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Stephens KE, Moore C, Vinson DA, White BE, Renfro Z, Zhou W, Ji Z, Ji H, Zhu H, Guan Y, Taverna SD. Identification of Regulatory Elements in Primary Sensory Neurons Involved in Trauma-Induced Neuropathic Pain. Mol Neurobiol 2024; 61:1845-1859. [PMID: 37792259 PMCID: PMC10896855 DOI: 10.1007/s12035-023-03673-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Chronic pain is a significant public health issue that is often refractory to existing therapies. Here we use a multiomic approach to identify cis-regulatory elements that show differential chromatin accessibility and reveal transcription factor (TF) binding motifs with functional regulation in the rat dorsal root ganglion (DRG), which contain cell bodies of primary sensory neurons, after nerve injury. We integrated RNA-seq to understand how differential chromatin accessibility after nerve injury may influence gene expression. Using TF protein arrays and chromatin immunoprecipitation-qPCR, we confirmed C/EBPγ binding to a differentially accessible sequence and used RNA-seq to identify processes in which C/EBPγ plays an important role. Our findings offer insights into TF motifs that are associated with chronic pain. These data show how interactions between chromatin landscapes and TF expression patterns may work together to determine gene expression programs in rat DRG neurons after nerve injury.
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Affiliation(s)
- Kimberly E Stephens
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA.
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
| | - Cedric Moore
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- , Present address: 20400 Century Blvd, Suite 120, Germantown, MD, USA
| | - David A Vinson
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA
| | - Bryan E White
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA
| | - Zachary Renfro
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA
- Present address: School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Weiqiang Zhou
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Zhicheng Ji
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Present address: Department of Biostatistics and Bioinformatics, School of Medicine, Duke University, Durham, NC, USA
| | - Hongkai Ji
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Yun Guan
- Department of Anesthesiology and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Neurological Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
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Vinson DA, Stephens KE, O’Meally RN, Bhat S, Dancy BCR, Cole RN, Yegnasubramanian S, Taverna SD. De novo methylation of histone H3K23 by the methyltransferases EHMT1/GLP and EHMT2/G9a. Epigenetics Chromatin 2022; 15:36. [PMID: 36411491 PMCID: PMC9677696 DOI: 10.1186/s13072-022-00468-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022] Open
Abstract
Epigenetic modifications to histone proteins serve an important role in regulating permissive and repressive chromatin states, but despite the identification of many histone PTMs and their perceived role, the epigenetic writers responsible for generating these chromatin signatures are not fully characterized. Here, we report that the canonical histone H3K9 methyltransferases EHMT1/GLP and EHMT2/G9a are capable of catalyzing methylation of histone H3 lysine 23 (H3K23). Our data show that while both enzymes can mono- and di-methylate H3K23, only EHMT1/GLP can tri-methylate H3K23. We also show that pharmacologic inhibition or genetic ablation of EHMT1/GLP and/or EHMT2/G9a leads to decreased H3K23 methylation in mammalian cells. Taken together, this work identifies H3K23 as a new direct methylation target of EHMT1/GLP and EHMT2/G9a, and highlights the differential activity of these enzymes on H3K23 as a substrate.
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Affiliation(s)
- David A. Vinson
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.241054.60000 0004 4687 1637Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Robert N. O’Meally
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Shri Bhat
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Blair C. R. Dancy
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.507680.c0000 0001 2230 3166Walter Reed Army Institute of Research, Silver Spring, MD 20910-7500 USA
| | - Robert N. Cole
- grid.21107.350000 0001 2171 9311Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Sean D. Taverna
- grid.21107.350000 0001 2171 9311Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Stephens KE, Zhou W, Renfro Z, Ji Z, Ji H, Guan Y, Taverna SD. Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain. J Neuroinflammation 2021; 18:185. [PMID: 34446036 PMCID: PMC8390277 DOI: 10.1186/s12974-021-02228-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Efforts to understand genetic variability involved in an individual's susceptibility to chronic pain support a role for upstream regulation by epigenetic mechanisms. METHODS To examine the transcriptomic and epigenetic basis of chronic pain that resides in the peripheral nervous system, we used RNA-seq and ATAC-seq of the rat dorsal root ganglion (DRG) to identify novel molecular pathways associated with pain hypersensitivity in two well-studied persistent pain models induced by chronic constriction injury (CCI) of the sciatic nerve and intra-plantar injection of complete Freund's adjuvant (CFA) in rats. RESULTS Our RNA-seq studies identify a variety of biological process related to synapse organization, membrane potential, transmembrane transport, and ion binding. Interestingly, genes that encode transcriptional regulators were disproportionately downregulated in both models. Our ATAC-seq data provide a comprehensive map of chromatin accessibility changes in the DRG. A total of 1123 regions showed changes in chromatin accessibility in one or both models when compared to the naïve and 31 shared differentially accessible regions (DAR)s. Functional annotation of the DARs identified disparate molecular functions enriched for each pain model which suggests that chromatin structure may be altered differently following sciatic nerve injury and hind paw inflammation. Motif analysis identified 17 DNA sequences known to bind transcription factors in the CCI DARs and 33 in the CFA DARs. Two motifs were significantly enriched in both models. CONCLUSIONS Our improved understanding of the changes in chromatin accessibility that occur in chronic pain states may identify regulatory genomic elements that play essential roles in modulating gene expression in the DRG.
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Affiliation(s)
- Kimberly E Stephens
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA.
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
| | - Weiqiang Zhou
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Zachary Renfro
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Hongkai Ji
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Yun Guan
- Department of Anesthesia and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Neurological Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
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Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, Taverna SD, Zhang H, Ramazanoglu S, Hansen KD, Feinberg AP. Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. Genome Biol 2021; 22:116. [PMID: 33888138 PMCID: PMC8061076 DOI: 10.1186/s13059-021-02335-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/30/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focus on limited numbers of individuals and one to two brain regions. RESULTS Using GTEx samples, we generate a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12 to 23 donors. We identify differentially methylated regions between brain regions among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pairwise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identify unique CpG differentially methylated regions, many associated with ion transport. We also identify 81,130 regions of variably CpG methylated regions, i.e., variable methylation among individuals in the same brain region, which are enriched in regulatory regions and in CpG differentially methylated regions. Many variably methylated regions are unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. Variably methylated regions identified in the amygdala, anterior cingulate cortex, and hippocampus are enriched for heritability of schizophrenia. CONCLUSIONS These data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.
