Fluctuations of Histone Chemical Modifications in Breast, Prostate
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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. -
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. -
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. -
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 -
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. -
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. -
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). -
Chip Validated H4k12ac (Clone RM202) Antibody with Positive and Negative Primer Sets
www.chromatrap.com Clywedog Rd South Wrexham Industrial Estate Wrexham LL13 9XS, United Kingdom Tel: +44 (0) 1978 666239/40 Email: [email protected] ChIP Validated H4K12ac (Clone RM202) Antibody with Positive and Negative Primer Sets Catalogue no: 900025 Chromatrap®’s ChIP Validated H4K12ac Antibody with Positive and Negative Primer Set provides a complete set of tools to assist with a successful ChIP assay. Including: H4K12ac antibody, control rabbit IgG, positive and negative primer sets. The ChIP Validated H4K12ac Antibody with Positive and Negative Primer Sets is not suitable for use with non-human species. Background: Histone 4 (H4) is one of the core histone proteins, comprising the protein component of chromatin. H4 is ubiquitous within chromosomes and can be found bound to most gene sequences throughout the genome. Lysine 12 on histone 4 (H4K12) can only be acetylated and is not associated with methylation. The histone modification H4K12ac is associated with active promoter regions and has roles in activating the transcription of genes, in particular genes with roles in memory and learning. H4K12ac can have an influence on paternal inheritance in the zygote, indicating the importance of this mark for embryo development. A rabbit IgG is included in this Antibody Primer Set as a negative control for the ChIP experiment. The H4K12ac positive primer set recognises the GREB1 gene. The negative primer set recognises the SAT2 gene. Suggested Usage: Component Suggested Dilution Figure H4K12ac 2:1 (antibody: chromatin) 1 Rabbit IgG 2:1 (antibody: chromatin) 1 Positive Primer Set Dilute from 4M (provided) to 1M working concentration Negative Primer Set Dilute from 4M (provided) to 1M working concentration Please note: Optimal dilutions should be determined by the user. -
H4k12ac Is Regulated by Estrogen Receptor-Alpha and Is Associated with BRD4 Function and Inducible Transcription
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No. 9 H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription Sankari Nagarajan1, Eva Benito2, Andre Fischer2,3 and Steven A. Johnsen1 1 Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany 2 Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany 3 Research Group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany Correspondence to: Steven A. Johnsen, email: [email protected] Keywords: Histone acetylation, bromodomain, estrogen, epigenetics, chromatin Received: December 04, 2014 Accepted: January 28, 2015 Published: January 31, 2015 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 Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previous studies established an important role of bromodomain-containing protein-4 (BRD4) in promoting estrogen-regulated transcription and proliferation of ER+ breast cancer cells. Here, we investigated the association between genome-wide occupancy of histone H4 acetylation at lysine 12 (H4K12ac) and BRD4 in the context of estrogen- induced transcription. Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner. -
New Insights Into the Role of Histone Changes in Aging
International Journal of Molecular Sciences Review New Insights into the Role of Histone Changes in Aging Sun-Ju Yi and Kyunghwan Kim * Department of Biology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Chungbuk, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-(43)-2612292 Received: 14 October 2020; Accepted: 2 November 2020; Published: 3 November 2020 Abstract: Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area. Keywords: aging; histone level; histone modification; histone variant; chromatin remodeling; epigenetics 1. Introduction An individual organism undergoes a series of developmental stages, including birth, growth, maturity, aging, and death. Aging is the gradual and continuous decline or loss of function at the cellular, tissue, and organismal levels with the passage of time. Aging is considered to begin in early adulthood, but is regarded as an integral part of life since other stages also affect the aging process [1]. -
Restoring Tip60 HAT/HDAC2 Balance in the Neurodegenerative Brain Relieves Epigenetic Transcriptional Repression and Reinstates C
This Accepted Manuscript has not been copyedited and formatted. The final version may differ from this version. A link to any extended data will be provided when the final version is posted online. Research Articles: Cellular/Molecular Restoring Tip60 HAT/HDAC2 balance in the neurodegenerative brain relieves epigenetic transcriptional repression and reinstates cognition Priyalakshmi Panikker, Song-Jun Xu, Haolin Zhang, Jessica Sarthi, Mariah Beaver, Avni Sheth, Sunya Akhter and Felice Elefant Department of Biology, Drexel University, Philadelphia, PA 19104, USA DOI: 10.1523/JNEUROSCI.2840-17.2018 Received: 28 September 2017 Revised: 26 March 2018 Accepted: 6 April 2018 Published: 13 April 2018 AUTHOR CONTRIBUTION: P.P., and F.E. designed the research; P.P., S.X., H.Z., J.S., M.B., A.S., and S.A conducted the experiments; P.P., S.X., H.Z., J.S., and F.E. analyzed the data; P.P. and F.E. wrote the paper. Conflict of Interest: The authors declare no competing financial interests. The authors thank the Cell Imaging Center (CIC) at Drexel University for their imaging facilities and to Dr. Denise Garcia for generously contributing antibodies for human hippocampal immunohistochemistry. This work was supported by NIH grant R01HD057939 to F.E. Corresponding Author: Felice Elefant, Ph.D., 3245 Chestnut Street, PISB 312, Department of Biology, Drexel University, Philadelphia, PA 19104, USA.; Email: [email protected], FAX: 215-895-1273 Cite as: J. Neurosci ; 10.1523/JNEUROSCI.2840-17.2018 Alerts: Sign up at www.jneurosci.org/cgi/alerts to receive customized email alerts when the fully formatted version of this article is published. -
Comprehensive Analysis of Histone Post-Translational Modifications In
Luense et al. Epigenetics & Chromatin (2016) 9:24 DOI 10.1186/s13072-016-0072-6 Epigenetics & Chromatin RESEARCH Open Access Comprehensive analysis of histone post‑translational modifications in mouse and human male germ cells Lacey J. Luense1,4†, Xiaoshi Wang2,4†, Samantha B. Schon3,4†, Angela H. Weller1,4, Enrique Lin Shiao2,4,5, Jessica M. Bryant1,4,5,6, Marisa S. Bartolomei1,4, Christos Coutifaris3, Benjamin A. Garcia2,4* and Shelley L. Berger1,4* Abstract Background: During the process of spermatogenesis, male germ cells undergo dramatic chromatin reorganization, whereby most histones are replaced by protamines, as part of the pathway to compact the genome into the small nuclear volume of the sperm head. Remarkably, approximately 90 % (human) to 95 % (mouse) of histones are evicted during the process. An intriguing hypothesis is that post-translational modifications (PTMs) decorating histones play a critical role in epigenetic regulation of spermatogenesis and embryonic development following fertilization. Although a number of specific histone PTMs have been individually studied during spermatogenesis and in mature mouse and human sperm, to date, there is a paucity of comprehensive identification of histone PTMs and their dynamics during this process. Results: Here we report systematic investigation of sperm histone PTMs and their dynamics during spermatogen- esis. We utilized “bottom-up” nanoliquid chromatography–tandem mass spectrometry (nano-LC–MS/MS) to identify histone PTMs and to determine their relative abundance in distinct stages of mouse spermatogenesis (meiotic, round spermatids, elongating/condensing spermatids, and mature sperm) and in human sperm. We detected peptides and histone PTMs from all four canonical histones (H2A, H2B, H3, and H4), the linker histone H1, and multiple histone isoforms of H1, H2A, H2B, and H3 in cells from all stages of mouse spermatogenesis and in mouse sperm.