Transcription Shapes Genome-Wide Histone Acetylation Patterns
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Quantitative Proteomics Methods for the Analysis of Histone Post-Translational Modifications
Université de Montréal Quantitative Proteomics Methods for the Analysis of Histone Post-translational Modifications par Nebiyu Ali Abshiru Département de Chimie Faculté des arts et des sciences Thèse présentée à la Faculté des études supérieures et postdoctorales en vue de l’obtention du grade de philosophiae doctor (Ph.D.) en chimie Septembre 2015 ©Nebiyu Ali Abshiru, 2015 i Résumé Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. -
Recurrent Herpes Simplex Virus Type 1 (HSV-1) Infection Modulates Neuronal Aging Marks in in Vitro and in Vivo Models
International Journal of Molecular Sciences Article Recurrent Herpes Simplex Virus Type 1 (HSV-1) Infection Modulates Neuronal Aging Marks in In Vitro and In Vivo Models Giorgia Napoletani 1 , Virginia Protto 1 , Maria Elena Marcocci 1 , Lucia Nencioni 1 , Anna Teresa Palamara 1,2,† and Giovanna De Chiara 3,*,† 1 Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, 00185 Rome, Italy; [email protected] (G.N.); [email protected] (V.P.); [email protected] (M.E.M.); [email protected] (L.N.); [email protected] (A.T.P.) 2 Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy 3 Institute of Translational Pharmacology, National Research Council (CNR), 00133 Rome, Italy * Correspondence: [email protected] † Co-last authors. Abstract: Herpes simplex virus 1 (HSV-1) is a widespread neurotropic virus establishing a life-long latent infection in neurons with periodic reactivations. Recent studies linked HSV-1 to neurodegen- erative processes related to age-related disorders such as Alzheimer’s disease. Here, we explored whether recurrent HSV-1 infection might accelerate aging in neurons, focusing on peculiar marks of aged cells, such as the increase in histone H4 lysine (K) 16 acetylation (ac) (H4K16ac); the decrease Citation: Napoletani, G.; Protto, V.; of H3K56ac, and the modified expression of Sin3/HDAC1 and HIRA proteins. By exploiting both Marcocci, M.E.; Nencioni, L.; in vitro and in vivo models of recurrent HSV-1 infection, we found a significant increase in H4K16ac, Palamara, A.T.; De Chiara, G. -
Histone H3K4 Demethylation Is Negatively Regulated by Histone H3 Acetylation in Saccharomyces Cerevisiae
Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae Vicki E. Maltbya, Benjamin J. E. Martina, Julie Brind’Amourb,1, Adam T. Chruscickia,1, Kristina L. McBurneya, Julia M. Schulzec, Ian J. Johnsona, Mark Hillsd, Thomas Hentrichc, Michael S. Koborc, Matthew C. Lorinczb, and LeAnn J. Howea,2 Departments of aBiochemistry and Molecular Biology and bMedical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; cCenter for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4; and dTerry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3 Edited by Kevin Struhl, Harvard Medical School, Boston, MA, and approved September 12, 2012 (received for review February 6, 2012) Histone H3 lysine 4 trimethylation (H3K4me3) is a hallmark of of lysine-specific HDMs have been identified: amine oxidases, transcription initiation, but how H3K4me3 is demethylated during such as LSD1, and the JmjC (Jumonji C) domain–containing gene repression is poorly understood. Jhd2, a JmjC domain protein, demethylases. This latter class of demethylases can be split fur- was recently identified as the major H3K4me3 histone demethylase ther into several subfamilies, including the evolutionarily con- (HDM) in Saccharomyces cerevisiae. Although JHD2 is required for served JARID1 family of demethylases, which is characterized JHD2 removal of methylation upon gene repression, deletion of does not only by a JmjC domain but also by JmjN, AT-rich interactive, not result in increased levels of H3K4me3 in bulk histones, indicating C5HC2 zinc finger, and PHD finger domains (6). In the yeast S. that this HDM is unable to demethylate histones during steady-state cerevisiae, the lone member of the JARID1 family of demethy- conditions. -
Recognition of Histone Acetylation by the GAS41 YEATS Domain Promotes H2A.Z Deposition in Non-Small Cell Lung Cancer
Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer Chih-Chao Hsu,1,2,8 Jiejun Shi,3,8 Chao Yuan,1,2,7,8 Dan Zhao,4,5,8 Shiming Jiang,1,2 Jie Lyu,3 Xiaolu Wang,1,2 Haitao Li,4,5 Hong Wen,1,2 Wei Li,3 and Xiaobing Shi1,2,6 1Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 2Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 3Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; 4MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; 5Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; 6Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues and providing binding platforms for “reader” proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Re- cently, we identified the YEATS domain of AF9 (ALL1 fused gene from chromosome 9) as a novel acetyl-lysine- binding module and showed that the ENL (eleven-nineteen leukemia) YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. -
