How HP1 Post-Translational Modifications Regulate
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JB Review Biochemical and Structural Properties of Heterochromatin Protein 1: Understanding Its Role in Chromatin Assembly
J. Biochem. 2014;1Journal10 doi:10.1093/jb/mvu032 of Biochemistry Advance Access published June 4, 2014 JB Review Biochemical and structural properties of heterochromatin protein 1: understanding its role in chromatin assembly Received March 20, 2014; accepted April 9, 2014; published online May 13, 2014 Gohei Nishibuchi and Jun-ichi Nakayama* homologues and isoforms have been identified in eu- karyotic organisms, ranging from fission yeast to Graduate School of Natural Sciences, Nagoya City University, mammals, flies, and nematodes (69). In mammals, Nagoya 467-8501, Japan the three HP1 isoforms HP1a, HP1b and HP1g *Jun-ichi Nakayama, Graduate School of Natural Sciences, Nagoya (Fig. 1A) have different localization patterns within City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya cells (11, 12). Mice deficient for each HP1 isoform ex- 467-8501, Japan. Tel: þ81-52-872-5838, Fax: þ81-52-872-5866, email: [email protected] hibit different phenotypes (1315), indicating that the isoforms have distinct functions in forming higher- Heterochromatin protein 1 (HP1) is an evolutionarily order chromatin structures. conserved chromosomal protein that binds lysine HP1-family proteins share a basic structure consist- Downloaded from 9-methylated histone H3 (H3K9me), a hallmark of het- ing of an amino-terminal chromodomain (CD) and a erochromatin, and plays a crucial role in forming carboxyl-terminal chromo shadow domain (CSD) higher-order chromatin structures. HP1 has an N-ter- linked by an unstructured hinge region (16). The CD minal chromodomain and a C-terminal chromo shadow functions as a binding module that targets lysine domain, linked by an unstructured hinge region. -
Table S1. List of Proteins in the BAHD1 Interactome
Table S1. List of proteins in the BAHD1 interactome BAHD1 nuclear partners found in this work yeast two-hybrid screen Name Description Function Reference (a) Chromatin adapters HP1α (CBX5) chromobox homolog 5 (HP1 alpha) Binds histone H3 methylated on lysine 9 and chromatin-associated proteins (20-23) HP1β (CBX1) chromobox homolog 1 (HP1 beta) Binds histone H3 methylated on lysine 9 and chromatin-associated proteins HP1γ (CBX3) chromobox homolog 3 (HP1 gamma) Binds histone H3 methylated on lysine 9 and chromatin-associated proteins MBD1 methyl-CpG binding domain protein 1 Binds methylated CpG dinucleotide and chromatin-associated proteins (22, 24-26) Chromatin modification enzymes CHD1 chromodomain helicase DNA binding protein 1 ATP-dependent chromatin remodeling activity (27-28) HDAC5 histone deacetylase 5 Histone deacetylase activity (23,29,30) SETDB1 (ESET;KMT1E) SET domain, bifurcated 1 Histone-lysine N-methyltransferase activity (31-34) Transcription factors GTF3C2 general transcription factor IIIC, polypeptide 2, beta 110kDa Required for RNA polymerase III-mediated transcription HEYL (Hey3) hairy/enhancer-of-split related with YRPW motif-like DNA-binding transcription factor with basic helix-loop-helix domain (35) KLF10 (TIEG1) Kruppel-like factor 10 DNA-binding transcription factor with C2H2 zinc finger domain (36) NR2F1 (COUP-TFI) nuclear receptor subfamily 2, group F, member 1 DNA-binding transcription factor with C4 type zinc finger domain (ligand-regulated) (36) PEG3 paternally expressed 3 DNA-binding transcription factor with -
Functional Roles of Bromodomain Proteins in Cancer
cancers Review Functional Roles of Bromodomain Proteins in Cancer Samuel P. Boyson 1,2, Cong Gao 3, Kathleen Quinn 2,3, Joseph Boyd 3, Hana Paculova 3 , Seth Frietze 3,4,* and Karen C. Glass 1,2,4,* 1 Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; [email protected] 2 Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA; [email protected] 3 Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; [email protected] (C.G.); [email protected] (J.B.); [email protected] (H.P.) 4 University of Vermont Cancer Center, Burlington, VT 05405, USA * Correspondence: [email protected] (S.F.); [email protected] (K.C.G.) Simple Summary: This review provides an in depth analysis of the role of bromodomain-containing