Histone Onco-Modifications
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The C-Terminal Region of Histone H4 Recognized by Antinucleosome Th Cells in Identification of a Minimal T Cell Epitope
Identification of a Minimal T Cell Epitope Recognized by Antinucleosome Th Cells in the C-Terminal Region of Histone H4 This information is current as Patrice Decker, Anne Le Moal, Jean-Paul Briand and of October 2, 2021. Sylviane Muller J Immunol 2000; 165:654-662; ; doi: 10.4049/jimmunol.165.2.654 http://www.jimmunol.org/content/165/2/654 Downloaded from References This article cites 34 articles, 13 of which you can access for free at: http://www.jimmunol.org/content/165/2/654.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on October 2, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2000 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Identification of a Minimal T Cell Epitope Recognized by Antinucleosome Th Cells in the C-Terminal Region of Histone H41 Patrice Decker, Anne Le Moal, Jean-Paul Briand, and Sylviane Muller2 Autoreactive T cells responding to systemic autoantigens have been characterized in patients and mice with autoimmune diseases and in healthy individuals. -
How Human H1 Histone Recognizes DNA
molecules Article How Human H1 Histone Recognizes DNA Olesya P. Luzhetskaya, Sergey E. Sedykh and Georgy A. Nevinsky * Institute of Chemical Biology and Fundamental Medicine, SD of Russian Academy of Sciences, 8 Lavrentiev Ave., 630090 Novosibirsk, Russia; [email protected] (O.P.L.); [email protected] (S.E.S.) * Correspondence: [email protected]; Tel.: +7-383-363-51-26; Fax: +7-383-363-51-53 Received: 11 August 2020; Accepted: 1 October 2020; Published: 5 October 2020 Abstract: Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the affinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1–20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein–oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 0.2) 2 ± 10 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, × − d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their affinity by a factor of f = 3.0 0.2. This factor f corresponds ± to the Kd value = 1/f characterizing the affinity of one nucleotide of different ss d(pN)n for H1 at n = 2–6 (which are covered by this protein globule) is approximately 0.33 0.02 M. -
Interplay Between Epigenetics and Metabolism in Oncogenesis: Mechanisms and Therapeutic Approaches
OPEN Oncogene (2017) 36, 3359–3374 www.nature.com/onc REVIEW Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches CC Wong1, Y Qian2,3 and J Yu1 Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer. Oncogene (2017) 36, 3359–3374; doi:10.1038/onc.2016.485; published online 16 January 2017 INTRODUCTION metabolic genes have also been identified as driver genes It has been appreciated since the early days of cancer research mutated in some cancers, such as isocitrate dehydrogenase 1 16 17 that the metabolic profiles of tumor cells differ significantly from and 2 (IDH1/2) in gliomas and acute myeloid leukemia (AML), 18 normal cells. Cancer cells have high metabolic demands and they succinate dehydrogenase (SDH) in paragangliomas and fuma- utilize nutrients with an altered metabolic program to support rate hydratase (FH) in hereditary leiomyomatosis and renal cell 19 their high proliferative rates and adapt to the hostile tumor cancer (HLRCC). -
Predicting Double-Strand DNA Breaks Using Epigenome Marks Or DNA at Kilobase Resolution
bioRxiv preprint doi: https://doi.org/10.1101/149039; this version posted June 12, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution Rapha¨elMourad1 and Olivier Cuvier1 April 10, 2017 1 Laboratoire de Biologie Mol´eculaireEucaryote (LBME), CNRS, Universit´ePaul Sabatier (UPS), 31000 Toulouse, France Abstract Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, includ- ing exposure to ionizing radiation or reactive oxygen species. DSBs can cause abnormal chromosomal rearrangements which are linked to cancer development, and hence represent an important issue. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of DSB origin. However these techniques are costly and challenging. Hence we devised a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are available from the ENCODE project. We achieved excellent prediction accuracy (AUC = 0:97) at high resolution (< 1 kb), and showed that only chromatin accessibility and H3K4me1 mark were sufficient for highly accurate prediction (AUC = 0:95). We also demonstrated the better sensitivity of DSB predictions com- pared to BLESS experiments. We identified chromatin accessibility, activity and long-range contacts as best predictors. In addition, our work represents the first step toward unveiling the "cis-DNA repairing" code underlying DSBs, paving the way for future studies of cis-elements involved in DNA damage and repair. -
