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Randle RK, Amara VR, Popik W. IFI16 Is Indispensable for Promoting HIF-1α-Mediated APOL1 Expression in Human Podocytes under Hypoxic Conditions. Int J Mol Sci 2024; 25:3324. [PMID: 38542298 PMCID: PMC10970439 DOI: 10.3390/ijms25063324] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Genetic variants in the protein-coding regions of APOL1 are associated with an increased risk and progression of chronic kidney disease (CKD) in African Americans. Hypoxia exacerbates CKD progression by stabilizing HIF-1α, which induces APOL1 transcription in kidney podocytes. However, the contribution of additional mediators to regulating APOL1 expression under hypoxia in podocytes is unknown. Here, we report that a transient accumulation of HIF-1α in hypoxia is sufficient to upregulate APOL1 expression in podocytes through a cGAS/STING/IRF3-independent pathway. Notably, IFI16 ablation impedes hypoxia-driven APOL1 expression despite the nuclear accumulation of HIF-1α. Co-immunoprecipitation assays indicate no direct interaction between IFI16 and HIF-1α. Our studies identify hypoxia response elements (HREs) in the APOL1 gene enhancer/promoter region, showing increased HIF-1α binding to HREs located in the APOL1 gene enhancer. Luciferase reporter assays confirm the role of these HREs in transcriptional activation. Chromatin immunoprecipitation (ChIP)-qPCR assays demonstrate that IFI16 is not recruited to HREs, and IFI16 deletion reduces HIF-1α binding to APOL1 HREs. RT-qPCR analysis indicates that IFI16 selectively affects APOL1 expression, with a negligible impact on other hypoxia-responsive genes in podocytes. These findings highlight the unique contribution of IFI16 to hypoxia-driven APOL1 gene expression and suggest alternative IFI16-dependent mechanisms regulating APOL1 gene expression under hypoxic conditions.
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Affiliation(s)
- Richaundra K. Randle
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA;
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
| | - Venkateswara Rao Amara
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur 844102, Bihar, India
| | - Waldemar Popik
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
- Department of Internal Medicine, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA
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2
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Gussakovsky D, Booy EP, Brown MJF, McKenna SA. Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression. RNA 2023; 29:1185-1200. [PMID: 37156570 PMCID: PMC10351891 DOI: 10.1261/rna.079649.123] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
The SRP9/SRP14 heterodimer is a central component of signal recognition particle (SRP) RNA (7SL) processing and Alu retrotransposition. In this study, we sought to establish the role of nuclear SRP9/SRP14 in the transcriptional regulation of 7SL and BC200 RNA. 7SL and BC200 RNA steady-state levels, rate of decay, and transcriptional activity were evaluated under SRP9/SRP14 knockdown conditions. Immunofluorescent imaging, and subcellular fractionation of MCF-7 cells, revealed a distinct nuclear localization for SRP9/SRP14. The relationship between this localization and transcriptional activity at 7SL and BC200 genes was also examined. These findings demonstrate a novel nuclear function of SRP9/SRP14 establishing that this heterodimer transcriptionally regulates 7SL and BC200 RNA expression. We describe a model in which SRP9/SRP14 cotranscriptionally regulate 7SL and BC200 RNA expression. Our model is also a plausible pathway for regulating Alu RNA transcription and is consistent with the hypothesized roles of SRP9/SRP14 transporting 7SL RNA into the nucleolus for posttranscriptional processing, and trafficking of Alu RNA for retrotransposition.
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Affiliation(s)
- Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mira J F Brown
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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3
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Takamatsu N, Shirahata Y, Seki K, Nakamaru E, Ito M, Tsukamoto D. Heat shock factor 1 induces a short burst of transcription of the clock gene Per2 during interbout arousal in mammalian hibernation. J Biol Chem 2023; 299:104576. [PMID: 36871756 PMCID: PMC10060108 DOI: 10.1016/j.jbc.2023.104576] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
During winter hibernation, a diverse range of small mammals can enter prolonged torpor. They spend the non-hibernation season as a homeotherm, but the hibernation season as a heterotherm. In the hibernation season, chipmunks (Tamias asiaticus) cycle regularly between 5-6 day long deep torpor with a body temperature (Tb) of 5-7 ºC and interbout arousal of ∼ 20 h, during which, their Tb returns to the normothermic level. Here, we investigated Per2 expression in the liver to elucidate the regulation of the peripheral circadian clock in a mammalian hibernator. In the non-hibernation season, as in mice, heat shock factor 1 (HSF1), activated by elevated Tb during the wake period, activated Per2 transcription in the liver, which contributed to synchronizing the peripheral circadian clock to the Tb rhythm. In the hibernation season, we determined that the Per2 mRNA was at low levels during deep torpor, but Per2 transcription was transiently activated by HSF1, which was activated by elevated Tb during interbout arousal. Nevertheless, we found that the mRNA from the core clock gene Bmal1 exhibited arrhythmic expression during interbout arousal. Since circadian rhythmicity is dependent on negative feedback loops involving the clock genes, these results suggest that the peripheral circadian clock in the liver is nonfunctional in the hibernation season.