proteins in cancer development. As readers of acetylated lysine on nucleosomal histones, bromod- omain proteins are poised to activate gene expression, and often promote cancer progression. We examined changes in gene expression patterns that are observed in bromodomain-containing proteins and associated with specific cancer types. We also mapped the protein–protein interaction network for the human bromodomain-containing proteins, discuss the cellular roles of these epigenetic regu- lators as part of nine different functional groups, and identify bromodomain-specific mechanisms in cancer development. Lastly, we summarize emerging strategies to target bromodomain proteins in cancer therapy, including those that may be essential for overcoming resistance. Overall, this review provides a timely discussion of the different mechanisms of bromodomain-containing pro- Citation: Boyson, S.P.; Gao, C.; teins in cancer, and an updated assessment of their utility as a therapeutic target for a variety of Quinn, K.; Boyd, J.; Paculova, H.; cancer subtypes. -
Maintenance of Self-Renewal Ability of Mouse Embryonic Stem Cells in The
MaintenanceBlackwellMalden,GTCGenes1365-2443©?117OriginalDnmt1/3a/3bA 2006 TsumuraBlackwell to USA ArticleCells Publishing et Publishing al. triple knockoutInc Ltd ES cells of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b Akiko Tsumura1,4, Tomohiro Hayakawa2, Yuichi Kumaki3,6, Shin-ichiro Takebayashi1, Morito Sakaue1, Chisa Matsuoka1, Kunitada Shimotohno4, Fuyuki Ishikawa5, En Li7, Hiroki R. Ueda3, Jun-ichi Nakayama2 and Masaki Okano1,* 1Laboratory for Mammalian Epigenetic Studies, 2Laboratory for Chromatin Dynamics, and 3Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan 4Department of Viral Oncology, Institute for Virus Research, Kyoto University, 53 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8501, Japan 5Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan 6INTEC Web and Genome Informatics Corp., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan 7Epigenetics Program, Novartis Institute for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b cooperatively regulate cytosine methylation in CpG dinucleotides in mammalian genomes, providing an epigenetic basis for gene silencing and maintenance of genome integrity. Proper CpG methylation is required for the normal growth of various somatic cell types, indicating its essential role in the basic cellular function of mammalian cells. Previous studies using Dnmt1–/– or Dnmt3a–/–Dnmt3b–/– ES cells, however, have shown that undifferentiated embryonic stem (ES) cells can tolerate hypomethylation for their proliferation. In an attempt to investigate the effects of the complete loss of CpG DNA methyltransferase function, we established mouse ES cells lacking all three of these enzymes by gene targeting. -
The Heterochromatin Condensation State in Peripheral “Gene Poor” and Central “Gene Rich” Nuclear Regions of Less Differe
L al of euk rn em u i o a J Journal of Leukemia Karel Smetana, J Leuk 2014, 2:4 ISSN: 2329-6917 DOI: 10.4172/2329-6917.1000151 Research Article Open Access The Heterochromatin Condensation State in Peripheral “Gene Poor” and Central “Gene Rich” Nuclear Regions of Less Differentiated and Mature Human Leukemic Cells: A Mini-Review with Additional Original Observations Karel Smetana* Institute of Hematology and Blood Transfusion, Prague, Czech Republic *Corresponding author: Karel Smetana, Senior scientist Institute of Hematology and Blood Transfusion, U nemocnice 1, 128 20 Prague, Czech Republic, Tel: 420 739906473; E-mail: [email protected] Rec date: May 22, 2014; Acc date: Aug 28, 2014; Pub date: Aug 30, 2014 Copyright: © 2014 Karel Smenata. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract In the morphological cytology the heterochromatin is one of very useful tools for the cell identification including the differentiation and maturation stage. However, the heterochromatin condensation state was less studied although it appeared to be different in “gene rich” central and “gene poor” peripheral nuclear regions. The heavy heterochromatin condensation state in the central “gene rich” nuclear regions might reflect a marked structural stability and protect the genomic integrity. It must be also noted that the heterochromatin condensation state in these nuclear regions is more variable than in the nuclear periphery because of the presence of more as well as less condensed heterochromatin territories. -
