”. Genes within bivalent domains were B largely repressed, to almost the same ex- G9a KMT1C tent as genes that were marked by me Glp me me KMT1D H3K27me3 alone. In contrast, genes only Riz1 KMT8 me Ezh1 me me Eset KMT1E me me Fig. 1. Overview of histone methylation pro- Ezh2 KMT6 me me me Suv39h1/2 KMT1A/B me me me cesses. (A) Methylation of lysines H3K4 and H3K36 is generally correlated with transcriptional ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPA H3 S activity, and demethylation of H3K4 is required 9 27 for effective silencing. The specificities of H3K4 me me me me me Utx KDM6A and H3K36 HMTs are not unambiguously clear Lsd1 + AR KDM1* me me me Jmjd3 KDM6B yet. (B) Methylation of H3K9 and H3K27 are hallmarks of transcriptional repression, and the me me me Jmjd1a KDM3A antagonizing HDMs are categorized as transcrip- me me Jmjd2a/b KDM4A/B tional co-activators. H3K9me3 is a hallmark of me Jmjd2c/Gasc1 KDM4C constitutive heterochromatin; H3K27me3 is the readout of PcG mediated silencing. (C) In the tail of histone H4, only K20 is targeted by HMTs. CDH4K20me1 correlates with ongoing transcrip- me PrSet7 KMT5A me tion, whereas H4K20me3 is an integral part of me me me me heterochromatin mediated silencing. (D)Dot1L is Suv4-20h1/2 KMT5B/C Dot1L KMT4 me me me me me me the only HMT known to target H3K79 in the globular domain of H3. No HDM is known to K target either H4K20 or H3K79. HMTs are indi- ...GAKRHRKVLRDN H4 H3 cated above the histone tails, HDMs are below, 20 and hexagons represent the respective methyla- 79 tion status. Asterisks (*) indicate enzymes that target multiple lysine residues. Transcriptional repression by histone lysine methylation 337 associated with H3K4me3 were highly expressed (Bernstein et coding elements (Bejerano et al., 2004; Nobrega et al., 2003) and al., 2006a) (Fig. 2A). These results indicate that in bivalent being devoid of retrotransposons (Bernstein et al., 2006a; Simons domains the repressive H3K27me3 state generally overrules the et al., 2006; Tanay et al., 2007). As such, Bernstein et al. may thus activating effect
Load more

Recommended publications
  • Plant SET Domain-Containing Proteins: Structure, Function and Regulation
    Biochimica et Biophysica Acta 1769 (2007) 316–329 www.elsevier.com/locate/bbaexp Review Plant SET domain-containing proteins: Structure, function and regulation Danny W-K Ng, Tao Wang, Mahesh B. Chandrasekharan 1, Rodolfo Aramayo, ⁎ Sunee Kertbundit 2, Timothy C. Hall Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University, College Station, TX 77843-3155, USA Received 27 October 2006; received in revised form 3 April 2007; accepted 4 April 2007 Available online 12 April 2007 Abstract Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/ interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein–protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread.
    [Show full text]
  • Computational Investigation of Thiol-Based Redox Modifications in Proteins: Redox-Active Disulfides, Zn2+ Sites and Their Associations
    THESIS SUBMITTED IN TOTAL FULFILLMENT OF THE REQUIREMENTS OF THE DEGREE OF DOCTOR OF PHILOSOPHY Computational investigation of thiol‐based redox modifications in proteins: redox‐active disulfides, 2+ Zn sites and their associations Application of tools of bioinformatics in health and disease Dhakshinari Vihara Kumari Hulugalle March 2013 Victor Chang Cardiac Research Institute School of Medical Sciences, Faculty of Medicine, University of New South Wales PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: HULUGALLE First name: DHAKSHINARI Other name/s: VIHARA KUMARI PhD Abbreviation for degree as given in the University calendar: School: SCHOOL OF MEDICAL SCIENCES Faculty: MEDICINE Title: Computational investigation of thiol-based redox modifications in proteins: redox-active disulfides, Zn2+ sites and their associations Abstract 350 words maximum: (PLEASE TYPE) Thiol based redox signalling is an emerging area of research in protein science. Reversible disulfide bonding and Zn2+ expulsion are two important but less explored oxidative thiol modifications associated with redox signalling. They have numerous implications in health and disease. Three computational methods have previously been developed to predict redox-active disulfides in proteins: redox pair protein (RP) method, ‘forbidden disulfides’ (FD) method and torsional energy (TE) method. These methods and other tools of bioinformatics are used in my study to investigate redox-active disulfides, Zn2+ sites and the association between FDs and Zn fingers in protein structures. The first objective of my study was to apply the RP method to predict novel proteins containing likely redox-active disulfides. Over 300 novel RP proteins were found during this study. Significant conformational changes associated with disulfide redox activity in RP protein structures were also identified.
