1
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Li H, Ding Z, Fang ZY, Long N, Ang HY, Zhang Y, Fan YJ, Xu YZ. Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons. Nucleic Acids Res 2024; 52:6002-6016. [PMID: 38499485 PMCID: PMC11162794 DOI: 10.1093/nar/gkae185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Alternative splicing (AS) generates multiple RNA isoforms and increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch sites (BSs) in the alternatively spliced introns and predict thousands of them from six organisms, of which many are evolutionarily conserved. Intriguingly, a highly conserved stem-loop structure with concealed BSs is found in animal SF3B3 genes and colocalizes with a downstream poison exon (PE). Destabilization of this structure allows increased usage of the BSs and results in enhanced PE inclusion in human and Drosophila cells, leading to decreased expression of SF3B3. This structure is experimentally validated using an in-cell SHAPE-MaP assay. Through RNA interference screens of 28 RNA-binding proteins, we find that this stem-loop structure is sensitive to U2 factors. Furthermore, we find that SF3B3 also facilitates DNA repair and protects genome stability by enhancing interaction between ERCC6/CSB and arrested RNA polymerase II. Importantly, both Drosophila and human cells with the secondary structure mutated by genome editing exhibit altered DNA repair in vivo. This study provides a novel and common mechanism for AS regulation of PEs and reveals a physiological function of SF3B3 in DNA repair.
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Affiliation(s)
- Hao Li
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Zhan Ding
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Zhuo-Ya Fang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Ni Long
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Hao-Yang Ang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Yu Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei 430072, China
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2
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Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Ehmke N, Seelow D, Fradin M, Kornak U, Fischer-Zirnsak B. Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy. Hum Genet 2024; 143:683-694. [PMID: 38592547 PMCID: PMC11098864 DOI: 10.1007/s00439-024-02669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Generalized lipodystrophy is a feature of various hereditary disorders, often leading to a progeroid appearance. In the present study we identified a missense and a frameshift variant in a compound heterozygous state in SUPT7L in a boy with intrauterine growth retardation, generalized lipodystrophy, and additional progeroid features. SUPT7L encodes a component of the transcriptional coactivator complex STAGA. By transcriptome sequencing, we showed the predicted missense variant to cause aberrant splicing, leading to exon truncation and thereby to a complete absence of SUPT7L in dermal fibroblasts. In addition, we found altered expression of genes encoding DNA repair pathway components. This pathway was further investigated and an increased rate of DNA damage was detected in proband-derived fibroblasts and genome-edited HeLa cells. Finally, we performed transient overexpression of wildtype SUPT7L in both cellular systems, which normalizes the number of DNA damage events. Our findings suggest SUPT7L as a novel disease gene and underline the link between genome instability and progeroid phenotypes.
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Affiliation(s)
- Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Leonard A Koch
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
| | - Hristiana Lyubenova
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Oliver Küchler
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, F-35033, France
- Univercity Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, F-35000, France
| | - Erika Launay
- Service de Cytogénétique et Biologie cellulaire, Hôpital Pontchaillou - CHU Rennes, 2 rue Henri Le Guilloux - Rennes cedex 9, France, Rennes, F-35033, France
| | - Sebastian Brachs
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre Référence Déficiences Intellectuelles CRDI, Hôpital Sud - CHU Rennes, 16 boulevard de Bulgarie - BP 90347, Rennes cedex 2, Rennes, F-35203, France
- Service de Génétique, CH Saint Brieuc, St Brieuc, 22000, France
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany.
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3
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Modenini G, Abondio P, Sazzini M, Boattini A. Polymorphic transposable elements provide new insights on high-altitude adaptation in the Tibetan Plateau. Genomics 2024; 116:110854. [PMID: 38701989 DOI: 10.1016/j.ygeno.2024.110854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/23/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Several studies demonstrated that populations living in the Tibetan plateau are genetically and physiologically adapted to high-altitude conditions, showing genomic signatures ascribable to the action of natural selection. However, so far most of them relied solely on inferences drawn from the analysis of coding variants and point mutations. To fill this gap, we focused on the possible role of polymorphic transposable elements in influencing the adaptation of Tibetan and Sherpa highlanders. To do so, we compared high-altitude and middle/low-lander individuals of East Asian ancestry by performing in silico analyses and differentiation tests on 118 modern and ancient samples. We detected several transposable elements associated with high altitude, which map genes involved in cardiovascular, hematological, chem-dependent and respiratory conditions, suggesting that metabolic and signaling pathways taking part in these functions are disproportionately impacted by the effect of environmental stressors in high-altitude individuals. To our knowledge, our study is the first hinting to a possible role of transposable elements in the adaptation of Tibetan and Sherpa highlanders.