Chromatid Cohesion During Mitosis: Lessons from Meiosis
Journal of Cell Science 112, 2607-2613 (1999) 2607 Printed in Great Britain © The Company of Biologists Limited 1999 JCS0467 COMMENTARY Chromatid cohesion during mitosis: lessons from meiosis Conly L. Rieder1,2,3 and Richard Cole1 1Wadsworth Center, New York State Dept of Health, PO Box 509, Albany, New York 12201-0509, USA 2Department of Biomedical Sciences, State University of New York, Albany, New York 12222, USA 3Marine Biology Laboratory, Woods Hole, MA 02543-1015, USA *Author for correspondence (e-mail: [email protected]) Published on WWW 21 July 1999 SUMMARY The equal distribution of chromosomes during mitosis and temporally separated under various conditions. Finally, we meiosis is dependent on the maintenance of sister demonstrate that in the absence of a centromeric tether, chromatid cohesion. In this commentary we review the arm cohesion is sufficient to maintain chromatid cohesion evidence that, during meiosis, the mechanism underlying during prometaphase of mitosis. This finding provides a the cohesion of chromatids along their arms is different straightforward explanation for why mutants in proteins from that responsible for cohesion in the centromere responsible for centromeric cohesion in Drosophila (e.g. region. We then argue that the chromatids on a mitotic ord, mei-s332) disrupt meiosis but not mitosis. chromosome are also tethered along their arms and in the centromere by different mechanisms, and that the Key words: Sister-chromatid cohesion, Mitosis, Meiosis, Anaphase functional action of these two mechanisms can be onset INTRODUCTION (related to the fission yeast Cut1P; Ciosk et al., 1998). When Pds1 is destroyed Esp1 is liberated, and this event somehow The equal distribution of chromosomes during mitosis is induces a class of ‘glue’ proteins, called cohesins (e.g. -
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc Oncogenesis
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis By Yuting Sun This thesis is submitted in fulfilment of the requirements for the degree of Doctor of Philosophy at the University of New South Wales Children’s Cancer Institute Australia for Medical Research School of Women’s and Children’s Health, Faculty of Medicine University of New South Wales Australia August 2014 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Sun First name: Yuting Other name/s: Abbreviation for degree as given in the University calendar: PhD School : School of·Women's and Children's Health Faculty: Faculty of Medicine Title: The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis. Abstract 350 words maximum: (PLEASE TYPE) N-Myc Induces neuroblastoma by regulating the expression of target genes and proteins, and N-Myc protein is degraded by Fbxw7 and NEDD4 and stabilized by Aurora A. The class lla histone deacetylase HDAC5 suppresses gene transcription, and blocks myoblast and leukaemia cell differentiation. While histone H3 lysine 4 (H3K4) trimethylation at target gene promoters is a pre-requisite for Myc· induced transcriptional activation, WDRS, as a histone H3K4 methyltransferase presenter, is required for H3K4 methylation and transcriptional activation mediated by a histone H3K4 methyltransferase complex. Here, I investigated the roles of HDAC5 and WDR5 in N-Myc overexpressing neuroblastoma. I have found that N-Myc upregulates HDAC5 protein expression, and that HDAC5 represses NEDD4 gene expression, increases Aurora A gene expression and consequently upregulates N-Myc protein expression in neuroblastoma cells. -
(RRP1B) Modulates Metastasis Through Regulation of Histone Methylation