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Affiliation(s)
- Nobuhiko Takamatsu
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan.
| | - Yuiho Shirahata
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
| | - Kota Seki
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
| | - Erina Nakamaru
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
| | - Michihiko Ito
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
| | - Daisuke Tsukamoto
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara-shi, Kanagawa 252-0373, Japan
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4
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Amatori S, Fanelli M. The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues. Int J Mol Sci 2022; 23:1103. [PMID: 35163027 DOI: 10.3390/ijms23031103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer cells accumulate epigenomic aberrations that contribute to cancer initiation and progression by altering both the genomic stability and the expression of genes. The awareness of such alterations could improve our understanding of cancer dynamics and the identification of new therapeutic strategies and biomarkers to refine tumor classification and treatment. Formalin fixation and paraffin embedding (FFPE) is the gold standard to preserve both tissue integrity and organization, and, in the last decades, a huge number of biological samples have been archived all over the world following this procedure. Recently, new chromatin immunoprecipitation (ChIP) techniques have been developed to allow the analysis of histone post-translational modifications (PTMs) and transcription factor (TF) distribution in FFPE tissues. The application of ChIP to genome-wide chromatin studies using real archival samples represents an unprecedented opportunity to conduct retrospective clinical studies thanks to the possibility of accessing large cohorts of samples and their associated diagnostic records. However, although recent attempts to standardize have been made, fixation and storage conditions of clinical specimens are still extremely variable and can affect the success of chromatin studies. The procedures introduced in the last few years dealt with this problem proponing successful strategies to obtain high-resolution ChIP profiles from FFPE archival samples. In this review, we compare the different FFPE-ChIP techniques, highlighting their strengths, limitations, common features, and peculiarities, as well as pitfalls and caveats related to ChIP studies in FFPE samples, in order to facilitate their application.
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5
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Bilodeau S, Kurat CF, Lambert JP. Editorial: The Evolving Chromatin and Transcriptional Landscapes-Emerging Methods, Tools and Techniques. Front Cell Dev Biol 2021; 9:782776. [PMID: 34790670 PMCID: PMC8591211 DOI: 10.3389/fcell.2021.782776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, QC, Canada.,Centre de Recherche sur le Cancer de L'Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives de L'Université Laval, Québec, QC, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Christoph Franz Kurat
- Molecular Biology Division, Biomedical Center Munich, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jean-Philippe Lambert
- Centre de Recherche sur le Cancer de L'Université Laval, Québec, QC, Canada.,Centre de Recherche en Données Massives de L'Université Laval, Québec, QC, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, QC, Canada.,Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada
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6
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Khan N, Shahid S, Asif AR. Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome). Molecules 2021; 26:6694. [PMID: 34771102 DOI: 10.3390/molecules26216694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022] Open
Abstract
Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases.
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7
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Sharma M, Castro-Piedras I, Rasha F, Ramachandran S, Sennoune SR, Furr K, Almodovar S, Ganapathy V, Grisham MB, Rahman RL, Pruitt K. Dishevelled-1 DIX and PDZ domain lysine residues regulate oncogenic Wnt signaling. Oncotarget 2021; 12:2234-2251. [PMID: 34733415 PMCID: PMC8555683 DOI: 10.18632/oncotarget.28089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 11/26/2022] Open
Abstract
DVL proteins are central mediators of the Wnt pathway and relay complex input signals into different branches of the Wnt signaling network. However, molecular mechanism(s) that regulate DVL-mediated relay of Wnt signals still remains unclear. Here, for the first time, we elucidate the functional significance of three DVL-1 lysines (K/Lys) which are subject to post-translational acetylation. We demonstrate that K34 Lys residue in the DIX domain regulates subcellular localization of β-catenin, thereby influencing downstream Wnt target gene expression. Additionally, we show that K69 (DIX domain) and K285 (PDZ domain) regulate binding of DVL-1 to Wnt target gene promoters and modulate expression of Wnt target genes including CMYC, OCT4, NANOG, and CCND1, in cell line models and xenograft tumors. Finally, we report that conserved DVL-1 lysines modulate various oncogenic functions such as cell migration, proliferation, cell-cycle progression, 3D-spheroid formation and in-vivo tumor growth in breast cancer models. Collectively, these findings highlight the importance of DVL-1 domain-specific lysines which were recently shown to be acetylated and characterize their influence on Wnt signaling. These site-specific modifications may be subject to regulation by therapeutics already in clinical use (lysine deacetylase inhibitors such as Panobinostat and Vorinostat) or may possibly have prognostic utility in translational efforts that seek to modulate dysfunctional Wnt signaling.
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Affiliation(s)
- Monica Sharma
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Isabel Castro-Piedras
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Fahmida Rasha
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Sabarish Ramachandran
- Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Souad R. Sennoune
- Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kathryn Furr
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Sharilyn Almodovar
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Vadivel Ganapathy
- Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Matthew B. Grisham
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | | | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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8
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Li Y, Nakka K, Olender T, Gingras-Gelinas P, Wong MMK, Robinson DCL, Bandukwala H, Palii CG, Neyret O, Brand M, Blais A, Dilworth FJ. Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag. STAR Protoc 2021; 2:100751. [PMID: 34467227 PMCID: PMC8384913 DOI: 10.1016/j.xpro.2021.100751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/24/2022] Open
Abstract
Muscle stem cells (MuSCs) are a rare stem cell population that provides myofibers with a remarkable capacity to regenerate after tissue injury. Here, we have adapted the Cleavage Under Target and Tagmentation technology to the mapping of the chromatin landscape and transcription factor binding in 50,000 activated MuSCs isolated from injured mouse hindlimb muscles. We have applied this same approach to human CD34+ hematopoietic stem and progenitor cells. This protocol could be adapted to any rare stem cell population. For complete details on the use and execution of this protocol, please refer to Robinson et al. (2021). Isolation of muscle stem cells from cardiotoxin-injured tissue CUT&Tag-based mapping of epigenetic landscape and transcription factor enrichment Adaptation of a synthetic spike-in DNA for effective normalization across samples Pipeline for efficient analysis of CUT&Tag sequencing data hosted on Git-hub
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Affiliation(s)
- Yuefeng Li
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kiran Nakka
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Matthew Man-Kin Wong
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Daniel C L Robinson
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hina Bandukwala
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Odile Neyret
- Molecular Biology Platform, Institut de Recherche Clinique de Montreal, Montreal, QC, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Alexandre Blais
- Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,CI3, University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, ON, Canada
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, ON, Canada
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9
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Weems JC, Slaughter BD, Unruh JR, Weaver KJ, Miller BD, Delventhal KM, Conaway JW, Conaway RC. A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA polymerase II transcription. J Biol Chem 2021; 297:100862. [PMID: 34116057 PMCID: PMC8294581 DOI: 10.1016/j.jbc.2021.100862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022] Open
Abstract
The Elongin complex was originally identified as an RNA polymerase II (RNAPII) elongation factor and subsequently as the substrate recognition component of a Cullin-RING E3 ubiquitin ligase. More recent evidence indicates that the Elongin ubiquitin ligase assembles with the Cockayne syndrome B helicase (CSB) in response to DNA damage and can target stalled polymerases for ubiquitylation and removal from the genome. In this report, we present evidence that the CSB-Elongin ubiquitin ligase pathway has roles beyond the DNA damage response in the activation of RNAPII-mediated transcription. We observed that assembly of the CSB-Elongin ubiquitin ligase is induced not just by DNA damage, but also by a variety of signals that activate RNAPII-mediated transcription, including endoplasmic reticulum (ER) stress, amino acid starvation, retinoic acid, glucocorticoids, and doxycycline treatment of cells carrying several copies of a doxycycline-inducible reporter. Using glucocorticoid receptor (GR)-regulated genes as a model, we showed that glucocorticoid-induced transcription is accompanied by rapid recruitment of CSB and the Elongin ubiquitin ligase to target genes in a step that depends upon the presence of transcribing RNAPII on those genes. Consistent with the idea that the CSB-Elongin pathway plays a direct role in GR-regulated transcription, mouse cells lacking the Elongin subunit Elongin A exhibit delays in both RNAPII accumulation on and dismissal from target genes following glucocorticoid addition and withdrawal, respectively. Taken together, our findings bring to light a new role for the CSB-Elongin pathway in RNAPII-mediated transcription.