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Affiliation(s)
- Giorgia Modenini
- Dept. of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
| | - Paolo Abondio
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bologna, Italy
| | - Marco Sazzini
- Dept. of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy; Interdepartmental Centre - Alma Mater Research Institute on Global Changes and Climate Change, University of Bologna, Italy
| | - Alessio Boattini
- Dept. of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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4
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Anatskaya OV, Vinogradov AE. Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study. Int J Mol Sci 2024; 25:4185. [PMID: 38673782 PMCID: PMC11050069 DOI: 10.3390/ijms25084185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mesenchymal stem cells (MSC) attract an increasing amount of attention due to their unique therapeutic properties. Yet, MSC can undergo undesirable genetic and epigenetic changes during their propagation in vitro. In this study, we investigated whether polyploidy can compromise MSC oncological safety and therapeutic properties. For this purpose, we compared the impact of polyploidy on the transcriptome of cancer cells and MSC of various origins (bone marrow, placenta, and heart). First, we identified genes that are consistently ploidy-induced or ploidy-repressed through all comparisons. Then, we selected the master regulators using the protein interaction enrichment analysis (PIEA). The obtained ploidy-related gene signatures were verified using the data gained from polyploid and diploid populations of early cardiomyocytes (CARD) originating from iPSC. The multistep bioinformatic analysis applied to the cancer cells, MSC, and CARD indicated that polyploidy plays a pivotal role in driving the cell into hypertranscription. It was evident from the upregulation of gene modules implicated in housekeeping functions, stemness, unicellularity, DNA repair, and chromatin opening by means of histone acetylation operating via DNA damage associated with the NUA4/TIP60 complex. These features were complemented by the activation of the pathways implicated in centrosome maintenance and ciliogenesis and by the impairment of the pathways related to apoptosis, the circadian clock, and immunity. Overall, our findings suggest that, although polyploidy does not induce oncologic transformation of MSC, it might compromise their therapeutic properties because of global epigenetic changes and alterations in fundamental biological processes. The obtained results can contribute to the development and implementation of approaches enhancing the therapeutic properties of MSC by removing polyploid cells from the cell population.
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Affiliation(s)
- Olga V. Anatskaya
- Institute of Cytology Russian Academy of Sciences, 194064 St. Petersburg, Russia;
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5
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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6
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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7
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Hurd M, Pino J, Jang K, Allevato MM, Vorontchikhina M, Ichikawa W, Zhao Y, Gates R, Villalpando E, Hamilton MJ, Faiola F, Pan S, Qi Y, Hung YW, Girke T, Ann D, Seewaldt V, Martinez E. MYC acetylated lysine residues drive oncogenic cell transformation and regulate select genetic programs for cell adhesion-independent growth and survival. Genes Dev 2023; 37:865-882. [PMID: 37852796 PMCID: PMC10691474 DOI: 10.1101/gad.350736.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The MYC oncogenic transcription factor is acetylated by the p300 and GCN5 histone acetyltransferases. The significance of MYC acetylation and the functions of specific acetylated lysine (AcK) residues have remained unclear. Here, we show that the major p300-acetylated K148(149) and K157(158) sites in human (or mouse) MYC and the main GCN5-acetylated K323 residue are reversibly acetylated in various malignant and nonmalignant cells. Oncogenic overexpression of MYC enhances its acetylation and alters the regulation of site-specific acetylation by proteasome and deacetylase inhibitors. Acetylation of MYC at different K residues differentially affects its stability in a cell type-dependent manner. Lysine-to-arginine substitutions indicate that although none of the AcK residues is required for MYC stimulation of adherent cell proliferation, individual AcK sites have gene-specific functions controlling select MYC-regulated processes in cell adhesion, contact inhibition, apoptosis, and/or metabolism and are required for the malignant cell transformation activity of MYC. Each AcK site is required for anchorage-independent growth of MYC-overexpressing cells in vitro, and both the AcK148(149) and AcK157(158) residues are also important for the tumorigenic activity of MYC transformed cells in vivo. The MYC AcK site-specific signaling pathways identified may offer new avenues for selective therapeutic targeting of MYC oncogenic activities.
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Affiliation(s)
- Matthew Hurd
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Jeffrey Pino
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Kay Jang
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Michael M Allevato
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Marina Vorontchikhina
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Wataru Ichikawa
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Yifan Zhao
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Ryan Gates
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Emily Villalpando
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Michael J Hamilton
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Francesco Faiola
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Songqin Pan
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Yu-Wen Hung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Thomas Girke
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - David Ann
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Victoria Seewaldt
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Department of Population Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA;
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
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8
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Nikom D, Zheng S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat Rev Neurosci 2023; 24:457-473. [PMID: 37336982 DOI: 10.1038/s41583-023-00717-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.
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Affiliation(s)
- David Nikom
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA
| | - Sika Zheng
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA.
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA.
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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9
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Li X, Liu D, Wang Y, Chen Y, Wang C, Lin Z, Tian L. PHF5A as a new OncoTarget and therapeutic prospects. Heliyon 2023; 9:e18010. [PMID: 37483794 PMCID: PMC10362332 DOI: 10.1016/j.heliyon.2023.e18010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/24/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
PHF5A (PHD-finger domain protein 5A) is a highly conserved protein comprised of 110 amino acids that belong to PHD zinc finger proteins and is ubiquitously expressed in entire eukaryotic nuclei from yeast to man. PHF5A is an essential component of the SF3B splicing complex regulating protein-protein or protein-DNA interactions; particularly involved in pre-mRNA splicing. Besides its basic spliceosome-associated attributes encompassing the regulation of alternative splicing of specific genes, PHF5A also plays a pivotal role in cell cycle regulation and morphological development of cells along with their differentiation into particular tissues/organs, DNA damage repair, maintenance of pluripotent embryonic stem cells (CSCs) embryogenesis and regulation of chromatin-mediated transcription. Presently identification of spliceosome and non-spliceosome-associated attributes of PHF5A needs great attention based on its key involvement in the pathogenesis of cancer malignancies including the prognosis of lung adenocarcinoma, endometrial adenocarcinoma, breast, and colorectal cancer. PHF5A is an essential splicing factor or cofactor actively participating as an oncogenic protein in tumorigenesis via activation of downstream signaling pathway attributed to its regulation of dysregulated splicing or abnormal alternative splicing of targeted genes. Further, the participation of PHF5A in regulating the growth of cancer stem cells might not be ignored. The current review briefly overviews the structural and functional attributes of PHF5A along with its hitherto described role in the propagation of cancer malignancies and its future concern as a potential therapeutic target for cancer management/treatment.