Published OnlineFirst August 4, 2014; DOI: 10.1158/1541-7786.MCR-14-0167 Molecular Cancer Oncogenes and Tumor Suppressors Research Metastasis-Associated Protein Ribosomal RNA Processing 1 Homolog B (RRP1B) Modulates Metastasis through Regulation of Histone Methylation Minnkyong Lee1, Amy M. Dworkin1, Jens Lichtenberg1, Shashank J. Patel1, Niraj S. Trivedi2, Derek Gildea2, David M. Bodine1, and Nigel P.S. Crawford1 Abstract Overexpression of ribosomal RNA processing 1 homolog B (RRP1B) induces a transcriptional profile that accurately predicts patient outcome in breast cancer. However, the mechanism by which RRP1B modulates transcription is unclear. Here, the chromatin-binding properties of RRP1B were examined to define how it regulates metastasis-associated transcription. To identify genome-wide RRP1B-binding sites, high-throughput ChIP-seq was performed in the human breast cancer cell line MDA-MB-231 and HeLa cells using antibodies against endogenous RRP1B. Global changes in repressive marks such as histone H3 lysine 9 trimethylation (H3K9me3) were also examined by ChIP-seq. Analysis of these samples identified 339 binding regions in MDA- MB-231 cells and 689 RRP1B-binding regions in HeLa cells. Among these, 136 regions were common to both cell lines. Gene expression analyses of these RRP1B-binding regions revealed that transcriptional repression is the primary result of RRP1B binding to chromatin. ChIP-reChIP assays demonstrated that RRP1B co-occupies loci with decreased gene expression with the heterochromatin-associated proteins, tripartite motif-containing protein 28 (TRIM28/KAP1), and heterochromatin protein 1-a (CBX5/HP1a). RRP1B occupancy at these loci was also associated with higher H3K9me3 levels, indicative of heterochromatinization mediated by the TRIM28/HP1a complex. -
Mitosis Vs. Meiosis
Mitosis vs. Meiosis In order for organisms to continue growing and/or replace cells that are dead or beyond repair, cells must replicate, or make identical copies of themselves. In order to do this and maintain the proper number of chromosomes, the cells of eukaryotes must undergo mitosis to divide up their DNA. The dividing of the DNA ensures that both the “old” cell (parent cell) and the “new” cells (daughter cells) have the same genetic makeup and both will be diploid, or containing the same number of chromosomes as the parent cell. For reproduction of an organism to occur, the original parent cell will undergo Meiosis to create 4 new daughter cells with a slightly different genetic makeup in order to ensure genetic diversity when fertilization occurs. The four daughter cells will be haploid, or containing half the number of chromosomes as the parent cell. The difference between the two processes is that mitosis occurs in non-reproductive cells, or somatic cells, and meiosis occurs in the cells that participate in sexual reproduction, or germ cells. The Somatic Cell Cycle (Mitosis) The somatic cell cycle consists of 3 phases: interphase, m phase, and cytokinesis. 1. Interphase: Interphase is considered the non-dividing phase of the cell cycle. It is not a part of the actual process of mitosis, but it readies the cell for mitosis. It is made up of 3 sub-phases: • G1 Phase: In G1, the cell is growing. In most organisms, the majority of the cell’s life span is spent in G1. • S Phase: In each human somatic cell, there are 23 pairs of chromosomes; one chromosome comes from the mother and one comes from the father. -
Aging Mice Have Increased Chromosome Instability That Is Exacerbated by Elevated Mdm2 Expression
Oncogene (2011) 30, 4622–4631 & 2011 Macmillan Publishers Limited All rights reserved 0950-9232/11 www.nature.com/onc ORIGINAL ARTICLE Aging mice have increased chromosome instability that is exacerbated by elevated Mdm2 expression T Lushnikova1, A Bouska2, J Odvody1, WD Dupont3 and CM Eischen1 1Department of Pathology, Vanderbilt University School of Medicine, Nashville, TN, USA; 2Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA and 3Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA Aging is thought to negatively affect multiple cellular Introduction processes including the ability to maintain chromosome stability. Chromosome instability (CIN) is a common Genomic instability refers to the accumulation or property of cancer cells and may be a contributing factor acquisition of numerical and/or structural abnormali- to cellular transformation. The types of DNA aberrations ties in chromosomes. It has long been observed that that arise during aging before tumor development and that chromosome instability (CIN) is a hallmark of cancer contribute to tumorigenesis are currently unclear. Mdm2, cells and is postulated to be required for tumorigenesis a key regulator of the p53 tumor suppressor and (Lengauer et al., 1998; Negrini et al., 2010). Genomic modulator of DNA break repair, is frequently over- changes, such as chromosome breaks, translocations, expressed in malignancies and contributes to CIN. To genome rearrangements, aneuploidy and telomere short- determine the relationship between aging and CIN and the ening have been observed in aging organisms (Nisitani role of Mdm2, precancerous wild-type C57Bl/6 and et al., 1990; Tucker et al., 1999; Dolle and Vijg, 2002; littermate-matched Mdm2 transgenic mice at various Aubert and Lansdorp, 2008; Zietkiewicz et al., 2009). -