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Affiliation(s)
- Lindsay F. Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Peter F. Hickey
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Rakel Tryggvadóttir
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Colin M. Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Sean D. Taverna
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
| | - Sinan Ramazanoglu
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - GTEx Consortium
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
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Xu J, Zhao X, Mao F, Basrur V, Ueberheide B, Chait BT, Allis CD, Taverna SD, Gao S, Wang W, Liu Y. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies. Nucleic Acids Res 2021; 49:5407-5425. [PMID: 33412588 PMCID: PMC8191774 DOI: 10.1093/nar/gkaa1262] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023] Open
Abstract
Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1-another PcG protein interacting with the EZL1 complex-reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome.
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Affiliation(s)
| | | | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Proteomics Resource Facility, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatrix Ueberheide
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY 10065, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences and the Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shan Gao
- Correspondence may also be addressed to Shan Gao.
| | - Wei Wang
- Correspondence may also be addressed to Wei Wang.
| | - Yifan Liu
- To whom correspondence should be addressed. Tel: +1 323 865 3852;
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Waldrip ZJ, Jenjaroenpun P, DeYoung O, Nookaew I, Taverna SD, Raney KD, Tackett AJ. Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae. PeerJ 2020; 8:e9442. [PMID: 32821531 PMCID: PMC7395602 DOI: 10.7717/peerj.9442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/08/2020] [Indexed: 12/26/2022] Open
Abstract
The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts.
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Affiliation(s)
- Zachary J Waldrip
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Oktawia DeYoung
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
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West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics 2019; 14:130-145. [PMID: 30739529 DOI: 10.1080/15592294.2019.1580110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
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Affiliation(s)
- Kirk L West
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Stephanie D Byrum
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,b Arkansas Children's Research Institute , Little Rock , AR , USA
| | - Samuel G Mackintosh
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Rick D Edmondson
- c College of Medicine , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Sean D Taverna
- d Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , MD , USA.,e Center for Epigenetics , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Alan J Tackett
- a Department of Biochemistry and Molecular Biology , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,b Arkansas Children's Research Institute , Little Rock , AR , USA
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8
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Stephens KE, Zhou W, Ji Z, Chen Z, He S, Ji H, Guan Y, Taverna SD. Sex differences in gene regulation in the dorsal root ganglion after nerve injury. BMC Genomics 2019; 20:147. [PMID: 30782122 PMCID: PMC6381758 DOI: 10.1186/s12864-019-5512-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/05/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular basis underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain in rats after nerve injury. RESULTS We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1513 genes were differentially expressed between sexes. Genes which facilitated synaptic transmission in naïve and injured females did not show increased expression in males. CONCLUSIONS Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this major health issue.
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Affiliation(s)
- Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, School of Medicine, Center for Epigenetics, Johns Hopkins University, Baltimore, MD USA
| | - Weiqiang Zhou
- Department of Biostatics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Zhicheng Ji
- Department of Biostatics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Zhiyong Chen
- Department of Anesthesia and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD USA
| | - Shaoqiu He
- Department of Anesthesia and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD USA
| | - Hongkai Ji
- Department of Biostatics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Yun Guan
- Department of Anesthesia and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, School of Medicine, Center for Epigenetics, Johns Hopkins University, Baltimore, MD USA
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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10
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Stephens KE, Chen Z, Sivanesan E, Raja SN, Linderoth B, Taverna SD, Guan Y. RNA-seq of spinal cord from nerve-injured rats after spinal cord stimulation. Mol Pain 2018; 14:1744806918817429. [PMID: 30451078 PMCID: PMC6293371 DOI: 10.1177/1744806918817429] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/28/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
Spinal cord stimulation has become an important modality in pain treatment especially for neuropathic pain conditions refractory to pharmacotherapy. However, the molecular control of inhibitory and excitatory mechanisms observed after spinal cord stimulation are poorly understood. Here, we used RNA-seq to identify differences in the expression of genes and gene networks in spinal cord tissue from nerve-injured rats with and without repetitive conventional spinal cord stimulation treatment. Five weeks after chronic constrictive injury to the left sciatic nerve, male and female rats were randomized to receive repetitive spinal cord stimulation or no treatment. Rats receiving spinal cord stimulation underwent epidural placement of a miniature stimulating electrode and received seven sessions of spinal cord stimulation (50 Hz, 80% motor threshold, 0.2 ms, constant current bipolar stimulation, 120 min/session) over four consecutive days. Within 2 h after the last spinal cord stimulation treatment, the L4-L6 spinal segments ipsilateral to the side of nerve injury were harvested and used to generate libraries for RNA-seq. Our RNA-seq data suggest further increases of many existing upregulated immune responses in chronic constrictive injury rats after repetitive spinal cord stimulation, including transcription of cell surface receptors and activation of non-neuronal cells. We also demonstrate that repetitive spinal cord stimulation represses transcription of several key synaptic signaling genes that encode scaffold proteins in the post-synaptic density. Our transcriptional studies suggest a potential relationship between specific genes and the therapeutic effects observed in patients undergoing conventional spinal cord stimulation after nerve injury. Furthermore, our results may help identify new therapeutic targets for improving the efficacy of conventional spinal cord stimulation and other chronic pain treatments.
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Affiliation(s)
- Kimberly E Stephens
- Department of Pharmacology and Molecular Sciences,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
- Center for Epigenetics, School of Medicine, Johns
Hopkins University, Baltimore, MA, USA
- Department of Anesthesia and Critical Care Medicine,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Zhiyong Chen
- Department of Anesthesia and Critical Care Medicine,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
- Institute of Basic Medical Sciences, Department of
Human Anatomy, Histology and Embryology, Neuroscience Center, Chinese
Academy of Medical Sciences, School of Basic Medicine, Peking Union
Medical College, Beijing, China
| | - Eellan Sivanesan
- Department of Anesthesia and Critical Care Medicine,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Srinivasa N Raja
- Department of Anesthesia and Critical Care Medicine,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Bengt Linderoth
- Division of Functional Neurosurgery, Department of
Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
- Center for Epigenetics, School of Medicine, Johns
Hopkins University, Baltimore, MA, USA
| | - Yun Guan
- Department of Anesthesia and Critical Care Medicine,
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
- School of Medicine, Department of Neurological
Surgery, Johns Hopkins University, Baltimore, MA, USA
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11
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Xiong J, Gao S, Dui W, Yang W, Chen X, Taverna SD, Pearlman RE, Ashlock W, Miao W, Liu Y. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res 2016; 44:10091-10105. [PMID: 27488188 PMCID: PMC5137421 DOI: 10.1093/nar/gkw684] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 02/06/2023] Open
Abstract
The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.