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Affiliation(s)
- Xiaojiang Li
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Dalong Liu
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yun Wang
- Department of Thoracic Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yu Chen
- Department of Orthopedics, LiaoYuanCity TCM Hospital, LiaoYuan, 136200, China
| | - Chenyang Wang
- Department of Orthopedics, LiaoYuanCity TCM Hospital, LiaoYuan, 136200, China
| | - Zhicheng Lin
- Department of Internal Medicine, Baishan Hospital of Traditional Chinese Medicine, Baishan, 134300, China
| | - Lin Tian
- Department of Lung Oncology, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
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10
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Bartelt LC, Switonski PM, Adamek G, Carvalho J, Duvick LA, Jarrah SI, McLoughlin HS, Scoles DR, Pulst SM, Orr HT, Hull C, Lowe CB, La Spada AR. Purkinje-Enriched snRNA-seq in SCA7 Cerebellum Reveals Zebrin Identity Loss as a Central Feature of Polyglutamine Ataxias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533345. [PMID: 37214832 PMCID: PMC10197555 DOI: 10.1101/2023.03.19.533345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disorder caused by a CAG-polyglutamine repeat expansion. SCA7 patients display a striking loss of Purkinje cell (PC) neurons with disease progression; however, PCs are rare, making them difficult to characterize. We developed a PC nuclei enrichment protocol and applied it to single-nucleus RNA-seq of a SCA7 knock-in mouse model. Our results unify prior observations into a central mechanism of cell identity loss, impacting both glia and PCs, driving accumulation of inhibitory synapses and altered PC spiking. Zebrin-II subtype dysregulation is the predominant signal in PCs, leading to complete loss of zebrin-II striping at motor symptom onset in SCA7 mice. We show this zebrin-II subtype degradation is shared across Polyglutamine Ataxia mouse models and SCA7 patients. It has been speculated that PC subtype organization is critical for cerebellar function, and our results suggest that a breakdown of zebrin-II parasagittal striping is pathological.
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Affiliation(s)
- Luke C. Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine; Irvine, CA 92697, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Pawel M. Switonski
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grażyna Adamek
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Juliana Carvalho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa A. Duvick
- Institute for Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sabrina I. Jarrah
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Daniel R. Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Stefan M. Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Harry T. Orr
- Institute for Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Court Hull
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Craig B. Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R. La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine; Irvine, CA 92697, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
- UCI Center for Neurotherapeutics, University of California, Irvine; Irvine, CA 92697, USA
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11
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Li M, Cheng Q, Wang X, Yang Y. Research progress and therapeutic prospect of PHF5A acting as a new target for malignant tumors. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:647-655. [PMID: 36581580 PMCID: PMC10264978 DOI: 10.3724/zdxbyxb-2022-0459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/01/2022] [Indexed: 11/30/2022]
Abstract
PHD-finger domain protein 5A (PHF5A) is a member of the PHD-finger like protein superfamily and widely expressed in the nucleus of eukaryotes. The PHD-finger like domain is a protein-DNA or protein-protein interaction region. In addition to regulate alternative splicing of target genes as a spliceosome protein subunit, PHF5A is also involved in pluripotency maintenance of embryonic stem cells, chromatin remodeling, DNA damage repair, embryogenesis and histomorphological development. Recently, increasing studies have focused on exploring spliceosome-related and non-spliceosome-related functions of PHF5A and its relationship with the tumorigenesis, development and patient prognosis of various malignant tumors, such as breast cancer, lung cancer and colorectal cancer. The underlying mechanisms of PHF5A may include mediating aberrant alternative splicing of target genes, activating downstream signaling pathways as an oncogene/protein, and regulating abnormal gene transcription as a nuclear transcription factor or cofactor. Besides, PHF5A was also found to be involved in the growth regulation of cancer stem cells. In this review, we aimed to delineate the structural and functional characteristics of PHF5A, to summarize its role in the occurrence and development of malignant tumors hitherto described, and to provide potential targets for anti-tumor therapy.