Re-Coding the ‘Corrupt’ Code: CRISPR-Cas9 Interventions in Human Germ Line Editing
Re-coding the ‘corrupt’ code: CRISPR-Cas9 interventions in human germ line editing CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation Master Thesis Tilburg University- Law and Technology 2018-19 Tilburg Institute for Law, Technology, and Society (TILT) October 2019 Student: Srishti Tripathy Supervisors: Prof. Dr. Robin Pierce SRN: 2012391 Dr. Emre Bayamlioglu ANR: 659785 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation This page is intentionally left blank 2 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation 3 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation Table of Contents CHAPTER 1: Introduction .............................................................................................................. 6 1.1 Introduction and Review - “I think I’m crazy enough to do it” ......................................................................... 6 1.2 Research Question and Sub Questions .......................................................................................................................... 9 1.4 Methodology ............................................................................................................................................................................. 9 1.4 Thesis structure: ................................................................................................................................................................. -
Application of Histone Modification-Specific Interaction Domains As an Alternative to Antibodies
Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Method Application of histone modification-specific interaction domains as an alternative to antibodies Goran Kungulovski,1 Ina Kycia,1,4 Raluca Tamas,1 Renata Z. Jurkowska,1 Srikanth Kudithipudi,1 Chisato Henry,2 Richard Reinhardt,3 Paul Labhart,2 and Albert Jeltsch1 1Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany; 2Active Motif, Carlsbad, California 92008, USA; 3Max-Planck-Genomzentrum Koln,€ 50829 Koln,€ Germany Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we suc- cessfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies. [Supplemental material is available for this article.] The unstructured N-terminal tails of histones protrude from the yielding false negative results. When undocumented, the cross- core nucleosome and harbor complex patterns of post-translational reactivity with related or unrelated marks and the combinatorial modifications (PTMs) (Kouzarides 2007; Margueron and Reinberg effect of neighboring marks compromise the application of anti- 2010; Bannister and Kouzarides 2011; Tan et al. -
The Role of Histone H2av Variant Replacement and Histone H4 Acetylation in the Establishment of Drosophila Heterochromatin
The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin Jyothishmathi Swaminathan, Ellen M. Baxter, and Victor G. Corces1 Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA Activation and repression of transcription in eukaryotes involve changes in the chromatin fiber that can be accomplished by covalent modification of the histone tails or the replacement of the canonical histones with other variants. Here we show that the histone H2A variant of Drosophila melanogaster, H2Av, localizes to the centromeric heterochromatin, and it is recruited to an ectopic heterochromatin site formed by a transgene array. His2Av behaves genetically as a PcG gene and mutations in His2Av suppress position effect variegation (PEV), suggesting that this histone variant is required for euchromatic silencing and heterochromatin formation. His2Av mutants show reduced acetylation of histone H4 at Lys 12, decreased methylation of histone H3 at Lys 9, and a reduction in HP1 recruitment to the centromeric region. H2Av accumulation or histone H4 Lys 12 acetylation is not affected by mutations in Su(var)3-9 or Su(var)2-5. The results suggest an ordered cascade of events leading to the establishment of heterochromatin and requiring the recruitment of the histone H2Av variant followed by H4 Lys 12 acetylation as necessary steps before H3 Lys 9 methylation and HP1 recruitment can take place. [Keywords: Chromatin; silencing; transcription; histone; nucleus] Received September 8, 2004; revised version accepted November 4, 2004. The basic unit of chromatin is the nucleosome, which is guchi et al. 2004). The role of histone variants, and spe- made up of 146 bp of DNA wrapped around a histone cially those of H3 and H2A, in various nuclear processes octamer composed of two molecules each of the histones has been long appreciated (Wolffe and Pruss 1996; Ah- H2A, H2B, H3, and H4. -