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Affiliation(s)
- Jie Xiong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,These authors contributed equally to this work as first authors
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China,These authors contributed equally to this work as first authors
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences and The Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ronald E. Pearlman
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wendy Ashlock
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,Correspondence may also be addressed to Wei Miao.
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,To whom correspondence should be addressed. Tel: +1 734 6154239;
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12
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Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLife 2016; 5. [PMID: 27892853 PMCID: PMC5182062 DOI: 10.7554/elife.19090] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Piroska E Huvos
- Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, United States
| | | | - Nikhat Zafar
- J. Craig Venter Institute, Rockville, United States
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, United States
| | | | | | | | | | - Carsten Russ
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Qiandong Zeng
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Lin Fan
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Joshua Z Levin
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Terrance Shea
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sarah K Young
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ryan Hegarty
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Riza Daza
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sharvari Gujja
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jennifer R Wortman
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Bruce W Birren
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Chad Nusbaum
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Clayton M Carey
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Tomoko Noto
- Institute of Molecular Biotechnology, Vienna, Austria
| | | | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
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13
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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun 2016; 7:13387. [PMID: 27841353 PMCID: PMC5114558 DOI: 10.1038/ncomms13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
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Affiliation(s)
- Zhangli Su
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
| | - Jin-Hee Lee
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Kimberly A. Krautkramer
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy J. Thorpe
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Melissa D. Boersma
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Vyacheslav I. Kuznetsov
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | | | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - George N. Phillips
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
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14
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Waldrip ZJ, Byrum SD, Storey AJ, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics 2014; 9:1207-11. [PMID: 25147920 PMCID: PMC4169012 DOI: 10.4161/epi.29919] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/24/2014] [Accepted: 07/12/2014] [Indexed: 01/23/2023] Open
Abstract
Any given chromosomal activity (e.g., transcription) is governed predominantly by the local epiproteome. However, defining local epiproteomes has been limited by a lack of effective technologies to isolate discrete sections of chromatin and to identify with precision specific proteins and histone posttranslational modifications (PTMs). We report the use of the Cas9 and guide RNA (gRNA) components of the CRISPR system for gRNA-directed purification of a discrete section of chromatin. Quantitative mass spectrometry provides for unambiguous identification of proteins and histone PTMs specifically associated with the enriched chromatin. This CRISPR-based Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) approach revealed changes in the local epiproteome of a promoter during activation of transcription. CRISPR-ChAP-MS thus has broad applications for discovering molecular components and dynamic regulation of any in vivo activity at a given chromosomal location.
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Affiliation(s)
- Zachary J Waldrip
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Stephanie D Byrum
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Aaron J Storey
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Jun Gao
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Alicia K Byrd
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Samuel G Mackintosh
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Wayne P Wahls
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Kevin D Raney
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
| | - Alan J Tackett
- University of Arkansas for Medical Sciences; Department of Biochemistry and Molecular Biology; Little Rock, AR USA
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15
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Brown LJ, Baranowski M, Wang Y, Schrey AK, Lenz T, Taverna SD, Cole PA, Sefkow M. Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins. Anal Biochem 2014; 467:14-21. [PMID: 25172130 DOI: 10.1016/j.ab.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022]
Abstract
S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 μM, 6.0 ± 2.9 μM, and 10.06 ± 2.87 μM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.
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Affiliation(s)
- Lindsey J Brown
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Yun Wang
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Thomas Lenz
- Caprotec Bioanalytics, 12489 Berlin, Germany
| | - Sean D Taverna
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Philip A Cole
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
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16
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Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis. eLife 2014; 3:e02996. [PMID: 25161194 PMCID: PMC4141274 DOI: 10.7554/elife.02996] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the well-established role of heterochromatin in protecting chromosomal integrity during meiosis and mitosis, the contribution and extent of heterochromatic histone posttranslational modifications (PTMs) remain poorly defined. Here, we gained novel functional insight about heterochromatic PTMs by analyzing histone H3 purified from the heterochromatic germline micronucleus of the model organism Tetrahymena thermophila. Mass spectrometric sequencing of micronuclear H3 identified H3K23 trimethylation (H3K23me3), a previously uncharacterized PTM. H3K23me3 became particularly enriched during meiotic leptotene and zygotene in germline chromatin of Tetrahymena and C. elegans. Loss of H3K23me3 in Tetrahymena through deletion of the methyltransferase Ezl3p caused mislocalization of meiosis-induced DNA double-strand breaks (DSBs) to heterochromatin, and a decrease in progeny viability. These results show that an evolutionarily conserved developmental pathway regulates H3K23me3 during meiosis, and our studies in Tetrahymena suggest this pathway may function to protect heterochromatin from DSBs. DOI:http://dx.doi.org/10.7554/eLife.02996.001 Inside the nucleus of a cell, the DNA is wound around histone proteins. This forms a structure called chromatin that allows the long DNA strands to fit inside the cell. Variations in chromatin structure also help the cell to control the functional properties of DNA. For example, a large proportion of chromatin in the cell is in the form of heterochromatin, which is very densely packed, and is associated with many roles such as gene silencing and keeping DNA intact during reproduction. Many animals and plants have two copies of each DNA molecule: one inherited from the mother, and one from the father of the organism. Reproductive cells undergo a process called recombination when they form, where the matching copies of each DNA molecule break in a number of places and rejoin to form a new ‘blend’ of their mother's and their father's DNA, which is passed on to their own offspring. In contrast, most heterochromatin is inherited without recombining, preserving it in an unaltered form. This