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Affiliation(s)
- Man Li
- 1. Department of Medical Oncology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, Anhui Province, China
| | - Qianqian Cheng
- 1. Department of Medical Oncology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, Anhui Province, China
| | - Xiaojing Wang
- 2. Anhui Clinical and Preclinical Key Laboratory of Respiratory Disease, Bengbu 233004, Anhui Province, China
- 3. Molecular Diagnosis Center, Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, Anhui Province, China
| | - Yan Yang
- 1. Department of Medical Oncology, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, Anhui Province, China
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12
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Cryo-EM structure of human SAGA transcriptional coactivator complex. Cell Discov 2022; 8:125. [PMID: 36414614 PMCID: PMC9681738 DOI: 10.1038/s41421-022-00489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022] Open
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13
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Hinds JW, Feris EJ, Wilkins OM, Deary LT, Wang X, Cole MD. S146L in MYC is a context-dependent activating substitution in cancer development. PLoS One 2022; 17:e0272771. [PMID: 36018850 PMCID: PMC9417018 DOI: 10.1371/journal.pone.0272771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/26/2022] [Indexed: 11/19/2022] Open
Abstract
MYC is one of the most dysregulated oncogenes and is thought to be fundamental to tumor formation and/or maintenance in many cancer types. This dominant pro-tumor activity makes MYC an attractive target for cancer therapy. However, MYC is a transcription factor lacking enzymatic activity, and the structure of one of its two domains is unknown e.g., its transactivation domain. Consequently, few direct MYC-targeting therapies have been developed, and none have been successful in the clinic. Nevertheless, significant effort has been devoted to understanding the mechanisms of oncogenic MYC activity with the objective of uncovering novel vulnerabilities of MYC-dependent cancers. These extensive investigations have revealed in detail how MYC translocation, amplification, and other upstream perturbations contribute to MYC activity in cancer. However, missense mutations of the MYC gene have remained relatively understudied for their potential role in MYC-mediated oncogenesis. While the function of several low-frequency mutations in MYC have been described, our understanding of other equally or more frequent mutations is incomplete. Herein, we define the function of a recurrent missense mutation in MYC resulting in the substitution S146L. This mutation enhances the interaction between MYC and its cofactor TRRAP and may enhance oncogenic MYC activity in certain cellular contexts.
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Affiliation(s)
- John W. Hinds
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Edmond J. Feris
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Owen M. Wilkins
- Center for Quantitative Biology (CQB), Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, Unites States of America
| | - Luke T. Deary
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Xiaofeng Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Michael D. Cole
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
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14
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RNA splicing: a dual-edged sword for hepatocellular carcinoma. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:173. [PMID: 35972700 DOI: 10.1007/s12032-022-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/30/2022] [Indexed: 10/15/2022]
Abstract
RNA splicing is the fundamental process that brings diversity at the transcriptome and proteome levels. The spliceosome complex regulates minor and major processes of RNA splicing. Aberrant regulation is often associated with different diseases, including diabetes, stroke, hypertension, and cancer. In the majority of cancers, dysregulated alternative RNA splicing (ARS) events directly affect tumor progression, invasiveness, and often lead to poor survival of the patients. Alike the rest of the gastrointestinal malignancies, in hepatocellular carcinoma (HCC), which alone contributes to ~ 75% of the liver cancers, a large number of ARS events have been observed, including intron retention, exon skipping, presence of alternative 3'-splice site (3'SS), and alternative 5'-splice site (5'SS). These events are reported in spliceosome and non-spliceosome complexes genes. Molecules such as MCL1, Bcl-X, and BCL2 in different isoforms can behave as anti-apoptotic or pro-apoptotic, making the spliceosome complex a dual-edged sword. The anti-apoptotic isoforms of such molecules bring in resistance to chemotherapy or cornerstone drugs. However, in contrast, multiple malignant tumors, including HCC that target the pro-apoptotic favoring isoforms/variants favor apoptotic induction and make chemotherapy effective. Herein, we discuss different splicing events, aberrations, and antisense oligonucleotides (ASOs) in modulating RNA splicing in HCC tumorigenesis with a possible therapeutic outcome.
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15
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Kusakabe M, Kakumu E, Kurihara F, Tsuchida K, Maeda T, Tada H, Kusao K, Kato A, Yasuda T, Matsuda T, Nakao M, Yokoi M, Sakai W, Sugasawa K. Histone deacetylation regulates nucleotide excision repair through an interaction with the XPC protein. iScience 2022; 25:104040. [PMID: 35330687 PMCID: PMC8938288 DOI: 10.1016/j.isci.2022.104040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/07/2022] [Accepted: 03/04/2022] [Indexed: 12/05/2022] Open
Abstract
The XPC protein complex plays a central role in DNA lesion recognition for global genome nucleotide excision repair (GG-NER). Lesion recognition can be accomplished in either a UV-DDB-dependent or -independent manner; however, it is unclear how these sub-pathways are regulated in chromatin. Here, we show that histone deacetylases 1 and 2 facilitate UV-DDB-independent recruitment of XPC to DNA damage by inducing histone deacetylation. XPC localizes to hypoacetylated chromatin domains in a DNA damage-independent manner, mediated by its structurally disordered middle (M) region. The M region interacts directly with the N-terminal tail of histone H3, an interaction compromised by H3 acetylation. Although the M region is dispensable for in vitro NER, it promotes DNA damage removal by GG-NER in vivo, particularly in the absence of UV-DDB. We propose that histone deacetylation around DNA damage facilitates the recruitment of XPC through the M region, contributing to efficient lesion recognition and initiation of GG-NER. Histone deacetylation by HDAC1/2 promotes the DNA lesion recognition by XPC The HDAC1/2 activators, MTA proteins, also promote the recruitment of XPC XPC tends to localize in hypoacetylated chromatin independently of DNA damage Disordered middle region of XPC interacts with histone H3 tail and promotes GG-NER
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16
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Enhancing Therapeutic Approaches for Melanoma Patients Targeting Epigenetic Modifiers. Cancers (Basel) 2021; 13:cancers13246180. [PMID: 34944799 PMCID: PMC8699560 DOI: 10.3390/cancers13246180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
Melanoma is the least common but deadliest type of skin cancer. Melanomagenesis is driven by a series of mutations and epigenetic alterations in oncogenes and tumor suppressor genes that allow melanomas to grow, evolve, and metastasize. Epigenetic alterations can also lead to immune evasion and development of resistance to therapies. Although the standard of care for melanoma patients includes surgery, targeted therapies, and immune checkpoint blockade, other therapeutic approaches like radiation therapy, chemotherapy, and immune cell-based therapies are used for patients with advanced disease or unresponsive to the conventional first-line therapies. Targeted therapies such as the use of BRAF and MEK inhibitors and immune checkpoint inhibitors such as anti-PD-1 and anti-CTLA4 only improve the survival of a small subset of patients. Thus, there is an urgent need to identify alternative standalone or combinatorial therapies. Epigenetic modifiers have gained attention as therapeutic targets as they modulate multiple cellular and immune-related processes. Due to melanoma's susceptibility to extrinsic factors and reversible nature, epigenetic drugs are investigated as a therapeutic avenue and as adjuvants for targeted therapies and immune checkpoint inhibitors, as they can sensitize and/or reverse resistance to these therapies, thus enhancing their therapeutic efficacy. This review gives an overview of the role of epigenetic changes in melanoma progression and resistance. In addition, we evaluate the latest advances in preclinical and clinical research studying combinatorial therapies and discuss the use of epigenetic drugs such as HDAC and DNMT inhibitors as potential adjuvants for melanoma patients.
