DOCSLIB.ORG

Nucleosome Competition Reveals Processive Acetylation by the SAGA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nucleosome Competition Reveals Processive Acetylation by the SAGA Nucleosome competition reveals processive PNAS PLUS acetylation by the SAGA HAT module Alison E. Ringela, Anne M. Cieniewiczb,c, Sean D. Tavernab,c, and Cynthia Wolbergera,c,1 aDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205; bDepartment of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205; and cCenter for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 Edited by Carl Wu, Howard Hughes Medical Institute, Ashburn, VA, and approved September 1, 2015 (received for review April 30, 2015) The Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex histone acetyltransferase (HAT) complexes also contain reader hyperacetylates histone tails in vivo in a manner that depends modules that recognize the H3K4me3 mark (16, 17). upon histone 3 lysine 4 trimethylation (H3K4me3), a histone mark The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is a enriched at promoters of actively transcribed genes. SAGA contains highly conserved transcriptional coactivator (18) that is involved in a separable subcomplex known as the histone acetyltransferase the transcription of nearly all yeast genes (19, 20) and mediates (HAT) module that contains the HAT, Gcn5, bound to Sgf29, Ada2, crosstalk between H3K4me3 and histone hyperacetylation. The and Ada3. Sgf29 contains a tandem Tudor domain that recognizes HAT activity of SAGA resides in a four-protein subcomplex H3K4me3-containing peptides and is required for histone hyper- known as the “HAT module” (21, 22), which contains the catalytic acetylation in vivo. However, the mechanism by which H3K4me3 subunit Gcn5 (23–25), Ada2, Ada3 (26, 27), and Sgf29 (21, 28). recognition leads to lysine hyperacetylation is unknown, as in The association of Gcn5 with the other HAT module subunits vitro studies show no effect of the H3K4me3 modification on modulates Gcn5 activity and specificity. Gcn5 on its own acetylates histone peptide acetylation by Gcn5. To determine how H3K4me3 free histones but not nucleosomes (22, 23, 25) and preferentially binding by Sgf29 leads to histone hyperacetylation by Gcn5, we modifies histone H3 at K14 (25, 29). A complex containing Gcn5 used differential fluorescent labeling of histones to monitor acety- bound to Ada2 and Ada3 is more active overall and modifies lation of individual subpopulations of methylated and unmodified nucleosomal substrates (22, 25). Binding to Ada2/Ada3 also nucleosomes in a mixture. We find that the SAGA HAT module broadens the lysine specificity of Gcn5 to acetylate multiple lysine BIOCHEMISTRY preferentially acetylates H3K4me3 nucleosomes in a mixture con- residues on the histone H3 tail (22, 25). Sgf29 contains a tandem taining excess unmodified nucleosomes and that this effect requires Tudor domain that binds to H3K4me3 (17, 30) and is required for the Tudor domain of Sgf29. The H3K4me3 mark promotes processive, maintaining wild-type levels of histone H3 acetylation in vivo multisite acetylation of histone H3 by Gcn5 that can account for the (30–32). However, in vitro studies comparing acetylation kinetics different acetylation patterns established by SAGA at promoters by the SAGA complex on peptide substrates in the presence or versus coding regions. Our results establish a model for Sgf29 absence of Sgf29 do not show a rate enhancement when the function at gene promoters and define a mechanism governing H3K4me3 modification is present (30). Because these experi- crosstalk between histone modifications. ments were limited in scope to peptide substrates and measured acetylation using relatively insensitive end-point assays (30), acetyltransferase | histone crosstalk | histone modifications | the full impact of H3K4me3 on HAT module activity may transcription | coactivator Significance he different patterns of histone posttranslational modifications Tdistributed across the genome are proposed to constitute a Crosstalk between histone modifications regulates transcription “histone code” that orchestrates distinct transcriptional programs by establishing spatial and temporal relationships between his- by recruiting specific effector proteins (1–4). The phenome- tone marks. Despite discoveries of reader domains that physically non of histone code “crosstalk,” whereby one type of histone associate with chromatin-modifying enzymes, the mechanisms by modification directs the establishment of another, or through which recognition of one modification