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Affiliation(s)
- Juston C Weems
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kyle J Weaver
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Brandon D Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Kym M Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA.
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10
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Akagi R, Kubo T, Hatori Y, Miyamoto T, Inouye S. Heme oxygenase-1 induction by heat shock in rat hepatoma cell line is regulated by the coordinated function of HSF1, NRF2, AND BACH1. J Biochem 2021; 170:501-510. [PMID: 34061198 DOI: 10.1093/jb/mvab065] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 11/12/2022] Open
Abstract
The mechanism of heme oxygenase-1 (HO-1) induction by heat shock (HS) loading remains unclear. Here, we investigated the contribution of transcription factors to HS-induced HO-1 expression, using a rat hepatoma cell line (H-4-II-E). Our results demonstrated that HS treatment resulted in a marked induction of HO-1. Immunohistochemical analysis showed a slight mismatch in the expression levels of HO-1 and HSP70 by HS among cells, suggesting a conflict between multiple induction mechanisms. We observed HS-induced nuclear localization of, not only phosphorylated HSF1, but also NRF2, which is a typical transcription factor activated by oxidative stress. HSF1 knockdown in H-4-II-E markedly reduced HO-1 induction by HS, while NRF2 knockdown resulted in a partial effect. The chromatin immunoprecipitation assay demonstrated that HS loading resulted in significant binding of HSF1 to the HSE in the promoter proximal region of HO-1 gene and another HSE located close to the MARE in the -4 kb upstream enhancer region 1, where NRF2 also bound, together with BACH1, a negative transcription factor of HO-1. These observations indicate that HO-1 induction by HS is mainly mediated by HSF1 binding to the proximal HSE. NRF2 binding to MARE by HS is predominantly suppressed by an increased binding of BACH1.
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Affiliation(s)
- Reiko Akagi
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153, Japan
| | - Takanori Kubo
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153, Japan
| | - Yuta Hatori
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153, Japan
| | - Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-City, Ibaraki 305-8575, Japan
| | - Sachiye Inouye
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University 1-1-1 Daigakudohri, Sanyo-onoda-shi 756-0884, Japan
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11
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Ogura K, Matsui H, Yamamoto M, Noutoshi Y, Toyoda K, Taguchi F, Ichinose Y. Vfr targets promoter of genes encoding methyl-accepting chemotaxis protein in Pseudomonas syringae pv. tabaci 6605. Biochem Biophys Rep 2021; 26:100944. [PMID: 33659714 PMCID: PMC7890371 DOI: 10.1016/j.bbrep.2021.100944] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/22/2020] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
Virulence factor regulator (Vfr) is an indispensable transcription factor in the expression of virulence in the phytopathogenic bacteria Pseudomonassyringae. However, the function of Vfr is not known so far. The deletion of vfr resulted in the loss of surface swarming motility and reduced the virulence in P. syringae pv. tabaci (Pta) 6605. In order to identify the target genes of Vfr, we screened the sequences that bind to Vfr by chromatin immune precipitation (ChIP) and sequencing methods using the closely related bacterium P. syringae pv. syringae (Pss) B728a. For this purpose we first generated a strain that possesses the recombinant gene vfr::FLAG in Pss B728a, and performed ChIP using an anti-FLAG antibody. Immunoprecipitated DNA was purified and sequenced with Illumina HiSeq. The Vfr::FLAG-specific peaks were further subjected to an electrophoresis mobility-shift assay, and the promoter regions of locus tag for Psyr_0578 , Psyr_1776, and Psyr_2237 were identified as putative target genes of Vfr. These genes encode plant pathogen–specific methyl-accepting chemotaxis proteins (Mcp). These mcp genes seem to be involved in the Vfr-regulated expression of virulence. Identification of target gene of Vfr in Pseudomonas syringae by ChIP-seq and EMSA. Vfr targets 3 methyl-accepting chemotaxis proteins (mcp) genes. Existence of putative Vfr binding sequences in the promoter of 3 mcp genes.