REVIEW Chromatin Modifications and DNA Double-Strand Breaks
Leukemia (2007) 21, 195–200 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu REVIEW Chromatin modifications and DNA double-strand breaks: the current state of play TC Karagiannis1,2 and A El-Osta3 1Molecular Radiation Biology, Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; 2Department of Pathology, The University of Melbourne, Parkville, Melbourne, Victoria, Australia and 3Epigenetics in Human Health and Disease, Baker Medical Research Institute, The Alfred Medical Research and Education Precinct, Prahran, Victoria, Australia The packaging and compaction of DNA into chromatin is mutated (ATM) and ataxia telangiectasia-related (also known as important for all DNA-metabolism processes such as transcrip- Rad3-related, ATR), which are members of the phosphoinositide tion, replication and repair. The involvement of chromatin 4,5 modifications in transcriptional regulation is relatively well 3-kinase (PI(3)K) superfamily. They catalyse the phosphoryla- characterized, and the distinct patterns of chromatin transitions tion of numerous downstream substrates that are involved in 4,5 that guide the process are thought to be the result of a code on cell-cycle regulation, DNA repair and apoptosis. the histone proteins (histone code). In contrast to transcription, In mammalian cells, DSBs are repaired by one of two distinct the intricate link between chromatin and responses to DNA and complementary pathways – homologous recombination damage has been given attention only recently. It is now (HR) and non-homologous end-joining (NHEJ).6,7 Briefly, NHEJ emerging that specific ATP-dependent chromatin remodeling involves processing of the broken DNA terminii to make them complexes (including the Ino80, Swi/Snf and RSC remodelers) 3 and certain constitutive (methylation of lysine 79 of histone H3) compatible, followed by a ligation step. -
Annotated Classic Histone Code and Transcription
Annotated Classic Histone Code and Transcription Jerry L. Workman1,* 1Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA *Correspondence: [email protected] We are pleased to present a series of Annotated Classics celebrating 40 years of exciting biology in the pages of Cell. This install- ment revisits “Tetrahymena Histone Acetyltransferase A: A Homolog to Yeast Gcn5p Linking Histone Acetylation to Gene Activa- tion” by C. David Allis and colleagues. Here, Jerry Workman comments on how the discovery of Tetrahymena histone acetyltrans- ferase A, a homolog to a yeast transcriptional adaptor Gcn5p, by Allis led to the establishment of links between histone acetylation and gene activation. Each Annotated Classic offers a personal perspective on a groundbreaking Cell paper from a leader in the field with notes on what stood out at the time of first reading and retrospective comments regarding the longer term influence of the work. To see Jerry L. Workman’s thoughts on different parts of the manuscript, just download the PDF and then hover over or double- click the highlighted text and comment boxes on the following pages. You can also view Workman’s annotation by opening the Comments navigation panel in Acrobat. Cell 158, August 14, 2014, 2014 ©2014 Elsevier Inc. Cell, Vol. 84, 843±851, March 22, 1996, Copyright 1996 by Cell Press Tetrahymena Histone Acetyltransferase A: A Homolog to Yeast Gcn5p Linking Histone Acetylation to Gene Activation James E. Brownell,* Jianxin Zhou,* Tamara Ranalli,* 1995; Edmondson et al., submitted). Thus, the regulation Ryuji Kobayashi,² Diane G. Edmondson,³ of histone acetylation is an attractive control point for Sharon Y. -
Active Motif Technical Data Sheet (TDS)
Histone H4K8ac antibody (pAb) Catalog Nos: 61103, 61104 Quantities: 100 µg, 10 µg RRID: AB_2793506 Purification: Protein A Chromatography Isotype: IgG Host: Rabbit Application(s): ChIP, ChIP-Seq, DB, ICC, IF, WB Concentration: 1 µg/µl Reactivity: Human, Mouse, Wide Range Predicted Molecular Weight: 8 kDa Background: Histone H4 is one of the core components of the nucleosome. The nucleosome is the smallest subunit of chromatin and consists of 147 base pairs of DNA wrapped around an octamer of core histone proteins (two each of Histone H2A, Histone H2B, Histone H3 and Histone H4). Histone H1 is a linker histone, present at the interface between the nucleosome core and DNA entry/exit points; it is responsible for establishing higher-order chromatin structure. Chromatin is subject to a variety of chemical modifications, including post-translational modifications of the histone proteins