    [Show full text]
  • Hub Domains and Intrinsically Disordered Proteins
    REVIEWS αα-Hub domains and intrinsically disordered proteins: A decisive combo Received for publication, October 7, 2020, and in revised form, December 22, 2020 Published, Papers in Press, December 29, 2020, https://doi.org/10.1074/jbc.REV120.012928 Katrine Bugge1,2 , Lasse Staby1,2 , Edoardo Salladini1 , Rasmus G. Falbe-Hansen1 , Birthe B. Kragelund1,2,* , and Karen Skriver1,* From the 1REPIN and The Linderstrøm-Lang Centre for Protein Science; 2Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark Edited by Ronald Wek Hub proteins are central nodes in protein–protein interaction adaptability, multivalency, and high chemical modification networks with critical importance to all living organisms. potential (9–11). Indeed, ID appears to be a prerequisite for Recently, a new group of folded hub domains, the αα-hubs, was fidelity in signaling pathways through exploitation of the many defined based on a shared αα-hairpin supersecondary structural different mechanisms encoded in these properties (12, 13). foundation. The members PAH, RST, TAFH, NCBD, and HHD Recognition of IDRs in and by hubs depends on short linear are found in large proteins such as Sin3, RCD1, TAF4, CBP, and motifs (SLiMs), which are stretches of 2 to 12 residues with harmonin, which organize disordered transcriptional regulators only a few highly conserved positions (14, 15). It has been and membrane scaffolds in interactomes of importance to hu- proposed that the eukaryotic SLiMome consists of up to 1 man diseases and plant quality. In this review, studies of struc- million different SLiMs (16), but SLiMs active in hub in- tures, functions, and complexes across the αα-hubs are described teractions have very similar features (17).
    [Show full text]
  • Atlas Journal
    Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 5, Sep-Oct 2008 Previous Issue / Next Issue Genes XAF1 (XIAP associated factor-1) (17p13.2). Stéphanie Plenchette, Wai Gin Fong, Robert G Korneluk. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 668-673. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/XAF1ID44095ch17p13.html WWP1 (WW domain containing E3 ubiquitin protein ligase 1) (8q21.3). Ceshi Chen. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 674-680. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/WWP1ID42993ch8q21.html TSPAN1 (tetraspanin 1) (1p34.1). David Murray, Peter Doran. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 681-683. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TSPAN1ID44178ch1p34.html TCL1B (T-cell leukemia/lymphoma 1B) (14q32.13). Herbert Eradat, Michael A Teitell. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 684-686. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TCL1BID354ch14q32.html PVRL4 (poliovirus receptor-related 4) (1q23.3). Marc Lopez. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 687-690. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/PVRL4ID44141ch1q23.html PTTG1IP (pituitary tumor-transforming 1 interacting protein) (21q22.3). Vicki Smith, Chris McCabe. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 691-694.
    [Show full text]
  • Antibodies Products
    Chapter 2 : Gentaur Products List • WDSUB1 contains 1 SAM sterile alpha motif domain 1 U Defects in DLG3 are the cause of mental retardation X • Sodium hydrogen exchangers NHEs such as SLC9A8 are box domain and 7 WD repeats The function of WDSUB1 linked type 90 MRX90 integral transmembrane proteins that exchange extracellular remains unknown • SLC25A20 is one of several closely related mitochondrial Na for intracellular H NHEs have multiple functions including • RNF217 is an E3 ubiquitin protein ligase which accepts membrane carrier proteins that shuttle substrates between intracellular pH ho ubiquitin from E2 ubiquitin conjugating enzymes in the form cytosol and the intramitochondrial matrix space It mediates • SLCO1C1 is a member of the organic anion transporter of a thioester and then directly transfers the ubiquitin to the transport of acylcarn family SLCO1C1 is a transmembrane receptor that mediates targeted substrates • The sodium iodide symporter NIS or SLC5A5 is a key the sodium independent uptake of thyroid hormones in brain • TRIM60 contains a RING finger domain a motif present in a plasma membrane protein that mediates active I uptake in tissues This protein has part variety of functionally distinct proteins and known to be thyroid lactating breast and other tissues with an • SLC35A5 belongs to the nucleotide sugar transporter involved in protein protein and protein DNA interactions The electrogenic stoichiometry of 2 Na family SLC35A subfamily It is a multi pass membrane protein encoded by thi • SLC2A9 is a member of the SLC2A