is important since recombination in heterochromatin can create genetic abnormalities. Adding small chemical modifications—such as methyl groups—to the histone proteins at the core of the chromatin can change how the DNA is packed. However, the histone modifications that yield different chromatin structures, and the effect of these modifications, are not very well understood. Papazyan et al. have taken advantage of a distinct feature of the protozoan Tetrahymena thermophila: a single-celled organism that divides its chromatin into two different nuclei. The smaller micronuclei contain only heterochromatin, and Papazyan et al. discovered that the histone H3 protein in the micronuclei is modified by methyl groups at a specific site that had not been studied before. Furthermore, this protozoan makes more of these modifications when it reproduces. An enzyme called Ezl3p adds these methyl groups, and without this enzyme T. thermophila reproduces more slowly and has offspring that are less likely to survive and more likely to be infertile. Papazyan et al. provide evidence that these characteristics arise because the cells without the histone modification are unable to prevent DNA breaks from occurring in heterochromatin during recombination. The same histone modification also occurs when the microscopic worm Caenorhabditis elegans reproduces, suggesting that this method of DNA protection has been conserved throughout evolution. Papazyan et al. propose that the histone modification may prevent another enzyme that induces DNA breaks from accessing the heterochromatin in reproductive cells; but more work is required to support this hypothesis. These findings reveal the importance of a new histone modification during reproduction, and could provide new directions for infertility research. DOI:http://dx.doi.org/10.7554/eLife.02996.002
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Affiliation(s)
- Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ekaterina Voronina
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Balitmore, United States Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jessica R Chapman
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Teresa R Luperchio
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Tonya M Gilbert
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Elizabeth Meier
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Karen L Reddy
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Robert S Coyne
- Department of Genomic Medicine, J. Craig Venter Institute, Rockville, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, United States Department of Pathology, University of Virginia, Charlottesville, United States
| | - Yifan Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
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17
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Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD. The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3. Mol Cell Proteomics 2014; 13:2896-910. [PMID: 25106422 DOI: 10.1074/mcp.m114.038174] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In yeast, the conserved histone acetyltransferase (HAT) Gcn5 associates with Ada2 and Ada3 to form the catalytic module of the ADA and SAGA transcriptional coactivator complexes. Gcn5 also contains an acetyl-lysine binding bromodomain that has been implicated in regulating nucleosomal acetylation in vitro, as well as at gene promoters in cells. However, the contribution of the Gcn5 bromodomain in regulating site specificity of HAT activity remains unclear. Here, we used a combined acid-urea gel and quantitative mass spectrometry approach to compare the HAT activity of wild-type and Gcn5 bromodomain-mutant ADA subcomplexes (Gcn5-Ada2-Ada3). Wild-type ADA subcomplex acetylated H3 lysines with the following specificity; H3K14 > H3K23 > H3K9 ≈ H3K18 > H3K27 > H3K36. However, when the Gcn5 bromodomain was defective in acetyl-lysine binding, the ADA subcomplex demonstrated altered site-specific acetylation on free and nucleosomal H3, with H3K18ac being the most severely diminished. H3K18ac was also severely diminished on H3K14R, but not H3K23R, substrates in wild-type HAT reactions, further suggesting that Gcn5-catalyzed acetylation of H3K14 and bromodomain binding to H3K14ac are important steps preceding H3K18ac. In sum, this work details a previously uncharacterized cross-talk between the Gcn5 bromodomain "reader" function and enzymatic HAT activity that might ultimately affect gene expression. Future studies of how mutations in bromodomains or other histone post-translational modification readers can affect chromatin-templated enzymatic activities will yield unprecedented insight into a potential "histone/epigenetic code." MS data are available via ProteomeXchange with identifier PXD001167.
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Affiliation(s)
- Anne M Cieniewicz
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Linley Moreland
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Alison E Ringel
- ‖Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; **Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Samuel G Mackintosh
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Ana Raman
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Tonya M Gilbert
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Cynthia Wolberger
- §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ‖Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; **Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Alan J Tackett
- ¶Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205;
| | - Sean D Taverna
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
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18
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Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BCR, Wade H, Tackett AJ, Strahl BD, Taverna SD. A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. Mol Cell Proteomics 2014; 13:2883-95. [PMID: 25104842 DOI: 10.1074/mcp.m114.038224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical binding assays, and genetic analyses to classify NuA3 into two functionally distinct forms: NuA3a and NuA3b. Although NuA3a uses the PHD finger of Yng1 to interact with H3K4me3 at the 5'-end of open reading frames, NuA3b contains the unique member, Pdp3, which regulates an interaction between NuA3b and H3K36me3 at the transcribed regions of genes through its PWWP domain. We find that deletion of PDP3 decreases NuA3-directed transcription and results in growth defects when combined with transcription elongation mutants, suggesting NuA3b acts as a positive elongation factor. Finally, we determine that NuA3a, but not NuA3b, is synthetically lethal in combination with a deletion of the histone acetyltransferase GCN5, indicating NuA3b has a specialized role at coding regions that is independent of Gcn5 activity. Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156.
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Affiliation(s)
- Tonya M Gilbert
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Stephen L McDaniel
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Stephanie D Byrum
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Jessica A Cades
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Blair C R Dancy
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Herschel Wade
- **Department of Biophysics and Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Alan J Tackett
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Brian D Strahl
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599; ‡‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Sean D Taverna
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
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19
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Prusevich P, Kalin JH, Ming SA, Basso M, Givens J, Li X, Hu J, Taylor MS, Cieniewicz AM, Hsiao PY, Huang R, Roberson H, Adejola N, Avery LB, Casero RA, Taverna SD, Qian J, Tackett AJ, Ratan RR, McDonald OG, Feinberg AP, Cole PA. A selective phenelzine analogue inhibitor of histone demethylase LSD1. ACS Chem Biol 2014; 9:1284-93. [PMID: 24707965 PMCID: PMC4076021 DOI: 10.1021/cb500018s] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Lysine-specific
demethylase 1 (LSD1) is an epigenetic enzyme that
oxidatively cleaves methyl groups from monomethyl and dimethyl Lys4
of histone H3 (H3K4Me1, H3K4Me2) and can contribute to gene silencing.
This study describes the design and synthesis of analogues of a monoamine
oxidase antidepressant, phenelzine, and their LSD1 inhibitory properties.