Hst3 Is Turned Over by a Replication Stress-Responsive SCF Phospho
Hst3 is turned over by a replication stress-responsive SCFCdc4 phospho-degron Ellen R. Edenberga, Ajay A. Vashishtb, Benjamin R. Topacioa, James A. Wohlschlegelb, and David P. Toczyskia,1 aDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and bDepartment of Biological Chemistry, University of California, Los Angeles, CA 90095 Edited* by Stephen J. Elledge, Harvard Medical School, Boston, MA, and approved March 10, 2014 (received for review August 13, 2013) Hst3 is the histone deacetylase that removes histone H3K56 several E3 ubiquitin ligases to identify the one responsible for acetylation. H3K56 acetylation is a cell-cycle– and damage-regu- targeting Hst3 for degradation and found that Hst3 is partially lated chromatin marker, and proper regulation of H3K56 acetyla- stabilized at the nonpermissive temperature of temperature- tion is important for replication, genomic stability, chromatin sensitive mutants in CDC53 (the cullin scaffold for all SCF assembly, and the response to and recovery from DNA damage. ligases) and CDC4 (encoding an essential F-box protein) (Fig. Understanding the regulation of enzymes that regulate H3K56 1A). Inactivation of SCFCdc4 also stabilized Hst3 after treatment acetylation is of great interest, because the loss of H3K56 acetyla- B HST3 with hydroxyurea (HU) to induce replication stress (Fig. 1 ). tion leads to genomic instability. is controlled at both the Cdc4 transcriptional and posttranscriptional level. Here, we show that SCF recognizes its substrates through a phospho-degron – Hst3 is targeted for turnover by the ubiquitin ligase SCFCdc4 (20 22). To understand how Hst3 was targeted for turnover both after phosphorylation of a multisite degron. -
SETD2 Mutations in Primary Central Nervous System Tumors Angela N
Viaene et al. Acta Neuropathologica Communications (2018) 6:123 https://doi.org/10.1186/s40478-018-0623-0 RESEARCH Open Access SETD2 mutations in primary central nervous system tumors Angela N. Viaene1, Mariarita Santi1, Jason Rosenbaum2, Marilyn M. Li1, Lea F. Surrey1 and MacLean P. Nasrallah2,3* Abstract Mutations in SETD2 are found in many tumors, including central nervous system (CNS) tumors. Previous work has shown these mutations occur specifically in high grade gliomas of the cerebral hemispheres in pediatric and young adult patients. We investigated SETD2 mutations in a cohort of approximately 640 CNS tumors via next generation sequencing; 23 mutations were detected across 19 primary CNS tumors. Mutations were found in a wide variety of tumors and locations at a broad range of allele frequencies. SETD2 mutations were seen in both low and high grade gliomas as well as non-glial tumors, and occurred in patients greater than 55 years of age, in addition to pediatric and young adult patients. High grade gliomas at first occurrence demonstrated either frameshift/truncating mutations or point mutations at high allele frequencies, whereas recurrent high grade gliomas frequently harbored subclones with point mutations in SETD2 at lower allele frequencies in the setting of higher mutational burdens. Comparison with the TCGA dataset demonstrated consistent findings. Finally, immunohistochemistry showed decreased staining for H3K36me3 in our cohort of SETD2 mutant tumors compared to wildtype controls. Our data further describe the spectrum of tumors in which SETD2 mutations are found and provide a context for interpretation of these mutations in the clinical setting. Keywords: SETD2, Histone, Brain tumor, Glioma, Epigenetics, H3K36me3 Introduction (H3K36me3) in humans. -
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. -
Watanabe S, Resch M, Lilyestrom W, Clark N
NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2010 November 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2010 ; 1799(5-6): 480±486. doi:10.1016/j.bbagrm.2010.01.009. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Shinya Watanabe1,*, Michael Resch2,*, Wayne Lilyestrom2, Nicholas Clark2, Jeffrey C. Hansen2, Craig Peterson1, and Karolin Luger2,3 1 Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St.; Worcester, Massachusetts 01605 2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870 3 Howard Hughes Medical Institute Abstract The posttranslational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome free regions. Here we show by x-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans (‘oligomerization’) are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome free regions accessible to the DNA replication and repair machinery. -
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. -