    [Show full text]
  • AML1-ETO Decreases ETO-2 (MTG16) Interactions with Nuclear Receptor Corepressor, an Effect That Impairs Granulocyte Differentiation
    [CANCER RESEARCH 64, 4547–4554, July 1, 2004] AML1-ETO Decreases ETO-2 (MTG16) Interactions with Nuclear Receptor Corepressor, an Effect That Impairs Granulocyte Differentiation Vinzon Iban˜ez,1 Arun Sharma,1 Silvia Buonamici,1 Amit Verma,1 Sudhakar Kalakonda,3 Jianxiang Wang,4 ShriHari Kadkol,2 and Yogen Saunthararajah1 1Section of Hematology/Oncology, Department of Medicine, and 2Department of Pathology, University of Illinois, Chicago, Illinois; 3Department of Ophthalmology, University of Maryland, Baltimore, Maryland; and 4Laboratory of Hematological Malignancy, State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences ABSTRACT mology domain. NHR2 is an amphipathic helix structure that mediates homodimerization and binding of ETO to homologous family mem- The t(8;21) chromosome abnormality in acute myeloid leukemia targets bers (2). NHR3 is a coiled-coiled region that plays a role in interac- the AML1 and ETO genes to produce the leukemia fusion protein AML1- tions with N-CoR (3). NHR4 contains two MYND zinc finger motifs, ETO. Another member of the ETO family, ETO-2/MTG16, is highly which are necessary for binding to N-CoR (3–7); it is also known as expressed in murine and human hematopoietic cells, bears >75% homol- ogy to ETO, and like ETO, contains a conserved MYND domain that the MYND domain. interacts with the nuclear receptor corepressor (N-CoR). AML1-ETO ETO-2, like ETO, demonstrates corepressor function (8). This prevents granulocyte but not macrophage differentiation of murine function is likely to be mediated through the interactions of ETO-2 32Dcl3 granulocyte/macrophage progenitors. One possible mechanism with histone deacetylases 1, 2, 3, 6, and 8 and the ubiquitously is recruitment of N-CoR to aberrantly repress AML1 target genes.
    [Show full text]
  • Targeted Inhibition of the Plasmodium Falciparum Vitamin B6 Producing Enzyme Pdx1 and the Biochemical and Functional Consequences Thereof
    Targeted inhibition of the Plasmodium falciparum Vitamin B6 producing enzyme Pdx1 and the biochemical and functional consequences thereof Shaun Bernard Reeksting Submitted in partial fulfilment of the requirements for the degree Philosophiae Doctor in the Faculty of Natural and Agricultural Sciences Department of Biochemistry University of Pretoria South Africa June 2013 © University of Pretoria Submission declaration I, Shaun Bernard Reeksting, declare that this thesis, which I hereby submit for the degree Philosophiae Doctor in the Department of Biochemistry, at the University of Pretoria, is my own work and has not previously been submitted by me for a degree at this or any other tertiary institution. Signature: …………………………… Date: ………………………… ii © University of Pretoria Plagiarism declaration I understand what plagiarism is and am aware of the University‘s policy in this regard. I declare that this thesis is my own original work. Where other people‘s work has been used (either from printed source, internet or any other source), this has been properly acknowledged and referenced in accordance with departmental regulations. I have not used work previously produced by another student or any other person to hand in as my own. I have not allowed and will not allow anyone to copy my work with the intention of passing it off as his or her own work. Student‘s signature Date iii © University of Pretoria Summary Malaria is caused by the parasite Plasmodium falciparum and still plagues many parts of the world. To date, efforts to control the spread of the parasites have been largely ineffective. Due to development of resistance by the parasites to current therapeutics there is an urgent need for new classes of therapeutics.