A novel phenelzine analogue (bizine) containing a phenyl-butyrylamide
appendage was shown to be a potent LSD1 inhibitor in vitro and was selective versus monoamine oxidases A/B and the LSD1 homologue,
LSD2. Bizine was found to be effective at modulating bulk histone
methylation in cancer cells, and ChIP-seq experiments revealed a statistically
significant overlap in the H3K4 methylation pattern of genes affected
by bizine and those altered in LSD1–/– cells. Treatment
of two cancer cell lines, LNCaP and H460, with bizine conferred a
reduction in proliferation rate, and bizine showed additive to synergistic
effects on cell growth when used in combination with two out of five
HDAC inhibitors tested. Moreover, neurons exposed to oxidative stress
were protected by the presence of bizine, suggesting potential applications
in neurodegenerative disease.
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Affiliation(s)
| | | | | | - Manuela Basso
- Burke
Medical Research Institute, Departments of Neurology and Neuroscience, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Jeffrey Givens
- Department
of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rajiv R. Ratan
- Burke
Medical Research Institute, Departments of Neurology and Neuroscience, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Oliver G. McDonald
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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20
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Abstract
Here, we describe an approach to isolate native chromatin sections without genomic engineering for label-free proteomic identification of associated proteins and histone post-translational modifications. A transcription activator-like (TAL) protein A fusion protein was designed to recognize a unique site in the yeast GAL1 promoter. The TAL-PrA fusion enabled chromatin affinity purification (ChAP) of a small section of native chromatin upstream from the GAL1 locus, permitting mass spectrometric (MS) identification of proteins and histone post-translational modifications regulating galactose-induced transcription. This TAL-ChAP-MS approach allows the biochemical isolation of a specific native genomic locus for proteomic studies and will provide for unprecedented objective insight into protein and epigenetic mechanisms regulating site-specific chromosome metabolism.
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Affiliation(s)
- Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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21
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Yan G, Eller MS, Elm C, Larocca CA, Ryu B, Panova IP, Dancy BM, Bowers EM, Meyers D, Lareau L, Cole PA, Taverna SD, Alani RM. Selective inhibition of p300 HAT blocks cell cycle progression, induces cellular senescence, and inhibits the DNA damage response in melanoma cells. J Invest Dermatol 2013; 133:2444-2452. [PMID: 23698071 PMCID: PMC4380234 DOI: 10.1038/jid.2013.187] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 03/08/2013] [Accepted: 03/21/2013] [Indexed: 01/04/2023]
Abstract
Epigenetic events, including covalent post-translational modifications of histones, have been demonstrated to have critical roles in tumor development and progression. The transcriptional coactivator p300/CBP possesses both histone acetyltransferase (HAT) activity and scaffolding properties that directly influence the transcriptional activation of targeted genes. We have used a potent and specific inhibitor of p300/CBP HAT activity, C646, in order to evaluate the functional contributions of p300/CBP HAT to tumor development and progression. Here we report that C646 inhibits the growth of human melanoma and other tumor cells and promotes cellular senescence. Global assessment of the p300 HAT transcriptome in human melanoma identified functional roles in promoting cell cycle progression, chromatin assembly, and activation of DNA repair pathways through direct transcriptional regulatory mechanisms. In addition, C646 is shown to promote sensitivity to DNA damaging agents, leading to the enhanced apoptosis of melanoma cells after combination treatment with cisplatin. Together, our data suggest that p300 HAT activity mediates critical growth regulatory pathways in tumor cells and may serve as a potential therapeutic target for melanoma and other malignancies by promoting cellular responses to DNA damaging agents that are currently ineffective against specific cancers.
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Affiliation(s)
- Gai Yan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark S Eller
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Courtney Elm
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cecilia A Larocca
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Byungwoo Ryu
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Izabela P Panova
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Beverley M Dancy
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erin M Bowers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lisa Lareau
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Rhoda M Alani
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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22
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Papazvan R, Voronina E, Chapman JR, Gilbert TM, Meier E, Shabanowitz J, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3 at lysine 23 in meiotic heterochromatin. Epigenetics Chromatin 2013. [PMCID: PMC3600677 DOI: 10.1186/1756-8935-6-s1-o13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Dancy BCR, Ming SA, Papazyan R, Jelinek CA, Majumdar A, Sun Y, Dancy BM, Drury WJ, Cotter RJ, Taverna SD, Cole PA. Azalysine analogues as probes for protein lysine deacetylation and demethylation. J Am Chem Soc 2012; 134:5138-48. [PMID: 22352831 PMCID: PMC3313494 DOI: 10.1021/ja209574z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reversible lysine acetylation and methylation regulate the function of a wide variety of proteins, including histones. Here, we have synthesized azalysine-containing peptides in acetylated and unacetylated forms as chemical probes of the histone deacetylases (HDAC8, Sir2Tm, and SIRT1) and the histone demethylase, LSD1. We have shown that the acetyl-azalysine modification is a fairly efficient substrate for the sirtuins, but a weaker substrate for HDAC8, a classical HDAC. In addition to deacetylation by sirtuins, the acetyl-azalysine analogue generates a novel ADP-ribose adduct that was characterized by mass spectrometry, Western blot analysis, and nuclear magnetic resonance spectroscopy. This peptide-ADP-ribose adduct is proposed to correspond to a derailed reaction intermediate, providing unique evidence for the direct 2'-hydroxyl attack on the O-alkylimidate intermediate that is formed in the course of sirtuin catalyzed deacetylation. An unacetylated azalysine-containing H3 peptide proved to be a potent inhibitor of the LSD1 demethylase, forming an FAD adduct characteristic of previously reported related structures, providing a new chemical probe for mechanistic analysis.