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Affiliation(s)
- Keisuke Ogura
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
| | - Fumiko Taguchi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan.,Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama, 700-8530, Japan
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12
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Mostafa MM, Bansal A, Michi AN, Sasse SK, Proud D, Gerber AN, Newton R. Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells. J Biol Chem 2021; 296:100065. [PMID: 33184061 PMCID: PMC7949084 DOI: 10.1074/jbc.ra120.015755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/24/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Ligand-activated glucocorticoid receptor (GR) elicits variable glucocorticoid-modulated transcriptomes in different cell types. However, some genes, including Krüppel-like factor 9 (KLF9), a putative transcriptional repressor, demonstrate conserved responses. We show that glucocorticoids induce KLF9 expression in the human airways in vivo and in differentiated human bronchial epithelial (HBE) cells grown at air-liquid interface (ALI). In A549 and BEAS-2B pulmonary epithelial cells, glucocorticoids induce KLF9 expression with similar kinetics to primary HBE cells in submersion culture. A549 and BEAS-2B ChIP-seq data reveal four common glucocorticoid-induced GR binding sites (GBSs). Two GBSs mapped to the 5'-proximal region relative to KLF9 transcription start site (TSS) and two occurred at distal sites. These were all confirmed in primary HBE cells. Global run-on (GRO) sequencing indicated robust enhancer RNA (eRNA) production from three of these GBSs in BEAS-2B cells. This was confirmed in A549 cells, plus submersion, and ALI culture of HBE cells. Cloning each GBS into luciferase reporters revealed glucocorticoid-induced activity requiring a glucocorticoid response element (GRE) within each distal GBS. While the proximal GBSs drove modest reporter induction by glucocorticoids, this region exhibited basal eRNA production, RNA polymerase II enrichment, and looping to the TSS, plausibly underlying constitutive KLF9 expression. Post glucocorticoid treatment, interactions between distal and proximal GBSs and the TSS correlated with KLF9 induction. CBP/P300 silencing reduced proximal GBS activity, but negligibly affected KLF9 expression. Overall, a model for glucocorticoid-mediated regulation of KLF9 involving multiple GBSs is depicted. This work unequivocally demonstrates that mechanistic insights gained from cell lines can translate to physiologically relevant systems.
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Affiliation(s)
- Mahmoud M Mostafa
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Akanksha Bansal
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Aubrey N Michi
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - David Proud
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robert Newton
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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13
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Stieg DC, Cooper KF, Strich R. The extent of cyclin C promoter occupancy directs changes in stress-dependent transcription. J Biol Chem 2020; 295:16280-16291. [PMID: 32934007 DOI: 10.1074/jbc.ra120.015215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 kinase module (CKM) is a detachable Mediator subunit composed of cyclin C and one each of paralogs Cdk8/Cdk19, Med12/Med12L, and Med13/Med13L. Our previous RNA-Seq studies demonstrated that cyclin C represses a subset of hydrogen peroxide-induced genes under normal conditions but is involved in activating other loci following stress. Here, we show that cyclin C directs this transcriptional reprograming through changes in its promoter occupancy. Following peroxide stress, cyclin C promoter occupancy increased for genes it activates while decreasing at loci it represses under normal conditions. Promoter occupancy of other CKM components generally mirrored cyclin C, indicating that the CKM moves as a single unit. It has previously been shown that some cyclin C leaves the nucleus following cytotoxic stress to induce mitochondrial fragmentation and apoptosis. We observed that CKM integrity appeared compromised at a subset of repressed promoters, suggesting a source of cyclin C that is targeted for nuclear release. Interestingly, mTOR inhibition induced a new pattern of cyclin C promoter occupancy indicating that this control is fine-tuned to the individual stress. Using inhibitors, we found that Cdk8 kinase activity is not required for CKM movement or repression but was necessary for full gene activation. In conclusion, this study revealed that different stress stimuli elicit specific changes in CKM promoter occupancy correlating to altered transcriptional outputs. Finally, although CKM components were recruited or expelled from promoters as a unit, heterogeneity was observed at individual promoters, suggesting a mechanism to generate gene- and stress-specific responses.
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Affiliation(s)
- David C Stieg
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Katrina F Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA
| | - Randy Strich
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey, USA.
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14
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Steinauer N, Guo C, Zhang J. The transcriptional corepressor CBFA2T3 inhibits all- trans-retinoic acid-induced myeloid gene expression and differentiation in acute myeloid leukemia. J Biol Chem 2020; 295:8887-8900. [PMID: 32434928 PMCID: PMC7335779 DOI: 10.1074/jbc.ra120.013042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/14/2020] [Revised: 05/17/2020] [Indexed: 01/10/2023] Open
Abstract
CBFA2/RUNX1 partner transcriptional co-repressor 3 (CBFA2T3, also known as MTG16 or ETO2) is a myeloid translocation gene family protein that functions as a master transcriptional corepressor in hematopoiesis. Recently, it has been shown that CBFA2T3 maintains leukemia stem cell gene expression and promotes relapse in acute myeloid leukemia (AML). However, a role for CBFA2T3 in myeloid differentiation of AML has not been reported. Here, we show that CBFA2T3 represses retinoic acid receptor (RAR) target gene expression and inhibits all-trans-retinoic acid (ATRA)-induced myeloid differentiation of AML cells. ChIP-Seq revealed that CBFA2T3 targets the RARα/RXRα cistrome in U937 AML cells, predominantly at myeloid-specific enhancers associated with terminal differentiation. CRISPR/Cas9-mediated abrogation of CBFA2T3 resulted in spontaneous and ATRA-induced activation of myeloid-specific genes in a manner correlated with myeloid differentiation. Importantly, these effects were reversed by CBFA2T3 re-expression. Mechanistic studies showed that CBFA2T3 inhibits RAR target gene transcription by acting at an early step to regulate histone acetyltransferase recruitment, histone acetylation, and chromatin accessibility at RARα target sites, independently of the downstream, RAR-mediated steps of transcription. Finally, we validated the inhibitory effect of CBFA2T3 on RAR in multiple AML subtypes and patient samples. To our knowledge, this is the first study to show that CBFA2T3 down-regulation is both necessary and sufficient for enhancing ATRA-induced myeloid gene expression and differentiation of AML cells. Our findings suggest that CBFA2T3 can serve as a potential target for enhancing AML responsiveness to ATRA differentiation therapies.