    [Show full text]
  • Suppression of Neuroblastoma Tumorigenesis Using Enu Mutagenesis in the Th-Mycn Mouse Model of Neuroblastoma
    SUPPRESSION OF NEUROBLASTOMA TUMORIGENESIS USING ENU MUTAGENESIS IN THE TH-MYCN MOUSE MODEL OF NEUROBLASTOMA A thesis submitted to the University of New South Wales in fulfilment of the requirements for the degree of Doctor of Philosophy Jayne Murray Children’s Cancer Institute and School of Women’s and Children’s Health Faculty of Medicine University of New South Wales December 2017 i THESIS/DISSERTION SHEET PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Murray First name: Jayne Other name/s: Elizabeth Abbreviation for degree as given in the University calendar: PhD School: School of Women’s and Children’s Health Faculty: Faculty of Medicine Title: Suppression of neuroblastoma tumorigenesis using ENU mutagenesis in the Th-MYCN mouse model of neuroblastoma Abstract 350 words maximum: (PLEASE TYPE) Neuroblastoma, a disease of the neural crest and the most common solid tumour of infancy, accounts for 7-10% of all childhood cancer. The disease arises from primitive cells within the neural crest, and can develop at any point along the sympathetic nervous system, including sites within the abdomen, pelvis, neck and thoracic cavity. Neuroblastoma tumours with MYCN oncogene amplification are highly aggressive, leading to a dismal outcome in most patients. A mouse model of neuroblastoma previously generated by targeting the human MYCN oncogene to neural crest cells (Th-MYCN), leads to 100% of MYCN homozygous mice developing tumours at an early age. This thesis describes a forward genetic screen involving the use of N-ethyl-N-nitrosourea (ENU) to generate heritable mutations causing delayed tumorigenesis in this model, as well as genomic sequencing to identify the mutated gene(s) responsible for the delayed tumorigenesis observed.
    [Show full text]
  • (12) Patent Applicatio in Publication (10) Pub
    US 20070202 107A1 (19) United States (12) Patent Applicatio in Publication (10) Pub. No.: US 2007/0202107 A1 Whyte et al. (43) Pub. Date: Aug. 30, 2007 (54) NOVEL KINASES Publication Classification (75) Inventors: Davids Whyte, Belmont, CA (US); (51) Int . Cl. Gerard Manning, Menlo Park, CA A6IK 38/55 (2006.01) (US): Sean Caenepeel, Walnut Creek, CI2O I/68 (2006.01) CA (US) GOIN 33/574 (2006.01) C07H 21/04 (2006.01) Correspondence Address: CI2P 21/06 (2006.01) FOLEY AND LARDNER LLP A61 K 39/395 (2006.01) SUTE 500 CI2N 9/12 (2006.01) 3000 K STREET NW (52) U.S. Cl. .................... 424/146.1; 435/723: 435/69.1; WASHINGTON, DC 20007 (US) 435/194; 435/320.1; 435/325: 9 514/2; 530/388.26; 536/23.2; (73) Assignee: Sugen, Inc. 435/6 21) Appl. No.: 11/407,888 (21) App (57) ABSTRACT (22) Filed: Apr. 21, 2006 Related U.S. ApplicationO Data Theotide present sequences invention encoding relates the kinaseto kinase polypeptides, polypeptides, as wellnucle R he diagnosis an (62) Pig- - - of applit N 10/618,941,10 filede on Jul. varioustreatment products of various and kinase-related methods useful diseases for t and conditions.gnosis s , no Through the use of a bioinformatics strategy, mammalian (60) Provisional application No. 60/395,632, filed on Jul. members of the of PTK's and STK's have been identified 15, 2002. and their protein structure predicted. >CRIKH SEQID#NA GAACCCATTGCCAGCCGGGCCTCCAGGCTGAATCTGTTCTTCCAGGGGAAACCACCCTTTATGACTCAACAGCAGATGTCTCCTCTTTCCCGAGAAGGGATAGGGCGGAACAGATCGCAGACCTGGGGGTTCGCAGAGCCGCCAGTGGGGAGATGTTGAAGTTCAAATATGGAGCGCGGAATCCTTTGGATGCTGGTGCTGCT
    [Show full text]
  • A New Gene Inventory of the Ubiquitin and Ubiquitin-Like Conjugation Pathways in Giardia Intestinalis
    ORIGINAL ARTICLE Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 115: e190242, 2020 1|12 A new gene inventory of the ubiquitin and ubiquitin-like conjugation pathways in Giardia intestinalis Isabel Cristina Castellanos1, Eliana Patricia Calvo2/+, Moisés Wasserman3 1Universidad Escuela de Administración de Negocios, Departamento de Ciencias Básicas, Bogotá, Colombia 2Universidad El Bosque, Laboratorio de Virología, Bogotá, Colombia 3Universidad Nacional de Colombia, Laboratorio de Investigaciones Básicas en Bioquímica, Bogotá, Colombia BACKGROUND Ubiquitin (Ub) and Ub-like proteins (Ub-L) are critical regulators of complex cellular processes such as the cell cycle, DNA repair, transcription, chromatin remodeling, signal translation, and protein degradation. Giardia intestinalis possesses an experimentally proven Ub-conjugation system; however, a limited number of enzymes involved in this process were identified using basic local alignment search tool (BLAST). This is due to the limitations of BLAST’s ability to identify homologous functional regions when similarity between the sequences dips to < 30%. In addition Ub-Ls and their conjugating enzymes have not been fully elucidated in Giardia. OBJETIVE To identify the enzymes involved in the Ub and Ub-Ls conjugation processes using intelligent systems based on the hidden Markov models (HMMs). METHODS We performed an HMM search of functional Pfam domains found in the key enzymes of these pathways in Giardia’s proteome. Each open reading frame identified was analysed by sequence homology, domain architecture, and transcription levels. FINDINGS We identified 118 genes, 106 of which corresponded to the ubiquitination process (Ub, E1, E2, E3, and DUB enzymes). The E3 ligase group was the largest group with 82 members; 71 of which harbored a characteristic RING domain.