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Affiliation(s)
| | | | | | | | - Ananya Majumdar
- The Johns Hopkins Biomolecular NMR Center, Johns Hopkins University, Baltimore, MD 21218
| | | | | | | | | | | | - Philip A. Cole
- Corresponding Author: Philip A. Cole, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N. Wolfe St, 316 Hunterian Building, Baltimore, MD 21205, Tel: 410-614-8849/614-0540, Fax: 410-955-3023,
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24
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Li R, Zhu J, Xie Z, Liao G, Liu J, Chen MR, Hu S, Woodard C, Lin J, Taverna SD, Desai P, Ambinder RF, Hayward GS, Qian J, Zhu H, Hayward SD. Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe 2012; 10:390-400. [PMID: 22018239 DOI: 10.1016/j.chom.2011.08.013] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/25/2011] [Accepted: 08/26/2011] [Indexed: 11/25/2022]
Abstract
Herpesviruses, which are major human pathogens, establish life-long persistent infections. Although the α, β, and γ herpesviruses infect different tissues and cause distinct diseases, they each encode a conserved serine/threonine kinase that is critical for virus replication and spread. The extent of substrate conservation and the key common cell-signaling pathways targeted by these kinases are unknown. Using a human protein microarray high-throughput approach, we identify shared substrates of the conserved kinases from herpes simplex virus, human cytomegalovirus, Epstein-Barr virus (EBV), and Kaposi's sarcoma-associated herpesvirus. DNA damage response (DDR) proteins were statistically enriched, and the histone acetyltransferase TIP60, an upstream regulator of the DDR pathway, was required for efficient herpesvirus replication. During EBV replication, TIP60 activation by the BGLF4 kinase triggers EBV-induced DDR and also mediates induction of viral lytic gene expression. Identification of key cellular targets of the conserved herpesvirus kinases will facilitate the development of broadly effective antiviral strategies.
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Affiliation(s)
- Renfeng Li
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
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25
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Byrum SD, Taverna SD, Tackett AJ. Quantitative analysis of histone exchange for transcriptionally active chromatin. J Clin Bioinforma 2011; 1:17. [PMID: 21884633 PMCID: PMC3164610 DOI: 10.1186/2043-9113-1-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 07/07/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Genome-wide studies use techniques, like chromatin immunoprecipitation, to purify small chromatin sections so that protein-protein and protein-DNA interactions can be analyzed for their roles in modulating gene transcription. Histone post-translational modifications (PTMs) are key regulators of gene transcription and are therefore prime targets for these types of studies. Chromatin purification protocols vary in the amount of chemical cross-linking used to preserve in vivo interactions. A balanced level of chemical cross-linking is required to preserve the native chromatin state during purification, while still allowing for solubility and interaction with affinity reagents. FINDINGS We previously used an isotopic labeling technique combining affinity purification and mass spectrometry called transient isotopic differentiation of interactions as random or targeted (transient I-DIRT) to identify the amounts of chemical cross-linking required to prevent histone exchange during chromatin purification. New bioinformatic analyses reported here reveal that histones containing transcription activating PTMs exchange more rapidly relative to bulk histones and therefore require a higher level of cross-linking to preserve the in vivo chromatin structure. CONCLUSIONS The bioinformatic approach described here is widely applicable to other studies requiring the analysis and purification of cognate histones and their modifications. Histones containing PTMs correlated to active gene transcription exchange more readily than bulk histones; therefore, it is necessary to use more rigorous in vivo chemical cross-linking to stabilize these marks during chromatin purification.
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Affiliation(s)
- Stephanie D Byrum
- University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Sean D Taverna
- Johns Hopkins School of Medicine, 855 North Wolfe Street, Baltimore, Maryland 21205, USA
| | - Alan J Tackett
- University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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26
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Blair LP, Avaritt NL, Huang R, Cole PA, Taverna SD, Tackett AJ. MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity. Epigenetics 2011; 6:490-9. [PMID: 21273814 DOI: 10.4161/epi.6.4.14531] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In eukaryotes, DNA is wrapped around proteins called histones and is condensed into chromatin. Post-translational modification of histones can result in changes in gene expression. One of the most well-studied histone modifications is the methylation of lysine 4 on histone H3 (H3K4). This residue can be mono-, di- or tri-methylated and these varying methylation states have been associated with different levels of gene expression. Understanding exactly what the purpose of these methylation states is, in terms of gene expression, has been a topic of much research in recent years. Enzymes that can add (methyltransferases) and remove (demethylases) these modifications are of particular interest. The first demethylase discovered, LSD1, is the most well-classified and has been implicated in contributing to human cancers and to DNA damage response pathways. Currently, there are limited methods for accurately studying the activity of demethylases in vitro or in vivo. In this work, we present MassSQUIRM (mass spectrometric quantitation using isotopic reductive methylation), a quantitative method for studying the activity of demethylases capable of removing mono- and di-methyl marks from lysine residues. We focus specifically on LSD1 due to its potential as a prime therapeutic target for human disease. This quantitative approach will enable better characterization of the activity of LSD1 and other chromatin modifying enzymes in vitro, in vivo or in response to inhibitors.
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Affiliation(s)
- Lauren P Blair
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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27
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Byrum S, Mackintosh SG, Edmondson RD, Cheung WL, Taverna SD, Tackett AJ. Analysis of Histone Exchange during Chromatin Purification. ACTA ACUST UNITED AC 2011; 1:61-65. [PMID: 21709819 DOI: 10.5584/jiomics.v1i1.26] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Central to the study of chromosome biology are techniques that permit the purification of small chromatin sections for analysis of associated DNA and proteins, including histones. Chromatin purification protocols vary greatly in the extent of chemical cross-linking used to prevent protein dissociation/re-association during isolation. Particularly for genome-wide analyses, chromatin purification requires a balanced level of fixation that captures native protein-protein and protein/DNA interactions, yet leaving chromatin sections soluble and accessible to affinity reagents. We have applied a relative quantification methodology called I-DIRT (isotopic differentiation of interactions as random or targeted) for optimizing levels of chemical cross-linking for affinity purification of cognate chromatin sections. We show that fine-tuning of chemical cross-linking is necessary for isolation of chromatin sections when minimal histone/protein exchange is required.
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Affiliation(s)
- Stephanie Byrum
- University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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28
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Smart SK, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Mapping the local protein interactome of the NuA3 histone acetyltransferase. Protein Sci 2009; 18:1987-97. [PMID: 19621382 DOI: 10.1002/pro.212] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein-protein interactions modulate cellular functions ranging from the activity of enzymes to signal transduction cascades. A technology termed transient isotopic differentiation of interactions as random or targeted (transient I-DIRT) is described for the identification of stable and transient protein-protein interactions in vivo. The procedure combines mild in vivo chemical cross-linking and non-stringent affinity purification to isolate low abundance chromatin-associated protein complexes. Using isotopic labeling and mass spectrometric readout, purified proteins are categorized with respect to the protein 'bait' as stable, transient, or contaminant. Here we characterize the local interactome of the chromatin-associated NuA3 histone lysine-acetyltransferase protein complex. We describe transient associations with the yFACT nucleosome assembly complex, RSC chromatin remodeling complex and a nucleosome assembly protein. These novel, physical associations with yFACT, RSC, and Nap1 provide insight into the mechanism of NuA3-associated transcription and chromatin regulation.