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Affiliation(s)
- Nickolas Steinauer
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Chun Guo
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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15
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Ciccone DN, Namiki Y, Chen C, Morshead KB, Wood AL, Johnston CM, Morris JW, Wang Y, Sadreyev R, Corcoran AE, Matthews AGW, Oettinger MA. The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF. J Biol Chem 2019; 294:13580-13592. [PMID: 31285261 PMCID: PMC6746451 DOI: 10.1074/jbc.ra118.007348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/28/2018] [Revised: 06/13/2019] [Indexed: 01/03/2023] Open
Abstract
Antigen receptor assembly in lymphocytes involves stringently-regulated coordination of specific DNA rearrangement events across several large chromosomal domains. Previous studies indicate that transcription factors such as paired box 5 (PAX5), Yin Yang 1 (YY1), and CCCTC-binding factor (CTCF) play a role in regulating the accessibility of the antigen receptor loci to the V(D)J recombinase, which is required for these rearrangements. To gain clues about the role of CTCF binding at the murine immunoglobulin heavy chain (IgH) locus, we utilized a computational approach that identified 144 putative CTCF-binding sites within this locus. We found that these CTCF sites share a consensus motif distinct from other CTCF sites in the mouse genome. Additionally, we could divide these CTCF sites into three categories: intergenic sites remote from any coding element, upstream sites present within 8 kb of the VH-leader exon, and recombination signal sequence (RSS)-associated sites characteristically located at a fixed distance (∼18 bp) downstream of the RSS. We noted that the intergenic and upstream sites are located in the distal portion of the VH locus, whereas the RSS-associated sites are located in the DH-proximal region. Computational analysis indicated that the prevalence of CTCF-binding sites at the IgH locus is evolutionarily conserved. In all species analyzed, these sites exhibit a striking strand-orientation bias, with >98% of the murine sites being present in one orientation with respect to VH gene transcription. Electrophoretic mobility shift and enhancer-blocking assays and ChIP–chip analysis confirmed CTCF binding to these sites both in vitro and in vivo.
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Affiliation(s)
- David N Ciccone
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yuka Namiki
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Changfeng Chen
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katrina B Morshead
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Andrew L Wood
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Colette M Johnston
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - John W Morris
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Anne E Corcoran
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Adam G W Matthews
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114.,Department of Biological Sciences and Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481
| | - Marjorie A Oettinger
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
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16
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Vo TM, Burchett R, Brun M, Monckton EA, Poon HY, Godbout R. Effects of nuclear factor I phosphorylation on calpastatin ( CAST) gene variant expression and subcellular distribution in malignant glioma cells. J Biol Chem 2019; 294:1173-1188. [PMID: 30504225 DOI: 10.1074/jbc.ra118.004787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Malignant glioma (MG) is the most lethal primary brain tumor. In addition to having inherent resistance to radiation treatment and chemotherapy, MG cells are highly infiltrative, rendering focal therapies ineffective. Genes involved in MG cell migration and glial cell differentiation are up-regulated by hypophosphorylated nuclear factor I (NFI), which is dephosphorylated by the phosphatase calcineurin in MG cells. Calcineurin is cleaved and thereby activated by calpain proteases, which are, in turn, inhibited by calpastatin (CAST). Here, we show that the CAST gene is a target of NFI and has NFI-binding sites in its intron 3 region. We also found that NFI-mediated regulation of CAST depends on NFI's phosphorylation state. We noted that occupation of CAST intron 3 by hypophosphorylated NFI results in increased activation of an alternative promoter. This activation resulted in higher levels of CAST transcript variants, leading to increased levels of CAST protein that lacks the N-terminal XL domain. CAST was primarily present in the cytoplasm of NFI-hypophosphorylated MG cells, with a predominantly perinuclear immunostaining pattern. NFI knockdown in NFI-hypophosphorylated MG cells increased CAST levels at the plasma membrane. These results suggest that NFI plays an integral role in the regulation of CAST variants and CAST subcellular distribution. Along with the previous findings indicating that NFI activity is regulated by calcineurin, these results provide a foundation for further investigations into the possibility of regulatory cross-talk between NFI and the CAST/calpain/calcineurin signaling pathway in MG cells.
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Affiliation(s)
- The Minh Vo
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Rebecca Burchett
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Miranda Brun
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Ho-Yin Poon
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada.
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17
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Liu X, Zhang W, Wu Z, Yang Y, Kang YJ. Copper levels affect targeting of hypoxia-inducible factor 1α to the promoters of hypoxia-regulated genes. J Biol Chem 2018; 293:14669-14677. [PMID: 30082314 DOI: 10.1074/jbc.ra118.001764] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/12/2018] [Indexed: 02/05/2023] Open
Abstract
Hypoxia-inducible factor 1α (HIF-1α) is a transcription factor that regulates cellular responses to hypoxia. It controls the expression of both BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 (BNIP3) and insulin-like growth factor 2 (IGF2). Previous studies have demonstrated that in hypoxia, copper is required for the expression of BNIP3 but not for that of IGF2 Here, using ChIP assays, computational analyses, luciferase reporter assays, and real-time quantitative RT-PCR, we sought to better understand how copper regulates the differential target gene selectivity of HIF-1α. Human umbilical vein endothelial cells (HUVECs) were exposed to CoCl2 or hypoxia conditions to increase HIF-1α accumulation. The binding of HIF-1α to hypoxia-responsive element (HRE) sites in the BNIP3 or IGF2 gene promoter in high- or low-copper conditions was examined. Our analyses revealed three and two potential HRE sites in the BNIP3 and IGF2 promoters, respectively. We identified that HRE (-412/-404) in the BNIP3 promoter and HRE (-354/-347) in the IGF2 promoter are the critical binding sites of HIF-1α. Tetraethelenepentamine (TEPA)-mediated reduction in copper concentration did not affect hypoxia- or CoCl2-induced HIF-1α accumulation. However, the copper reduction did suppress the binding of HIF-1α to the HRE (-412/-404) in BNIP3 but not the binding of HIF-1α to the HRE (-354/-347) in IGF2 In summary, our findings uncovered the mechanistic basis for differential HIF-1α-mediated regulation of BNIP3 and IGF2, indicating that copper regulates target gene selectivity of HIF-1α at least in part by affecting HIF-1α binding to its cognate HRE in the promoters of these two genes.