    [Show full text]
  • Characterization of the Protein Lysine Methyltransferase Smyd2
    CHARACTERIZATION OF THE PROTEIN LYSINE METHYLTRANSFERASE SMYD2 Sylvain Lanouette Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biochemistry Department of Biochemistry, Microbiology and Immunology Faculty of Medicine University of Ottawa © Sylvain Lanouette, Ottawa, Canada, 2015 ABSTRACT Our understanding of protein lysine methyltransferases and their substrates remains limited despite their importance as regulators of the proteome. The SMYD (SET and MYND domain) methyltransferase family plays pivotal roles in various cellular processes, including transcriptional regulation and embryonic development. Among them, SMYD2 is associated with oesophageal squamous cell carcinoma, bladder cancer and leukemia as well as with embryonic development. Initially identified as a histone methyltransferase, SMYD2 was later reported to methylate p53, the retinoblastoma protein pRb and the estrogen receptor ER and to regulate their activityOur proteomic and biochemical analyses demonstrated that SMYD2 also methylates the molecular chaperone HSP90 on K209 and K615. We also showed that HSP90 methylation is regulated by HSP90 co-chaperones, pH, and the demethylase LSD1. Further methyltransferase assays demonstrated that SMYD2 methylates lysine K* in proteins which include the sequence [LFM]-₁-K*-[AFYMSHRK]+₁-[LYK]+₂. This motif allowed us to show that SMYD2 methylates the transcriptional co-repressor SIN3B, the RNA helicase DHX15 and the myogenic transcription factors SIX1 and SIX2. Finally, muscle cell models suggest that SMYD2 methyltransferase activity plays a role in preventing premature myogenic differentiation of proliferating myoblasts by repressing muscle-specific genes. Our work thus shows that SMYD2 methyltransferase activity targets a broad array of substrates in vitro and in situ and is regulated by intricate mechanisms.
    [Show full text]
  • Evolutionary History of the Smyd Gene Family in Metazoans: a Framework to Identify the Orthologs of Human Smyd Genes in Drosophila and Other Animal Species
    RESEARCH ARTICLE Evolutionary History of the Smyd Gene Family in Metazoans: A Framework to Identify the Orthologs of Human Smyd Genes in Drosophila and Other Animal Species Eduardo Calpena1,2, Francesc Palau1,2¤, Carmen Espinós1,2, Máximo Ibo Galindo1,2* 1 Program in Rare and Genetic Diseases, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain, 2 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Valencia, Spain ¤ Current Address: Instituto Pediátrico de Enfermedades Raras, Hospital Sant Joan de Déu, Barcelona, Spain * [email protected] OPEN ACCESS Citation: Calpena E, Palau F, Espinós C, Galindo MI (2015) Evolutionary History of the Smyd Gene Family Abstract in Metazoans: A Framework to Identify the Orthologs of Human Smyd Genes in Drosophila and Other The Smyd gene family code for proteins containing a conserved core consisting of a SET Animal Species. PLoS ONE 10(7): e0134106. domain interrupted by a MYND zinc finger. Smyd proteins are important in epigenetic con- doi:10.1371/journal.pone.0134106 trol of development and carcinogenesis, through posttranslational modifications in histones Editor: ShaoJun Du, University of Maryland, UNITED and other proteins. Previous reports indicated that the Smyd family is quite variable in STATES metazoans, so a rigorous phylogenetic reconstruction of this complex gene family is of cen- Received: May 7, 2015 tral importance to understand its evolutionary history and functional diversification or con- Accepted: July 6, 2015 servation. We have performed a phylogenetic analysis of Smyd protein sequences, and our Published: July 31, 2015 results show that the extant metazoan Smyd genes can be classified in three main classes, Smyd3 (which includes chordate-specific Smyd1 and Smyd2 genes), Smyd4 and Smyd5.
    [Show full text]