triggers other kinds of which several histone modifications are recognized in tandem, has modifications have remained elusive. Gcn5 is the catalytic subunit emerged as an important and widespread mechanism regulating of the Spt-Ada-Gcn5 acetyltransferase (SAGA) histone acetyl- chromatin-templated processes (5, 6). The multifunctional com- transferase (HAT) module, which also recognizes histone 3 lysine 4 plexes that activate transcription are thought to mediate crosstalk trimethylation (H3K4me3) through the tandem Tudor domain- through “reader” domains that recognize particular chromatin containing protein Sgf29. Although previous studies could not marks as well as through catalytic subunits that deposit or remove connect H3K4me3 recognition to differences in acetylation by histone modifications (5, 7, 8). As a result, distinct combinations of Gcn5, we report enhanced processivity by the HAT module on histone posttranslational modifications that correlate with tran- methylated substrates using a previously unpublished histone scriptional output cluster across the genome (9–11). High levels of color-coding assay. Our work defines a mechanism for histone histone 3 lysine 4 trimethylation (H3K4me3) and histone H3 crosstalk that may account for genome-wide patterns of Gcn5- hyperacetylation are present at the promoters of actively tran- mediated acetylation. scribed genes (9, 11, 12), and multiple lines of evidence support the Author contributions: A.E.R., S.D.T., and C.W. designed research; A.E.R. and A.M.C. per- existence of regulatory mechanisms coupling the two modifica- formed research; A.E.R., A.M.C., S.D.T., and C.W. analyzed data; and A.E.R. and C.W. tions. Studies using tandem mass spectrometry to sequence whole wrote the paper. histone tails have shown that H3K4me3 is highly correlated with The authors declare no conflict of interest. hyperacetylation of the same H3 tail (13, 14). Deleting the yeast This article is a PNAS Direct Submission. Set1 methyltransferase, which trimethylates H3K4, leads to dra- Freely available online through the PNAS open access option. matically lower levels of histone H3 tail acetylation overall (13, 15). 1To whom correspondence should be addressed. Email: [email protected]. These results are consistent with a role for H3K4 methylation in This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. triggering hyperacetylation of histone H3; indeed, a number of 1073/pnas.1508449112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1508449112 PNAS Early Edition | 1of10 Downloaded by guest on September 26, 2021 HAT module and variants lacking either the Sgf29 tandem Tudor domain or the Gcn5 bromodomain were expressed as complexes in Escherichia coli and purified to homogeneity (Fig. 1). We first confirmed that S. pombe Sgf29 interacts specifically with H3K4me3 peptides in a pull-down assay. As shown in Fig. 2A, streptavidin beads coated with H3K4me3 peptides efficiently re- tain Sgf29, whereas unmodified H3 peptides do not. To determine the effect of H3K4me3 on the kinetics of pep- tide acetylation by Gcn5, we measured initial acetylation rates by the HAT module at increasing concentrations of either un- modified or H3K4me3 peptides in the presence of saturating amounts of acetyl-CoA. Compared with unmodified peptides, Fig. 1. Domain architecture of HAT module complexes. (Left) SDS/PAGE gel the presence of the H3K4me3 modification increases kcat/Km by of purified S. pombe HAT module complexes containing different domain 3.1-fold (Fig. 2B and Table 1). This change in kcat/Km is caused truncations in which all four subunits are present in roughly equimolar solely by a decrease in Km from 250 ± 40 μMto77± 10 μM, with quantities. (Right) Location of the catalytic domain, tandem Tudor domain, no corresponding change in kcat (Fig. 2B and Table 1). Deletion and bromodomain within the HAT module. of the Sgf29 tandem Tudor domain (ΔTudor) eliminates the difference in acetylation kinetics on H3K4me3 versus un- be much greater than previously determined. Thus, although modified peptides (Fig. 2C and Table 1), as is consistent with a k K multiple lines of evidence suggest that H3K4me3 regulates role for H3K4me3 binding in the observed difference in cat/ m. histone acetylation by SAGA in yeast and mammalian cells (17, We also ruled out the possibility that the H3K4me3 modification k K D 30, 31, 33), in vitro studies have failed to explain how H3K4me3 affects cat or m for acetyl-CoA (Fig. 2 and Table 2); our recognition by Sgf29 gives rise to different patterns of histone acet- finding is consistent with the proposed Gcn5 reaction mecha- ylation. As a result, the underlying mechanism governing crosstalk nism, in which the cofactor binds before the peptide (34, 35). between H3K4 trimethylation and acetylation by SAGA remains To confirm that acetylation by Gcn5 is not directly affected by poorly understood. truncating the Sgf29 tandem Tudor domain, we compared kcat K Δ To elucidate the mechanism underlying crosstalk between