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Affiliation(s)
- Xiaojuan Liu
- From the Regenerative Medicine Research Center, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
| | - Wenjing Zhang
- From the Regenerative Medicine Research Center, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
| | - Zhijuan Wu
- From the Regenerative Medicine Research Center, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
| | - Yutao Yang
- From the Regenerative Medicine Research Center, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
| | - Y James Kang
- From the Regenerative Medicine Research Center, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
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18
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Roeh S, Weber P, Rex-Haffner M, Deussing JM, Binder EB, Jakovcevski M. Sequencing on the SOLiD 5500xl System - in-depth characterization of the GC bias. Nucleus 2017; 8:370-380. [PMID: 28448740 DOI: 10.1080/19491034.2017.1320461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 10/19/2022] Open
Abstract
Different types of sequencing biases have been described and subsequently improved for a variety of sequencing systems, mostly focusing on the widely used Illumina systems. Similar studies are missing for the SOLiD 5500xl system, a sequencer which produced many data sets available to researchers today. Describing and understanding the bias is important to accurately interpret and integrate these published data in various ongoing research projects. We report a particularly strong GC bias for this sequencing system when analyzing a defined gDNA mix of 5 microbes with a wide range of different GC contents (20-72%) when comparing to the expected distribution and Illumina MiSeq data from the same DNA pool. Since we observed this bias already under PCR-free conditions, changing the PCR conditions during library preparation - a common strategy to handle bias in the Illumina system - was not relevant. Source of the bias appeared to be an uneven heat distribution during the SOLiD emulsion PCR (ePCR) - for enrichment of libraries prior loading - since ePCR in either small pouches or in 96-well plates improved the GC bias. Sequencing of chromatin immunoprecipitated DNA (ChIP-seq) is a common approach in epigenetics. ChIP-seq of the mixed source histone mark H3K9ac (acetyl Histone H3 lysine 9), typically found on promoter regions and on gene bodies, including CpG islands, performed on a SOLiD 5500xl machine, resulted in major loss of reads at GC rich loci (GC content ≥ 62%), not explained by low sequencing depth. This was improved with adaptations of the ePCR.
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Affiliation(s)
- Simone Roeh
- a Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Munich , Germany
| | - Peter Weber
- a Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Munich , Germany
| | - Monika Rex-Haffner
- a Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Munich , Germany
| | - Jan M Deussing
- b Department of Stress Neurobiology and Neurogenetics , Munich , Germany
| | - Elisabeth B Binder
- a Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Munich , Germany.,c Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
| | - Mira Jakovcevski
- a Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Munich , Germany.,b Department of Stress Neurobiology and Neurogenetics , Munich , Germany
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19
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Altonsy MO, Mostafa MM, Gerber AN, Newton R. Long-acting β 2-agonists promote glucocorticoid-mediated repression of NF-κB by enhancing expression of the feedback regulator TNFAIP3. Am J Physiol Lung Cell Mol Physiol 2016; 312:L358-L370. [PMID: 28039105 DOI: 10.1152/ajplung.00426.2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 12/27/2022] Open
Abstract
Glucocorticoids, or corticosteroids, are effective treatments for many chronic inflammatory diseases, and in mild/moderate asthma, long-acting β2-adrenoceptor agonists (LABAs) enhance the efficacy of inhaled corticosteroids (ICSs) more than increasing the ICS dose. In human bronchial epithelial, BEAS-2B, cells, expression of TNFα-induced protein-3 (TNFAIP3), or A20, a dual-ubiquitin ligase that provides feedback inhibition of NF-κB, was induced by budesonide, an ICS, and formoterol, a LABA, and was further enhanced by budesonide-formoterol combination. The proinflammatory cytokine TNF induced TNFAIP3 and TNF expression. Whereas subsequent budesonide treatment enhanced TNF-induced TNFAIP3 and reduced TNF expression, formoterol amplified these differential effects. In primary human airway smooth muscle cells, TNFAIP3 expression was induced by TNF. This was largely unaffected by budesonide but was acutely enhanced by budesonide-formoterol combination. In BEAS-2B cells, TNF recruited RELA, the main NF-κB transactivating subunit, to a 3' region of the TNF gene. RELA binding was reduced by budesonide, was further reduced by formoterol cotreatment, and was associated with reduced RNA polymerase II recruitment to the TNF gene. This is consistent with reduced TNF expression. TNFAIP3 knockdown enhanced TNF expression in the presence of TNF, TNF plus budesonide, and TNF plus budesonide-formoterol combination and confirms feedback inhibition. A luciferase reporter containing the TNF 3' RELA binding region recapitulated TNF inducibility and was inhibited by an IκB kinase inhibitor and TNFAIP3 overexpression. Repression of reporter activity by budesonide was increased by formoterol and involved TNFAIP3. Thus LABAs may improve the anti-inflammatory properties of ICSs by augmenting TNFAIP3 expression to negatively regulate NF-κB.