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17
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Herbst DA, Esbin MN, Louder RK, Dugast-Darzacq C, Dailey GM, Fang Q, Darzacq X, Tjian R, Nogales E. Structure of the human SAGA coactivator complex. Nat Struct Mol Biol 2021; 28:989-996. [PMID: 34811519 PMCID: PMC8660637 DOI: 10.1038/s41594-021-00682-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022]
Abstract
The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP6) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.
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Affiliation(s)
- Dominik A Herbst
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Meagan N Esbin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Robert K Louder
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Qianglin Fang
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Public Health, Sun Yat-sen University, Shenzhen, China
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
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18
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Switonski PM, Delaney JR, Bartelt LC, Niu C, Ramos-Zapatero M, Spann NJ, Alaghatta A, Chen T, Griffin EN, Bapat J, Sopher BL, La Spada AR. Altered H3 histone acetylation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7. Cell Rep 2021; 37:110062. [PMID: 34852229 PMCID: PMC8710427 DOI: 10.1016/j.celrep.2021.110062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/11/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
A common mechanism in inherited ataxia is a vulnerability of DNA damage. Spinocerebellar ataxia type 7 (SCA7) is a CAG-polyglutamine-repeat disorder characterized by cerebellar and retinal degeneration. Polyglutamine-expanded ataxin-7 protein incorporates into STAGA co-activator complex and interferes with transcription by altering histone acetylation. We performed chromatic immunoprecipitation sequencing ChIP-seq on cerebellum from SCA7 mice and observed increased H3K9-promoter acetylation in DNA repair genes, resulting in increased expression. After detecting increased DNA damage in SCA7 cells, mouse primary cerebellar neurons, and patient stem-cell-derived neurons, we documented reduced homology-directed repair (HDR) and single-strand annealing (SSA). To evaluate repair at endogenous DNA in native chromosome context, we modified linear amplification-mediated high-throughput genome-wide translocation sequencing and found that DNA translocations are less frequent in SCA7 models, consistent with decreased HDR and SSA. Altered DNA repair function in SCA7 may predispose the subject to excessive DNA damage, leading to neuron demise and highlights DNA repair as a therapy target. Switonski et al. performed ChIP-seq on cerebellar DNA from SCA7 mice and detect increased histone H3-promoter acetylation in DNA repair genes. They document DNA damage in SCA7 models and patient stem-cell-derived neurons. Using in vitro assays and genome-wide translocation sequencing, they observe altered DNA repair in SCA7.
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Affiliation(s)
- Pawel M Switonski
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Joe R Delaney
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Luke C Bartelt
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chenchen Niu
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Maria Ramos-Zapatero
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular & Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Akshay Alaghatta
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Toby Chen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emily N Griffin
- Department of Cellular & Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaidev Bapat
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bryce L Sopher
- Department of Neurology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Institute for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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19
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Vos SM. Chronicles of the human SAGA co-activator complex. Nat Struct Mol Biol 2021; 28:959-960. [PMID: 34819676 DOI: 10.1038/s41594-021-00696-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Apelt K, Lans H, Schärer OD, Luijsterburg MS. Nucleotide excision repair leaves a mark on chromatin: DNA damage detection in nucleosomes. Cell Mol Life Sci 2021; 78:7925-7942. [PMID: 34731255 PMCID: PMC8629891 DOI: 10.1007/s00018-021-03984-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) eliminates a broad spectrum of DNA lesions from genomic DNA. Genomic DNA is tightly wrapped around histones creating a barrier for DNA repair proteins to access DNA lesions buried in nucleosomal DNA. The DNA-damage sensors XPC and DDB2 recognize DNA lesions in nucleosomal DNA and initiate repair. The emerging view is that a tight interplay between XPC and DDB2 is regulated by post-translational modifications on the damage sensors themselves as well as on chromatin containing DNA lesions. The choreography between XPC and DDB2, their interconnection with post-translational modifications such as ubiquitylation, SUMOylation, methylation, poly(ADP-ribos)ylation, acetylation, and the functional links with chromatin remodelling activities regulate not only the initial recognition of DNA lesions in nucleosomes, but also the downstream recruitment and necessary displacement of GG-NER factors as repair progresses. In this review, we highlight how nucleotide excision repair leaves a mark on chromatin to enable DNA damage detection in nucleosomes.