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • New Developments in Epigenetics and Potential Clinical Applications
    NEW DEVELOPMENTS IN EPIGENETICS AND POTENTIAL CLINICAL APPLICATIONS Susan E. Bates, M.D. Columbia University Medical Center, New York, NY and J.J.P Bronx VA Medical Center, Bronx, NY TARGETING THE EPIGENOME What do we mean? “Targeting the Epigenome” - Meaning that we identify proteins that impact transcriptional controls that are important in cancer. “Epigenetics” – Meaning the right genes expressed at the right time, in the right place and in the right quantities. This process is ensured by an expanding list of genes that themselves must be expressed at the right time and right place. Think of it as a coordinated chromatin dance involving DNA, histone proteins, transcription factors, and over 700 proteins that modify them. Transcriptional Control: DNA Histone Tail Modification Nucleosomal Remodeling Non-Coding RNA HISTONE PROTEIN FAMILY 146 bp DNA wrap around an octomer of histone proteins H2A, H2B, H3, H4 are core histone families H1/H5 are linker histones >50 variants of the core histones Some with unique functions Post translational modification of “histone tails” key to gene expression Post-translational modifications include: – Acetylation – Methylation – Ubiquitination – Phosphorylation – Citrullation – SUMOylation – ADP-ribosylation THE HISTONE CODE Specific histone modifications determine function H3K9Ac, H3K27Ac, H3K36Ac H3K4Me3 – Gene activation H3K36Me2 – Inappropriate gene activation H3K27Me3 – Gene repression; Inappropriate gene repression H2AX S139Phosphorylation – associated with DNA double strand break, repair http://www.slideshare.net/jhowlin/eukaryotic-gene-regulation-part-ii-2013 KEY MODIFICATION - SPECIFIC FUNCTIONS H3K36Me: ac Active transcription, me H3K27Me: RNA elongation me Key Silencing ac ac me me Residue me me H3K4Me: H3K4 ac me Key Activating me me me Residue me H3K9 me H3K36 H3K9Ac:: H3K27 Activating Residue H3K18 H4K20 Activation me me me ac Modified from Mosammaparast N, et al.
    [Show full text]
  • Transcription Shapes Genome-Wide Histone Acetylation Patterns
    ARTICLE https://doi.org/10.1038/s41467-020-20543-z OPEN Transcription shapes genome-wide histone acetylation patterns Benjamin J. E. Martin 1, Julie Brind’Amour 2, Anastasia Kuzmin1, Kristoffer N. Jensen2, Zhen Cheng Liu1, ✉ Matthew Lorincz 2 & LeAnn J. Howe 1 Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between histone acetylation and transcription is causal or consequential has not been addressed. 1234567890():,; Using immunoblot and chromatin immunoprecipitation-sequencing in S. cerevisiae, here we show that the majority of histone acetylation is dependent on transcription. This dependency is partially explained by the requirement of RNA polymerase II (RNAPII) for the interaction of H4 histone acetyltransferases (HATs) with gene bodies. Our data also confirms the targeting of HATs by transcription activators, but interestingly, promoter-bound HATs are unable to acetylate histones in the absence of transcription. Indeed, HAT occupancy alone poorly predicts histone acetylation genome-wide, suggesting that HAT activity is regulated post- recruitment. Consistent with this, we show that histone acetylation increases at nucleosomes predicted to stall RNAPII, supporting the hypothesis that this modification is dependent on nucleosome disruption during transcription. Collectively, these data show that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases. 1 Department of Biochemistry and Molecular Biology, Life Sciences Institute, Molecular
    [Show full text]
  • 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 volvedinethylene-regulatedgeneactivationinamannerthatde- 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. Chromatin immunoprecipitation followed by correlated with the EIN2 protein levels and demonstrate that deep sequencing (ChIP-seq) and ChIP-reChIP-seq analyses revealed that EIN2-C is sufficient to rescue the levels of H3K14Ac and EIN2-C associates with histone partially through an interaction with H3K23Ac in ein2-5 at loci targeted using CRISPR/dCas9-EIN2-C.