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Affiliation(s)
- Sherri K Smart
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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29
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Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF, Allis CD. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev 2007; 21:1530-45. [PMID: 17575054 PMCID: PMC1891430 DOI: 10.1101/gad.1544207] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 05/01/2007] [Indexed: 01/17/2023]
Abstract
Methylated H3K27 is an important mark for Polycomb group (PcG) protein-mediated transcriptional gene silencing (TGS) in multicellular eukaryotes. Here a Drosophila E(z) homolog, EZL1, is characterized in the ciliated protozoan Tetrahymena thermophila and is shown to be responsible for H3K27 methylation associated with developmentally regulated heterochromatin formation and DNA elimination. Importantly, Ezl1p-catalyzed H3K27 methylation occurs in an RNA interference (RNAi)-dependent manner. H3K27 methylation also regulates H3K9 methylation in these processes. Furthermore, an "effector" of programmed DNA elimination, the chromodomain protein Pdd1p, is shown to bind both K27- and K9-methylated H3. These studies provide a framework for an RNAi-dependent, Polycomb group protein-mediated heterochromatin formation pathway in Tetrahymena and underscore the connection between the two highly conserved machineries in eukaryotes.
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Affiliation(s)
- Yifan Liu
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Sean D. Taverna
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
| | - Tara L. Muratore
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virgina 22904, USA
- Department of Pathology, Health Science Center, University of Virginia, Charlottesville, Virginia 22908, USA
| | - C. David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
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Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF, Allis CD. Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci U S A 2007; 104:2086-91. [PMID: 17284592 PMCID: PMC1892956 DOI: 10.1073/pnas.0610993104] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Individual posttranslational modifications (PTMs) on histones have well established roles in certain biological processes, notably transcriptional programming. Recent genomewide studies describe patterns of covalent modifications, such as H3 methylation and acetylation at promoters of specific target genes, or "bivalent domains," in stem cells, suggestive of a possible combinatorial interplay between PTMs on the same histone. However, detection of long-range PTM associations is often problematic in antibody-based or traditional mass spectrometric-based analyses. Here, histone H3 from a ciliate model was analyzed as an enriched source of transcriptionally active chromatin. Using a recently developed mass spectrometric approach, combinatorial modification states on single, long N-terminal H3 fragments (residues 1-50) were determined. The entire modification status of intact N termini was obtained and indicated correlations between K4 methylation and H3 acetylation. In addition, K4 and K27 methylation were identified concurrently on one H3 species. This methodology is applicable to other histones and larger polypeptides and will likely be a valuable tool in understanding the roles of combinatorial patterns of PTMs.
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Affiliation(s)
| | | | - Yifan Liu
- Laboratories of *Chromatin Biology and
| | - Alan J. Tackett
- Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10021
| | | | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904; and
| | - Brian T. Chait
- Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10021
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904; and
- Department of Pathology, Health Sciences Center, University of Virginia, Charlottesville, VA 22908
- **To whom correspondence may be addressed: E-mail:
or
| | - C. David Allis
- Laboratories of *Chromatin Biology and
- **To whom correspondence may be addressed: E-mail:
or
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Song X, Gjoneska E, Ren Q, Taverna SD, Allis CD, Gorovsky MA. Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol 2007; 27:2648-60. [PMID: 17242195 PMCID: PMC1899910 DOI: 10.1128/mcb.01910-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Phosphorylation of the C terminus SQ motif that defines H2A.X variants is required for efficient DNA double-strand break (DSB) repair in diverse organisms but has not been studied in ciliated protozoa. Tetrahymena H2A.X is one of two similarly expressed major H2As, thereby differing both from mammals, where H2A.X is a quantitatively minor component, and from Saccharomyces cerevisiae where it is the only type of major H2A. Tetrahymena H2A.X is phosphorylated in the SQ motif in both the mitotic micronucleus and the amitotic macronucleus in response to DSBs induced by chemical agents and in the micronucleus during prophase of meiosis, which occurs in the absence of a synaptonemal complex. H2A.X is phosphorylated when programmed DNA rearrangements occur in developing macronuclei, as for immunoglobulin gene rearrangements in mammals, but not during the DNA fragmentation that accompanies breakdown of the parental macronucleus during conjugation, correcting the previous interpretation that this process is apoptosis-like. Using strains containing a mutated (S134A) SQ motif, we demonstrate that phosphorylation of this motif is important for Tetrahymena cells to recover from exogenous DNA damage and is required for normal micronuclear meiosis and mitosis and, to a lesser extent, for normal amitotic macronuclear division; its absence, while not lethal, leads to the accumulation of DSBs in both micro- and macronuclei. These results demonstrate multiple roles of H2A.X phosphorylation in maintaining genomic integrity in different phases of the Tetrahymena life cycle.
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Affiliation(s)
- Xiaoyuan Song
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 2007; 24:785-796. [PMID: 17157260 PMCID: PMC4690528 DOI: 10.1016/j.molcel.2006.10.026] [Citation(s) in RCA: 233] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/22/2006] [Accepted: 10/19/2006] [Indexed: 12/31/2022]
Abstract
Posttranslational histone modifications participate in modulating the structure and function of chromatin. Promoters of transcribed genes are enriched with K4 trimethylation and hyperacetylation on the N-terminal tail of histone H3. Recently, PHD finger proteins, like Yng1 in the NuA3 HAT complex, were shown to interact with H3K4me3, indicating a biochemical link between K4 methylation and hyperacetylation. By using a combination of mass spectrometry, biochemistry, and NMR, we detail the Yng1 PHD-H3K4me3 interaction and the importance of NuA3-dependent acetylation at K14. Furthermore, genome-wide ChIP-Chip analysis demonstrates colocalization of Yng1 and H3K4me3 in vivo. Disrupting the K4me3 binding of Yng1 altered K14ac and transcription at certain genes, thereby demonstrating direct in vivo evidence of sequential trimethyl binding, acetyltransferase activity, and gene regulation by NuA3. Our data support a general mechanism of transcriptional control through which histone acetylation upstream of gene activation is promoted partially through availability of H3K4me3, "read" by binding modules in select subunits.