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Affiliation(s)
- Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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21
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Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
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22
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Juvinao-Quintero DL, Cardenas A, Perron P, Bouchard L, Lutz SM, Hivert MF. Associations between an integrated component of maternal glycemic regulation in pregnancy and cord blood DNA methylation. Epigenomics 2021; 13:1459-1472. [PMID: 34596421 DOI: 10.2217/epi-2021-0220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Previous studies suggest that fetal programming to hyperglycemia in pregnancy is due to modulation of DNA methylation (DNAm), but they have been limited in their maternal glycemic characterization. Methods: In the Gen3G study, we used a principal component analysis to integrate multiple glucose and insulin values measured during the second trimester oral glucose tolerance test. We investigated associations between principal components and cord blood DNAm levels in an epigenome-wide analysis among 430 mother-child pairs. Results: The first principal component was robustly associated with lower DNAm at cg26974062 (TXNIP; p = 9.9 × 10-9) in cord blood. TXNIP is a well-known DNAm marker for type 2 diabetes in adults. Conclusion: We hypothesize that abnormal glucose metabolism in pregnancy may program dysregulation of TXNIP across the life course.
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Affiliation(s)
- Diana L Juvinao-Quintero
- Division of Chronic Disease Research Across the Life Course, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health & Center for Computational Biology, University of California, Berkeley, CA 94720-7360, USA
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Department of Medical Biology, Centre Intégré Universitaire en Santé et Services Sociaux Saguenay-Lac-Saint-Jean, Hôpital Universitaire de Chicoutimi, Saguenay, QC, G7H 5H6, Canada.,Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sharon M Lutz
- Division of Chronic Disease Research Across the Life Course, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02215, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Life Course, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.,Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
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23
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Stanek TJ, Gennaro VJ, Tracewell MA, Di Marcantonio D, Pauley KL, Butt S, McNair C, Wang F, Kossenkov AV, Knudsen KE, Butt T, Sykes SM, McMahon SB. The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J 2021; 40:e102509. [PMID: 34155658 PMCID: PMC8365265 DOI: 10.15252/embj.2019102509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/10/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
The SAGA coactivator complex is essential for eukaryotic transcription and comprises four distinct modules, one of which contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II Ser2 phosphorylation and subsequent transcriptional elongation. In contrast to this H2B-associated role in transcription, we report here that human USP22 contributes to the early stages of stimulus-responsive transcription, where USP22 is required for pre-initiation complex (PIC) stability. Specifically, USP22 maintains long-range enhancer-promoter contacts and controls loading of Mediator tail and general transcription factors (GTFs) onto promoters, with Mediator core recruitment being USP22-independent. In addition, we identify Mediator tail subunits MED16 and MED24 and the Pol II subunit RBP1 as potential non-histone substrates of USP22. Overall, these findings define a role for human SAGA within the earliest steps of transcription.
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Affiliation(s)
- Timothy J Stanek
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Victoria J Gennaro
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mason A Tracewell
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Daniela Di Marcantonio
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kristen L Pauley
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sabrina Butt
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Stephen M Sykes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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24
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Begum NA, Haque F, Stanlie A, Husain A, Mondal S, Nakata M, Taniguchi T, Taniguchi H, Honjo T. Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition. EMBO J 2021; 40:e106393. [PMID: 33938017 PMCID: PMC8204862 DOI: 10.15252/embj.2020106393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement mediated by switch (S) region transcription, activation-induced cytidine deaminase (AID)-induced DNA breaks, and their resolution by non-homologous end joining (NHEJ)-mediated DNA repair. Due to the complex nature of the recombination process, numerous cofactors are intimately involved, making it important to identify rate-limiting factors that impact on DNA breaking and/or repair. Using an siRNA-based loss-of-function screen of genes predicted to encode PHD zinc-finger-motif proteins, we identify the splicing factor Phf5a/Sf3b14b as a novel modulator of the DNA repair step of CSR. Loss of Phf5a severely impairs AID-induced recombination, but does not perturb DNA breaks and somatic hypermutation. Phf5a regulates NHEJ-dependent DNA repair by preserving chromatin integrity to elicit optimal DNA damage response and subsequent recruitment of NHEJ factors at the S region. Phf5a stabilizes the p400 histone chaperone complex at the locus, which in turn promotes deposition of H2A variant such as H2AX and H2A.Z that are critical for the early DNA damage response and NHEJ, respectively. Depletion of Phf5a or p400 blocks the repair of both AID- and I-SceI-induced DNA double-strand breaks, supporting an important contribution of this axis to programmed as well as aberrant recombination.