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Affiliation(s)
- Mohammed O Altonsy
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Zoology, Sohag University, Sohag, Egypt
| | - Mahmoud M Mostafa
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado; and.,Department of Medicine, University of Colorado, Denver, Colorado
| | - Robert Newton
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada;
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20
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Wang J, Galvao J, Beach KM, Luo W, Urrutia RA, Goldberg JL, Otteson DC. Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells. J Biol Chem 2016; 291:18084-95. [PMID: 27402841 DOI: 10.1074/jbc.m116.732339] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 11/06/2022] Open
Abstract
Regenerative medicine holds great promise for the treatment of degenerative retinal disorders. Krüppel-like factors (KLFs) are transcription factors that have recently emerged as key tools in regenerative medicine because some of them can function as epigenetic reprogrammers in stem cell biology. Here, we show that KLF16, one of the least understood members of this family, is a POU4F2 independent transcription factor in retinal ganglion cells (RGCs) as early as embryonic day 15. When overexpressed, KLF16 inhibits RGC neurite outgrowth and enhances RGC growth cone collapse in response to exogenous ephrinA5 ligands. Ephrin/EPH signaling regulates RGC connectivity. The EphA5 promoter contains multiple GC- and GT-rich KLF-binding sites, which, as shown by ChIP-assays, bind KLF16 in vivo In electrophoretic mobility shift assays, KLF16 binds specifically to a single KLF site near the EphA5 transcription start site that is required for KLF16 transactivation. Interestingly, methylation of only six of 98 CpG dinucleotides within the EphA5 promoter blocks its transactivation by KLF16 but enables transactivation by KLF2 and KLF15. These data demonstrate a role for KLF16 in regulation of RGC neurite outgrowth and as a methylation-sensitive transcriptional regulator of EphA5 expression. Together, these data identify differential low level methylation as a novel mechanism for regulating KLF16-mediated EphA5 expression across the retina. Because of the critical role of ephrin/EPH signaling in patterning RGC connectivity, understanding the role of KLFs in regulating neurite outgrowth and Eph receptor expression will be vital for successful restoration of functional vision through optic nerve regenerative therapies.
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Affiliation(s)
- Jianbo Wang
- From the Departments of Physiological Optics and Vision Science and
| | - Joana Galvao
- the Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, California 94303, the Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, and
| | - Krista M Beach
- From the Departments of Physiological Optics and Vision Science and
| | - Weijia Luo
- Biology and Biochemistry, University of Houston, Houston, Texas 77204
| | - Raul A Urrutia
- the Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Epigenomics Translational Program, Center for Individualized Medicine, Departments of Medicine, Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Jeffrey L Goldberg
- the Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, California 94303, the Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, and
| | - Deborah C Otteson
- From the Departments of Physiological Optics and Vision Science and Biology and Biochemistry, University of Houston, Houston, Texas 77204,
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21
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Cheng D, Zhao Y, Wang S, Jia W, Kang J, Zhu J. Human Telomerase Reverse Transcriptase (hTERT) Transcription Requires Sp1/Sp3 Binding to the Promoter and a Permissive Chromatin Environment. J Biol Chem 2015; 290:30193-203. [PMID: 26487723 DOI: 10.1074/jbc.m115.662221] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 12/14/2022] Open
Abstract
The transcription of human telomerase gene hTERT is regulated by transcription factors (TFs), including Sp1 family proteins, and its chromatin environment. To understand its regulation in a relevant chromatin context, we employed bacterial artificial chromosome reporters containing 160 kb of human genomic sequence containing the hTERT gene. Upon chromosomal integration, the bacterial artificial chromosomes recapitulated endogenous hTERT expression, contrary to transient reporters. Sp1/Sp3 expression did not correlate with hTERT promoter activity, and these TFs bound to the hTERT promoters in both telomerase-positive and telomerase-negative cells. Mutation of the proximal GC-box resulted in a dramatic decrease of hTERT promoter activity, and mutations of all five GC-boxes eliminated its transcriptional activity. Neither mutations of GC-boxes nor knockdown of endogenous Sp1 impacted promoter binding by other TFs, including E-box-binding proteins, and histone acetylation and trimethylation of histone H3K9 at the hTERT promoter in telomerase-positive and -negative cells. The result indicated that promoter binding by Sp1/Sp3 was essential, but not a limiting step, for hTERT transcription. hTERT transcription required a permissive chromatin environment. Importantly, our data also revealed different functions of GC-boxes and E-boxes in hTERT regulation; although GC-boxes were essential for promoter activity, factors bound to the E-boxes functioned to de-repress hTERT promoter.
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Affiliation(s)
- De Cheng
- From the Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington 99210
| | - Yuanjun Zhao
- the Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, and
| | - Shuwen Wang
- From the Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington 99210
| | - Wenwen Jia
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiuhong Kang
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiyue Zhu
- From the Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington 99210, the Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, and
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22
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Mohibi S, Srivastava S, Wang-France J, Mirza S, Zhao X, Band H, Band V. Alteration/Deficiency in Activation 3 (ADA3) Protein, a Cell Cycle Regulator, Associates with the Centromere through CENP-B and Regulates Chromosome Segregation. J Biol Chem 2015; 290:28299-28310. [PMID: 26429915 DOI: 10.1074/jbc.m115.685511] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 02/01/2023] Open
Abstract
ADA3 (alteration/deficiency in activation 3) is a conserved component of several transcriptional co-activator and histone acetyltransferase (HAT) complexes. Recently, we generated Ada3 knock-out mice and demonstrated that deletion of Ada3 leads to early embryonic lethality. The use of Ada3(FL/FL) mouse embryonic fibroblasts with deletion of Ada3 using adenovirus Cre showed a critical role of ADA3 in cell cycle progression through mitosis. Here, we demonstrate an association of ADA3 with the higher order repeat region of the α-satellite region on human X chromosome centromeres that is consistent with its role in mitosis. Given the role of centromere proteins (CENPs) in mitosis, we next analyzed whether ADA3 associates with the centromere through CENPs. Both an in vivo proximity ligation assay and immunofluorescence studies confirmed the association of ADA3 with CENP-B protein, a highly conserved centromeric protein that binds to the 17-bp DNA sequences on α-satellite DNA. Deletional analysis showed that ADA3 directly associates with CENP-B through its N terminus, and a CENP-B binding-deficient mutant of ADA3 was incompetent in cell proliferation rescue. Notably, knockdown of ADA3 decreased binding of CENP-B onto the centromeres, suggesting that ADA3 is required for the loading of CENP-B onto the centromeres. Finally, we show that deletion of Ada3 from Ada3(FL/FL) mouse embryonic fibroblasts exhibited various chromosome segregation defects. Taken together, we demonstrate a novel ADA3 interaction with CENP-B-centromere that may account for its previously known function in mitosis. This study, together with its known function in maintaining genomic stability and its mislocalization in cancers, suggests an important role of ADA3 in mitosis.