and the methylation of cytosine residues in the DNA. Reported histone modifications include acetylation, methylation, phosphorylation, ubiquitylation, glycosylation, ADP-ribosylation, carbonylation and SUMOylation; they play a major role in regulating gene expression. Lysine N-ε-acetylation is a dynamic, reversible and tightly regulated protein and histone modification that plays a major role in chromatin remodeling and in the regulation of gene expression in various cellular functions. The chromatin-remodeling complex SWI/SNF is recruited to promoters through the interaction of the bromodomain of the protein BRG1, belonging to the SWI/SNF complex, and CBP-acetylated histone H4 Lysine 8, leading to a chromatin remodeling. Immunogen: This Histone H4 acetyl Lys8 antibody was raised against a peptide containing acetyl Lys8 of human Histone H4. -
Role of Hmof-Dependent Histone H4 Lysine 16 Acetylation in the Maintenance of TMS1/ASC Gene Activity
Research Article Role of hMOF-Dependent Histone H4 Lysine 16 Acetylation in the Maintenance of TMS1/ASC Gene Activity Priya Kapoor-Vazirani, Jacob D. Kagey, Doris R. Powell, and Paula M. Vertino Department of Radiation Oncology and the Winship Cancer Institute, Emory University, Atlanta, Georgia Abstract occurring aberrantly during carcinogenesis, is associated with gene Epigenetic silencing of tumor suppressor genes in human inactivation (4). Histone modifications can also act synergistically cancers is associated with aberrant methylation of promoter or antagonistically to define the transcription state of genes. region CpG islands and local alterations in histone mod- Acetylation of histones H3 and H4 is associated with transcrip- ifications. However, the mechanisms that drive these events tionally active promoters and an open chromatin configuration (5). remain unclear. Here, we establish an important role for Both dimethylation and trimethylation of histone H3 lysine 4 histone H4 lysine 16 acetylation (H4K16Ac) and the histone (H3K4me2and H3K4me3) have been linked to actively transcribing acetyltransferase hMOF in the regulation of TMS1/ASC,a genes, although recent studies indicate that CpG island–associated proapoptotic gene that undergoes epigenetic silencing in promoters are marked by H3K4me2regardless of the transcrip- human cancers. In the unmethylated and active state, the tional status (6, 7). In contrast, methylation of histone H3 lysine 9 TMS1 CpG island is spanned by positioned nucleosomes and and 27 are associated with transcriptionally inactive promoters and marked by histone H3K4 methylation. H4K16Ac was uniquely condensed closed chromatin (8, 9). Interplay between histone localized to two sharp peaks that flanked the unmethylated modifications and DNA methylation defines the transcriptional CpG island and corresponded to strongly positioned nucle- potential of a particular chromatin domain. -
Active Motif Technical Data Sheet (TDS)
Histone H4K8ac antibody (mAb) Catalog No: 61525 Quantity: 100 µg RRID: AB_2793669 Purification: Protein G Chromatography Clone: MABI 0408 Host: Mouse Isotype: IgG1 Concentration: 0.66 µg/µl Application(s): ChIP, DB, WB Molecular Weight: 8 kDa Reactivity: Human, Wide Range Predicted Background: Histone H4 is one of the core components of the nucleosome. The nucleosome is the smallest subunit of chromatin and consists of 147 base pairs of DNA wrapped around an octamer of core histone proteins (two each of Histone H2A, Histone H2B, Histone H3 and Histone H4). Histone H1 is a linker histone, present at the interface between the nucleosome core and DNA entry/exit points; it is responsible for establishing higher-order chromatin structure. Chromatin is subject to a variety of chemical modifications, including post-translational modifications of the histone proteins and the methylation of cytosine residues in the DNA. Reported histone modifications include acetylation, methylation, phosphorylation, ubiquitylation, glycosylation, ADP-ribosylation, carbonylation and SUMOylation; they play a major role in regulating gene expression. Lysine N-ε-acetylation is a dynamic, reversible and tightly regulated protein and histone modification that plays a major role in chromatin remodeling and in the regulation of gene expression in various cellular functions. The chromatin-remodeling complex SWI/SNF is recruited to promoters through the interaction of the bromodomain of the protein BRG1, belonging to the SWI/SNF complex, and CBP-acetylated histone H4 Lysine 8, leading to a chromatin remodeling. Immunogen: This antibody was raised against a synthetic peptide containing acetyl-lysine 8 of human Histone H4. Buffer: Purified IgG in PBS with 30% glycerol and 0.035% sodium azide.