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Affiliation(s)
- Nasim A Begum
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Farazul Haque
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Andre Stanlie
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- BioMedicine DesignPfizer Inc.CambridgeMAUSA
| | - Afzal Husain
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of BiochemistryFaculty of Life SciencesAligarh Muslim UniversityAligarhIndia
| | - Samiran Mondal
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of ChemistryRammohan CollegeKolkataIndia
| | - Mikiyo Nakata
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Takako Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Hisaaki Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Tasuku Honjo
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
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25
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Chen YJC, Dent SYR. Conservation and diversity of the eukaryotic SAGA coactivator complex across kingdoms. Epigenetics Chromatin 2021; 14:26. [PMID: 34112237 PMCID: PMC8194025 DOI: 10.1186/s13072-021-00402-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/03/2021] [Indexed: 12/27/2022] Open
Abstract
The SAGA complex is an evolutionarily conserved transcriptional coactivator that regulates gene expression through its histone acetyltransferase and deubiquitylase activities, recognition of specific histone modifications, and interactions with transcription factors. Multiple lines of evidence indicate the existence of distinct variants of SAGA among organisms as well as within a species, permitting diverse functions to dynamically regulate cellular pathways. Our co-expression analysis of genes encoding human SAGA components showed enrichment in reproductive organs, brain tissues and the skeletal muscle, which corresponds to their established roles in developmental programs, emerging roles in neurodegenerative diseases, and understudied functions in specific cell types. SAGA subunits modulate growth, development and response to various stresses from yeast to plants and metazoans. In metazoans, SAGA further participates in the regulation of differentiation and maturation of both innate and adaptive immune cells, and is associated with initiation and progression of diseases including a broad range of cancers. The evolutionary conservation of SAGA highlights its indispensable role in eukaryotic life, thus deciphering the mechanisms of action of SAGA is key to understanding fundamental biological processes throughout evolution. To illuminate the diversity and conservation of this essential complex, here we discuss variations in composition, essentiality and co-expression of component genes, and its prominent functions across Fungi, Plantae and Animalia kingdoms.
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Affiliation(s)
- Ying-Jiun C Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA.
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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26
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Soffers JHM, Workman JL. The SAGA chromatin-modifying complex: the sum of its parts is greater than the whole. Genes Dev 2021; 34:1287-1303. [PMID: 33004486 PMCID: PMC7528701 DOI: 10.1101/gad.341156.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review, Soffers and Workman discuss the initial discovery of the canonical SAGA complex, the subsequent studies that have shaped our view on the internal organization of its subunits into modules, and the latest structural work that visualizes the modules and provides insights into their function. There are many large protein complexes involved in transcription in a chromatin context. However, recent studies on the SAGA coactivator complex are generating new paradigms for how the components of these complexes function, both independently and in concert. This review highlights the initial discovery of the canonical SAGA complex 23 years ago, our evolving understanding of its modular structure and the relevance of its modular nature for its coactivator function in gene regulation.
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Affiliation(s)
- Jelly H M Soffers
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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27
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Adamus K, Reboul C, Voss J, Huang C, Schittenhelm RB, Le SN, Ellisdon AM, Elmlund H, Boudes M, Elmlund D. SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent. J Biol Chem 2021; 296:100671. [PMID: 33864814 PMCID: PMC8131915 DOI: 10.1016/j.jbc.2021.100671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/03/2022] Open
Abstract
The SAGA-like complex SLIK is a modified version of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. SLIK is formed through C-terminal truncation of the Spt7 SAGA subunit, causing loss of Spt8, one of the subunits that interacts with the TATA-binding protein (TBP). SLIK and SAGA are both coactivators of RNA polymerase II transcription in yeast, and both SAGA and SLIK perform chromatin modifications. The two complexes have been speculated to uniquely contribute to transcriptional regulation, but their respective contributions are not clear. To investigate, we assayed the chromatin modifying functions of SAGA and SLIK, revealing identical kinetics on minimal substrates in vitro. We also examined the binding of SAGA and SLIK to TBP and concluded that interestingly, both protein complexes have similar affinity for TBP. Additionally, despite the loss of Spt8 and C-terminus of Spt7 in SLIK, TBP prebound to SLIK is not released in the presence of TATA-box DNA, just like TBP prebound to SAGA. Furthermore, we determined a low-resolution cryo-EM structure of SLIK, revealing a modular architecture identical to SAGA. Finally, we performed a comprehensive study of DNA-binding properties of both coactivators. Purified SAGA and SLIK both associate with ssDNA and dsDNA with high affinity (KD = 10–17 nM), and the binding is sequence-independent. In conclusion, our study shows that the cleavage of Spt7 and the absence of the Spt8 subunit in SLIK neither drive any major conformational differences in its structure compared with SAGA, nor significantly affect HAT, DUB, or DNA-binding activities in vitro.
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Affiliation(s)
- Klaudia Adamus
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Cyril Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jarrod Voss
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Cheng Huang
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sarah N Le
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Andrew M Ellisdon
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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28
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Lim S, Ahn H, Duan R, Liu Y, Ryu HY, Ahn SH. The Spt7 subunit of the SAGA complex is required for the regulation of lifespan in both dividing and nondividing yeast cells. Mech Ageing Dev 2021; 196:111480. [PMID: 33831401 DOI: 10.1016/j.mad.2021.111480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Spt7 belongs to the suppressor of Ty (SPT) module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and is known as the yeast ortholog of human STAF65γ. Spt7 lacks intrinsic enzymatic activity but is responsible for the integrity and proper assembly of the SAGA complex. Here, we determined the role of the SAGA Spt7 subunit in cellular aging. We found that Spt7 was indispensable for a normal lifespan in both dividing and nondividing yeast cells. In the quiescent state of cells, Spt7 was required for the control of overall mRNA levels. In mitotically active cells, deletion of the SPT module had little effect on the recombination rate within heterochromatic ribosomal DNA (rDNA) loci, but loss of Spt7 profoundly elevated the plasmid-based DNA recombination frequency. Consistently, loss of Spt7 increased spontaneous Rad52 foci by approximately two-fold upon entry into S phase. These results provide evidence that Spt7 contributes to the regulation of the normal replicative lifespan (RLS) and chronological lifespan (CLS), possibly by controlling the DNA recombination rate and overall mRNA expression. We propose that the regulation of SAGA complex integrity by Spt7 might be involved in the conserved regulatory pathway for lifespan regulation in eukaryotes.