Hepatitis C Virus As a Unique Human Model Disease to Define
viruses Review Hepatitis C Virus as a Unique Human Model Disease to Define Differences in the Transcriptional Landscape of T Cells in Acute versus Chronic Infection David Wolski and Georg M. Lauer * Liver Center at the Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA * Correspondence: [email protected]; Tel.: +1-617-724-7515 Received: 27 June 2019; Accepted: 23 July 2019; Published: 26 July 2019 Abstract: The hepatitis C virus is unique among chronic viral infections in that an acute outcome with complete viral elimination is observed in a minority of infected patients. This unique feature allows direct comparison of successful immune responses with those that fail in the setting of the same human infection. Here we review how this scenario can be used to achieve better understanding of transcriptional regulation of T-cell differentiation. Specifically, we discuss results from a study comparing transcriptional profiles of hepatitis C virus (HCV)-specific CD8 T-cells during early HCV infection between patients that do and do not control and eliminate HCV. Identification of early gene expression differences in key T-cell differentiation molecules as well as clearly distinct transcriptional networks related to cell metabolism and nucleosomal regulation reveal novel insights into the development of exhausted and memory T-cells. With additional transcriptional studies of HCV-specific CD4 and CD8 T-cells in different stages of infection currently underway, we expect HCV infection to become a valuable model disease to study human immunity to viruses. Keywords: viral hepatitis; hepatitis C virus; T cells; transcriptional regulation; transcription factors; metabolism; nucleosome 1. -
Development and Validation of a Novel Immune-Related Prognostic Model
Wang et al. J Transl Med (2020) 18:67 https://doi.org/10.1186/s12967-020-02255-6 Journal of Translational Medicine RESEARCH Open Access Development and validation of a novel immune-related prognostic model in hepatocellular carcinoma Zheng Wang1, Jie Zhu1, Yongjuan Liu3, Changhong Liu2, Wenqi Wang2, Fengzhe Chen1* and Lixian Ma1* Abstract Background: Growing evidence has suggested that immune-related genes play crucial roles in the development and progression of hepatocellular carcinoma (HCC). Nevertheless, the utility of immune-related genes for evaluating the prognosis of HCC patients are still lacking. The study aimed to explore gene signatures and prognostic values of immune-related genes in HCC. Methods: We comprehensively integrated gene expression data acquired from 374 HCC and 50 normal tissues in The Cancer Genome Atlas (TCGA). Diferentially expressed genes (DEGs) analysis and univariate Cox regression analysis were performed to identify DEGs that related to overall survival. An immune prognostic model was constructed using the Lasso and multivariate Cox regression analyses. Furthermore, Cox regression analysis was applied to identify independent prognostic factors in HCC. The correlation analysis between immune-related signature and immune cells infltration were also investigated. Finally, the signature was validated in an external independent dataset. Results: A total of 329 diferentially expressed immune‐related genes were detected. 64 immune‐related genes were identifed to be markedly related to overall survival in HCC patients using univariate Cox regression analysis. Then we established a TF-mediated network for exploring the regulatory mechanisms of these genes. Lasso and multivariate Cox regression analyses were applied to construct the immune-based prognostic model, which consisted of nine immune‐related genes.