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Affiliation(s)
| | | | | | - Sameer Mirza
- Department of Genetics, Cell Biology, and Anatomy
| | | | - Hamid Band
- Department of Genetics, Cell Biology, and Anatomy; Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, and Pharmacology and Experimental Neuroscience, College of Medicine; Eppley Institute for Cancer and Allied Diseases; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, Nebraska 68198.
| | - Vimla Band
- Department of Genetics, Cell Biology, and Anatomy; Eppley Institute for Cancer and Allied Diseases; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, Nebraska 68198
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23
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Abstract
Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.
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Affiliation(s)
- Elizabeth A Hoffman
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
| | - Brian L Frey
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
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24
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Chakrabarti R, Sanyal S, Ghosh A, Bhar K, Das C, Siddhanta A. Phosphatidylinositol-4-phosphate 5-Kinase 1α Modulates Ribosomal RNA Gene Silencing through Its Interaction with Histone H3 Lysine 9 Trimethylation and Heterochromatin Protein HP1-α. J Biol Chem 2015; 290:20893-20903. [PMID: 26157143 DOI: 10.1074/jbc.m114.633727] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Indexed: 11/06/2022] Open
Abstract
Phosphoinositide signaling has been implicated in the regulation of numerous cellular processes including cytoskeletal dynamics, cellular motility, vesicle trafficking, and gene transcription. Studies have also shown that nuclear phosphoinositide(s) regulates processes such as mRNA export, cell cycle progression, gene transcription, and DNA repair. We have shown previously that the nuclear form of phosphatidylinositol-4-phosphate 5-kinase 1α (PIP5K), the enzyme responsible for phosphatidylinositol 4,5-bisphosphate synthesis, is modified by small ubiquitin-like modifier (SUMO)-1. In this study, we have shown that due to the site-specific Lys to Ala mutations of PIP5K at Lys-244 and Lys-490, it is unable to localize in the nucleus and nucleolus, respectively. Furthermore, by using chromatin immunoprecipitation assays, we have observed that PIP5K associates with the chromatin silencing complex constituted of H3K9me3 and heterochromatin protein 1α at multiple ribosomal DNA (rDNA) loci. These interactions followed a definite cyclical pattern of occupancy (mostly G1) and release from the rDNA loci (G1/S) throughout the cell cycle. Moreover, the immunoprecipitation results clearly demonstrate that PIP5K SUMOylated at Lys-490 interacts with components of the chromatin silencing machinery, H3K9me3 and heterochromatin protein 1α. However, PIP5K does not interact with the gene activation signature protein H3K4me3. This study, for the first time, demonstrates that PIP5K, an enzyme actively associated with lipid modification pathway, has additional roles in rDNA silencing.
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Affiliation(s)
| | - Sulagna Sanyal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Amit Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India and
| | - Kaushik Bhar
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India and
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India.
| | - Anirban Siddhanta
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India and.
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25
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Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T. Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. Epigenetics 2014; 9:1238-51. [PMID: 25055051 DOI: 10.4161/epi.29920] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 12/26/2022] Open
Abstract
Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.
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Affiliation(s)
- Nicholas Light
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale (Inserm); U1043; Toulouse, France
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Shu-Huang Chen
- McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tony Kwan
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
| | - Tomi Pastinen
- Department of Human Genetics; McGill University; Montréal, QC Canada; McGill University and Genome Québec Innovation Centre; McGill University; Montréal, QC Canada
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26
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Shi H, Ye T, Zhong B, Liu X, Jin R, Chan Z. AtHAP5A modulates freezing stress resistance in Arabidopsis through binding to CCAAT motif of AtXTH21. New Phytol 2014; 203:554-567. [PMID: 24739069 DOI: 10.1111/nph.12812] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/15/2014] [Indexed: 05/20/2023]
Abstract
Several eukaryotic Heme-associated proteins (HAPs) have been reported to bind specifically to DNA fragments containing CCAAT-box; however, the physiological functions and direct targets of these HAP proteins in plants remain unclear. In this study, we showed that AtHAP5A as a transcription factor interacted with CCAAT motif in vivo, and AtXTH21, one direct target of AtHAP5A, was involved in freezing stress resistance. The AtHAP5A overexpressing plants were more tolerant, whereas the loss-of-function mutant of AtHAP5A was more sensitive to freezing stress than wild-type plants. Chromatin immunoprecipitation (ChIP) assay demonstrated that AtHAP5A could bind to five fragments that contained CCAAT motifs in the AtXTH21 promoter. Similarly, the AtXTH21 overexpressing plants exhibited improved freezing resistance, while xth21 knockdown mutants displayed decreased freezing resistance. Notably, the modulated freezing resistance of AtHAP5A overexpressing plants and knockout mutant could be reversed by the xth21 mutant and AtXTH21 overexpressing plants, respectively, indicating that AtHAP5A might act upstream of AtXTH21 in freezing stress. Additionally, modulation of AtHAP5A and AtXTH21 expression had the same effects on abscisic acid (ABA) sensitivity and reactive oxygen species (ROS) metabolism. Taken together, these results demonstrated that AtHAP5A modulates freezing stress resistance in Arabidopsis through binding to the CCAAT motif of AtXTH21.
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Affiliation(s)
- Haitao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tiantian Ye
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bao Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xun Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Jin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
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