    [Show full text]
  • Learning Chroma\N States from Chip-‐Seq Data
    Learning Chroman States from ChIP-seq data Luca Pinello GC Yuan Lab Outline • Chroman structure, histone modificaons and combinatorial paerns • How to segment the genome in chroman states • How to use ChromHMM step by step • Further references 2 Epigene-cs and chroman structure • All (almost) the cells of our body share the same genome but have very different gene expression programs…. 3 h?p://jpkc.scu.edu.cn/ywwy/zbsw(E)/edetail12.htm The code over the code • The chroman structure and the accessibility are mainly controlled by: 1. Nucleosome posioning, 2. DNA methylaon, 3. Histone modificaons. 4 Histone Modificaons Specific histone modificaons or combinaons of modificaons confer unique biological func-ons to the region of the genome associated with them: • H3K4me3: promoters, gene acva.on • H3K27me3: promoters, poised enhancers, gene silencing • H2AZ: promoters • H3K4me1: enhancers • H3K36me3: transcribed regions • H3K9me3: gene silencing • H3k27ac: acve enhancers 5 Examples of *-Seq Measuring the genome genome fragmentation assembler DNA DNA reads “genome” ChIP-seq to measure histone data fragments Measuring the regulome (e.g., protein-binding of the genome) Chromatin Immunopreciptation genomic (ChIP) + intervals fragmentation Protein - peak caller bound by DNA bound DNA reads proteins REVIEWS fragments a also informative, as this ratio corresponds to the fraction ChIP–chip of nucleosomes with the particular modification at that location, averaged over all the cells assayed. One of the difficulties in conducting a ChIP–seq con- trol experiment is the large amount of sequencing that ChIP–seq may be necessary. For input DNA and bulk nucleosomes, many of the sequenced tags are spread evenly across the genome.
    [Show full text]
  • Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells Title During Mouse Spermatogenesis
    NAOSITE: Nagasaki University's Academic Output SITE Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells Title during Mouse Spermatogenesis. Song, Ning; Liu, Jie; An, Shucai; Nishino, Tomoya; Hishikawa, Yoshitaka; Author(s) Koji, Takehiko Citation Acta Histochemica et Cytochemica, 44(4), pp.183-190; 2011 Issue Date 2011-08-27 URL http://hdl.handle.net/10069/26169 Copyright (c) 2011 By the Japan Society of Histochemistry and Right Cytochemistry This document is downloaded at: 2020-09-18T06:01:32Z http://naosite.lb.nagasaki-u.ac.jp Advance Publication Acta Histochem. Cytochem. 44 (4): 183–190, 2011 doi:10.1267/ahc.11027 AHCActa0044-59911347-5800JapanTokyo,AHC1102710.1267/ahc.11027Regular Histochemica Society JapanArticle of Histochemistry et Cytochemica and Cytochemistry Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells during Mouse Spermatogenesis Ning Song1, Jie Liu2, Shucai An3, Tomoya Nishino1, Yoshitaka Hishikawa1 and Takehiko Koji1 1Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan, 2Department of Prosthodontics, College of Stomatology, Jiamusi University, Jiamusi, China and 3Department of General Surgery, First Affiliated Hospital, Medical College of Jiamusi University, Jiamusi, China 00 Received June 7, 2011; accepted June 29, 2011; published online July 20, 2011 © 2011Histone The Japanmodification Society has of beenHistochemistry implicated and in the regulation of mammalian spermatogenesis. However, the association of differently modified histone H3 with a specific stage of germ cells during spermatogenesis is not fully understood. In this study, we examined the localiza- tion of variously modified histone H3 in paraffin-embedded sections of adult mouse testis immunohistochemically, focusing on acetylation at lysine 9 (H3K9ac), lysine 18 (H3K18ac), and lysine 23 (H3K23ac); tri-methylation at lysine 4 (H3K4me3) and lysine 27 (H3K27me3); and phosphorylation at serine 10 (H3S10phos).
    [Show full text]
  • 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 volvedinethylene-regulatedgeneactivationinamannerthatde- 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. Chromatin immunoprecipitation followed by correlated with the EIN2 protein levels and demonstrate that deep sequencing (ChIP-seq) and ChIP-reChIP-seq analyses revealed that EIN2-C is sufficient to rescue the levels of H3K14Ac and EIN2-C associates with histone partially through an interaction with H3K23Ac in ein2-5 at loci targeted using CRISPR/dCas9-EIN2-C.