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Affiliation(s)
- Sean D Taverna
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Serge Ilin
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Jason C Tanny
- Laboratory of Chromatin Biology, The Rockefeller University
| | - Heather Lavender
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Haitao Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Lindsey Baker
- Laboratory of Chromatin Biology, The Rockefeller University
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington 98103
| | - Lauren P Blair
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | | | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University.
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Barber CM, Turner FB, Wang Y, Hagstrom K, Taverna SD, Mollah S, Ueberheide B, Meyer BJ, Hunt DF, Cheung P, Allis CD. The enhancement of histone H4 and H2A serine 1 phosphorylation during mitosis and S-phase is evolutionarily conserved. Chromosoma 2004; 112:360-71. [PMID: 15133681 DOI: 10.1007/s00412-004-0281-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 03/08/2004] [Accepted: 03/19/2004] [Indexed: 10/26/2022]
Abstract
Histone phosphorylation has long been associated with condensed mitotic chromatin; however, the functional roles of these modifications are not yet understood. Histones H1 and H3 are highly phosphorylated from late G2 through telophase in many organisms, and have been implicated in chromatin condensation and sister chromatid segregation. However, mutational analyses in yeast and biochemical experiments with Xenopus extracts have demonstrated that phosphorylation of H1 and H3 is not essential for such processes. In this study, we investigated additional histone phosphorylation events that may have redundant functions to H1 and H3 phosphorylation during mitosis. We developed an antibody to H4 and H2A that are phosphorylated at their respective serine 1 (S1) residues and found that H4S1/H2AS1 are highly phosphorylated in the mitotic chromatin of worm, fly, and mammals. Mitotic H4/H2A phosphorylation has similar timing and localization as H3 phosphorylation, and closely correlates with the chromatin condensation events during mitosis. We also detected a lower level of H4/H2A phosphorylation in 5-bromo-2-deoxyuridine-positive S-phase cells, which corroborates earlier studies that identified H4S1 phosphorylation on newly synthesized histones during S-phase. The evolutionarily conserved phosphorylation of H4/H2A during the cell cycle suggests that they may have a dual purpose in chromatin condensation during mitosis and histone deposition during S-phase.
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Affiliation(s)
- Cynthia M Barber
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
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Morshead KB, Ciccone DN, Taverna SD, Allis CD, Oettinger MA. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc Natl Acad Sci U S A 2003; 100:11577-82. [PMID: 14500909 PMCID: PMC208800 DOI: 10.1073/pnas.1932643100] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Indexed: 11/18/2022] Open
Abstract
In the earliest stages of antigen receptor assembly, D and J segments of the Ig heavy chain and T cell receptor beta loci are recombined in B and T cells, respectively, whereas the V segments are not. Distinct distribution patterns of various histone modifications and the nucleosome-remodeling factor BRG1 are found at "active" (DJ) and "inactive" (V) regions. Striking "hotspots" of histone H3 dimethylated at lysine 4 (di-Me H3-K4) are localized at the ends of the active DJ domains of both the Ig heavy chain and T cell receptor beta loci. BRG1 is not localized to specific sequences, as it is with transcriptional initiation, but rather associates with the entire active locus in a pattern that mirrors acetylation of histone H3. Within some inactive loci marked by H3-K9 dimethylation, two distinct levels of methylation are found in a nonrandom gene-segment-specific pattern. We suggest that the hotspots of di-Me H3-K4 are important marks for locus accessibility. The specific patterns of modification imply that the regulation of V(D)J recombination involves recruitment of specific methyltransferases in a localized manner.
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Affiliation(s)
- Katrina B Morshead
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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Abstract
Histone H3 lysine 9 methylation [Me(Lys9)H3] is an epigenetic mark for heterochromatin-dependent gene silencing, mediated by direct binding to chromodomain-containing proteins such as Heterochromatin Protein 1. In the ciliate Tetrahymena, two chromodomain proteins, Pdd1p and Pdd3p, are involved in the massive programmed DNA elimination that accompanies macronuclear development. We report that both proteins bind H3(Lys9)Me in vitro. In vivo, H3(Lys9)Me is confined to the time period and location where DNA elimination occurs, and associates with eliminated sequences. Loss of parental Pdd1p expression drastically reduces H3(Lys9)Me. Finally, tethering Pdd1p is sufficient to promote DNA excision. These results extend the range of H3(Lys9)Me involvement in chromatin activities outside transcriptional regulation and also strengthen the link between heterochromatin formation and programmed DNA elimination.
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Affiliation(s)
- Sean D Taverna
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
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Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis C, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 2001; 20:5232-41. [PMID: 11566886 PMCID: PMC125272 DOI: 10.1093/emboj/20.18.5232] [Citation(s) in RCA: 315] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent studies show that heterochromatin-associated protein-1 (HP1) recognizes a 'histone code' involving methylated Lys9 (methyl-K9) in histone H3. Using in situ immunofluorescence, we demonstrate that methyl-K9 H3 and HP1 co-localize to the heterochromatic regions of Drosophila polytene chromosomes. NMR spectra show that methyl-K9 binding of HP1 occurs via its chromo (chromosome organization modifier) domain. This interaction requires methyl-K9 to reside within the proper context of H3 sequence. NMR studies indicate that the methylated H3 tail binds in a groove of HP1 consisting of conserved residues. Using fluorescence anisotropy and isothermal titration calorimetry, we determined that this interaction occurs with a K(D) of approximately 100 microM, with the binding enthalpically driven. A V26M mutation in HP1, which disrupts its gene silencing function, severely destabilizes the H3-binding interface, and abolishes methyl-K9 H3 tail binding. Finally, we note that sequence diversity in chromo domains may lead to diverse functions in eukaryotic gene regulation. For example, the chromo domain of the yeast histone acetyltransferase Esa1 does not interact with methyl- K9 H3, but instead shows preference for unmodified H3 tail.
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Affiliation(s)
| | | | | | | | | | - Joel C. Eissenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908 and
Edward A.Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA Corresponding author e-mail:
S.A.Jacobs and S.D.Taverna contributed equally to this work
| | | | - Sepideh Khorasanizadeh
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908 and
Edward A.Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA Corresponding author e-mail:
S.A.Jacobs and S.D.Taverna contributed equally to this work
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