Deciphering the Histone Code to Build the Genome Structure
bioRxiv preprint doi: https://doi.org/10.1101/217190; this version posted November 20, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Deciphering the histone code to build the genome structure Kirti Prakasha,b,c,* and David Fournierd,* aPhysico-Chimie Curie, Institut Curie, CNRS UMR 168, 75005 Paris, France; bOxford Nanoimaging Ltd, OX1 1JD, Oxford, UK; cMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK; dFaculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; *Correspondence: [email protected], [email protected] Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutrali- sation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modi- fications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replica- tion and cell division. Finally, we propose a model where the histone code can set critical checkpoints for chromatin to fold reversibly be- tween different orders of the organisation in response to a biological stimulus. DNA | nucleosomes | histone modifications | chromatin domains | chro- mosomes | histone code | chromatin folding | genome structure Introduction The genetic information within chromosomes of eukaryotes is packaged into chromatin, a long and folded polymer of double-stranded DNA, histones and other structural and non- structural proteins. -
EIN2 Mediates Direct Regulation of Histone Acetylation in the Ethylene Response
EIN2 mediates direct regulation of histone acetylation in the ethylene response Fan Zhanga,b,1, Likai Wanga,b,1, Bin Qic, Bo Zhaoa,b, Eun Esther Koa,b, Nathaniel D. Riggana,b, Kevin China,b, and Hong Qiaoa,b,2 aInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712; bDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; and cDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309 Edited by Steven E. Jacobsen, University of California, Los Angeles, CA, and approved August 10, 2017 (received for review May 15, 2017) Ethylene gas is essential for developmental processes and stress of EBF1 and EBF2 (19, 20). In the nucleus, the EIN2-C transduces responses in plants. Although the membrane-bound protein EIN2 is signals to the transcription factors EIN3 and EIL1, which are key for critical for ethylene signaling, the mechanism by which the ethylene activation of expression of all ethylene-response genes (21, 22). We signal is transduced remains largely unknown. Here we show the recently discovered that acetylation at H3K23 and H3K14Ac is in- levels of H3K14Ac and H3K23Ac are correlated with the levels of volved in ethylene-regulated gene activation in a manner that de- EIN2 protein and demonstrate EIN2 C terminus (EIN2-C) is sufficient to pends on both EIN2 and EIN3 (23, 24). rescue the levels of H3K14/23Ac of ein2-5 at the target loci, using Here we show that the levels of H3K14/23Ac are positively CRISPR/dCas9-EIN2-C. -
Glycolytic Metabolism Influences Global Chromatin Structure
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No.6 Glycolytic metabolism influences global chromatin structure Xue-Song Liu, John B. Little, Zhi-Min Yuan Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA Correspondence to: Zhi-Min Yuan, e-mail: [email protected] Keywords: glycolysis, acetylation, chromatin structure, chemosensitivity Received: September 29, 2014 Accepted: December 15, 2014 Published: January 13, 2015 ABSTRACT Metabolic rewiring, specifically elevated glycolytic metabolism is a hallmark of cancer. Global chromatin structure regulates gene expression, DNA repair, and also affects cancer progression. But the interrelationship between tumor metabolism and chromatin architecture remain unclear. Here we show that increased glycolysis in cancer cells promotes an open chromatin configuration. Using complementary methods including Micrococcal nuclease (MNase) digestion assay, electron microscope and immunofluorescence staining, we demonstrate that glycolysis inhibition by pharmacological and genetic approaches was associated with induction of compacted chromatin structure. This condensed chromatin status appeared to result chiefly from histone hypoacetylation as restoration of histone acetylation with an HDAC inhibitor reversed the compacted chromatin state. Interestingly, glycolysis inhibition-induced chromatin condensation impeded DNA repair efficiency leading to increased sensitivity of cancer cells to DNA damage drugs, which may represent a novel molecular mechanism that can be exploited for cancer therapy. INTRODUCTION Tumor cells metabolize most glucose into lactate and thus generate abundant glycolytic intermediates as Pathologist have observed for long time that the precursors for macromolecular biosynthesis, which nucleus of cancer cells show distinct morphological enables tumor cells to meet their increased anabolic and alterations compared to the nucleus of normal cells, and energetic demands due to rapid tumor growth [8].