    [Show full text]
  • Fluctuations of Histone Chemical Modifications in Breast, Prostate
    biomolecules Review Fluctuations of Histone Chemical Modifications in Breast, Prostate, and Colorectal Cancer: An Implication of Phytochemicals as Defenders of Chromatin Equilibrium 1, 1, 1 2 Marek Samec y, Alena Liskova y, Lenka Koklesova , Veronika Mestanova , Maria Franekova 3, Monika Kassayova 4, Bianka Bojkova 4 , Sona Uramova 5, Pavol Zubor 6, Katarina Janikova 7, Jan Danko 1, Samson Mathews Samuel 8 , Dietrich Büsselberg 8,* and Peter Kubatka 3,* 1 Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; [email protected] (M.S.); [email protected] (A.L.); [email protected] (L.K.); [email protected] (J.D.) 2 Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; [email protected] 3 Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; [email protected] 4 Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; [email protected] (M.K.); [email protected] (B.B.) 5 Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; [email protected] 6 OBGY Health & Care, Ltd., 01026 Zilina, Slovakia; [email protected] 7 Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; [email protected] 8 Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; [email protected] * Correspondence: [email protected] (P.K.); [email protected] (D.B.); Tel.: 421-43/2633408 (P.K.) Co-first/equal authorship.
    [Show full text]
  • YEATS2 Links Histone Acetylation to Tumorigenesis of Non-Small Cell Lung Cancer
    ARTICLE DOI: 10.1038/s41467-017-01173-4 OPEN YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer Wenyi Mi 1,2, Haipeng Guan3,4, Jie Lyu 5, Dan Zhao3,4, Yuanxin Xi5, Shiming Jiang1,2, Forest H. Andrews6, Xiaolu Wang1,2, Mihai Gagea 7, Hong Wen1,2, Laszlo Tora 8,9,10,11, Sharon Y.R. Dent1,2,12, Tatiana G. Kutateladze6, Wei Li 5, Haitao Li 3,4 & Xiaobing Shi 1,2,12 Recognition of modified histones by “reader” proteins constitutes a key mechanism reg- ulating diverse chromatin-associated processes important for normal and neoplastic devel- opment. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively tran- scribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis. 1 Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA. 2 Center for Cancer Epigenetics, The University of Texas M.D.
    [Show full text]
  • Histone H3K23-Specific Acetylation by MORF Is Coupled to H3K14 Acylation
    ARTICLE https://doi.org/10.1038/s41467-019-12551-5 OPEN Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation Brianna J. Klein1,12, Suk Min Jang2,12, Catherine Lachance2, Wenyi Mi3, Jie Lyu 4,5, Shun Sakuraba 6, Krzysztof Krajewski7, Wesley W. Wang8, Simone Sidoli 9,11, Jiuyang Liu1, Yi Zhang 1, Xiaolu Wang3, Becka M. Warfield1, Andrew J. Kueh10, Anne K. Voss10, Tim Thomas10, Benjamin A. Garcia9, Wenshe R. Liu 8, Brian D. Strahl 7, Hidetoshi Kono 6, Wei Li 4,5, Xiaobing Shi 3, Jacques Côté 2*& Tatiana G. Kutateladze 1* 1234567890():,; Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyl- transferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.
    [Show full text]
  • Document Title
    H3K23ac polyclonal antibody Cat. No. C15310140-100 Type: Polyclonal Specificity: Human Size: 100 µl Isotype: NA Concentration: not determined Host: Rabbit Lot No.: A615-001 Purity: Whole antiserum Storage buffer: NA Storage conditions: NA Precautions: This product is for research use only. Not for use in diagnostic or therapeutic procedures. Description Polyclonal antibody raised in rabbit against histone H3 containing the acetylated lysine 23 (H3K23ac), using a KLH-conjugated synthetic peptide Applications Applications Suggested dilution References ELISA 1:100 - 1:500 Fig 1 Dot Blotting 1:1,000 Fig 2 Western Blotting 1:250 Fig 3 Target Description Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Acetylation of histone is associated with gene activation. Diagenode sa. BELIGUM | EUROPE Diagenode Inc. USA | NORTH AMERICA LIEGE SCIENCE PARK 400 Morris Avenue, Suite 101 Rue Bois Saint-Jean, 3 Denville, NJ 07834 - USA 4102 Seraing (Ougrée) - Belgium Tel: +1 862 209-4680 1 Tel: +32 4 364 20 50 Fax: +1 862 209-4681 Fax: +32 4 364 20 51 [email protected] | [email protected] [email protected] | [email protected] Validation Data Figure 1.
    [Show full text]