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Affiliation(s)
- Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hyojeong Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Ruxin Duan
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea.
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29
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Wang CC, Hsieh HY, Hsieh HL, Tu SL. The Physcomitrella patens chromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing. PLANT PHYSIOLOGY 2021; 185:1229-1241. [PMID: 33793927 PMCID: PMC8133547 DOI: 10.1093/plphys/kiaa103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Plants perceive dynamic light conditions and optimize their growth and development accordingly by regulating gene expression at multiple levels. Alternative splicing (AS), a widespread mechanism in eukaryotes that post-transcriptionally generates two or more messenger RNAs (mRNAs) from the same pre-mRNA, is rapidly controlled by light. However, a detailed mechanism of light-regulated AS is still not clear. In this study, we demonstrate that histone 3 lysine 36 trimethylation (H3K36me3) rapidly and differentially responds to light at specific gene loci with light-regulated intron retention (IR) of their transcripts in the moss Physcomitrella patens. However, the level of H3K36me3 following exposure to light is inversely related to that of IR events. Physcomitrella patens MORF-related gene 1 (PpMRG1), a chromatin adaptor, bound with higher affinity to H3K36me3 in light conditions than in darkness and was differentially targeted to gene loci showing light-responsive IR. Transcriptome analysis indicated that PpMRG1 functions in the regulation of light-mediated AS. Furthermore, PpMRG1 was also involved in red light-mediated phototropic responses. Our results suggest that light regulates histone methylation, which leads to alterations of AS patterns. The chromatin adaptor PpMRG1 potentially participates in light-mediated AS, revealing that chromatin-coupled regulation of pre-mRNA splicing is an important aspect of the plant's response to environmental changes.
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Affiliation(s)
- Chien-Chang Wang
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yu Hsieh
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
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30
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Metselaar PI, Hos C, Welting O, Bosch JA, Kraneveld AD, de Jonge WJ, Te Velde AA. Ambiguity about Splicing Factor 3b Subunit 3 (SF3B3) and Sin3A Associated Protein 130 (SAP130). Cells 2021; 10:cells10030590. [PMID: 33800128 PMCID: PMC7999425 DOI: 10.3390/cells10030590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/29/2022] Open
Abstract
In 2020, three articles were published on a protein that can activate the immune system by binding to macrophage-inducible C-type lectin receptor (Mincle). In the articles, the protein was referred to as ‘SAP130, a subunit of the histone deacetylase complex.’ However, the Mincle ligand the authors aimed to investigate is splicing factor 3b subunit 3 (SF3B3). This splicing factor is unrelated to SAP130 (Sin3A associated protein 130, a subunit of the histone deacetylase-dependent Sin3A corepressor complex). The conclusions in the three articles were formulated for SF3B3, while the researchers used qPCR primers and antibodies against SAP130. We retraced the origins of the ambiguity about the two proteins and found that Online Mendelian Inheritance in Man (OMIM) added a Nature publication on SF3B3 as a reference for Sin3A associated protein 130 in 2016. Subsequently, companies such as Abcam referred to OMIM and the Nature article in their products for both SF3B3 and SAP130. In turn, the mistake by OMIM followed in the persistent and confusing use of ‘SAP130′ (spliceosome-associated protein 130) as an alternative symbol for SF3B3. With this report, we aim to eliminate the persistent confusion and separate the literature regarding the two proteins.
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Affiliation(s)
- Paula I. Metselaar
- Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; (C.H.); (O.W.); (W.J.d.J.); (A.A.T.V.)
- Correspondence:
| | - Celine Hos
- Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; (C.H.); (O.W.); (W.J.d.J.); (A.A.T.V.)
| | - Olaf Welting
- Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; (C.H.); (O.W.); (W.J.d.J.); (A.A.T.V.)
| | - Jos A. Bosch
- Department of Psychology, University of Amsterdam, 1018WS Amsterdam, The Netherlands;
- Department of Medical Psychology, Amsterdam UMC, University of Amsterdam, 1001NK Amsterdam, The Netherlands
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands;
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; (C.H.); (O.W.); (W.J.d.J.); (A.A.T.V.)
| | - Anje A. Te Velde
- Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; (C.H.); (O.W.); (W.J.d.J.); (A.A.T.V.)
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31
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Aki SS, Yura K, Aoyama T, Tsuge T. SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2021; 134:279-289. [PMID: 33555481 DOI: 10.1007/s10265-021-01260-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
COP9 signalosome (CSN) is a nuclear complex composed of eight distinct subunits that governs vast developmental processes in Arabidopsis thaliana (L.) Heynh. The null alleles of csn mutants display pleiotropic phenotypes that result in seedling lethality. To date, several partially complemented transgenic plants, expressing the particular CSN subunit in its corresponding null mutant allele, were utilized to bypass seedling lethality and investigate CSN regulation at later stages of development. One such transgenic plant corresponding to CSN1 subunit, fus6/CSN1-3-4, accumulates wild-type level of CSN1 and displays normal plant architecture at vegetative stage. Here we show through histological analyses that fus6/CSN1-3-4 plants display impairment of pollen development at the bicellular stage. This defect is identical to that observed in RNAi plants of SAP130, encoding a subunit of the multiprotein splicing factor SF3b. We further dissected the previously reported interaction between CSN1 and SAP130, to reveal that approximately 100 amino-acid residues located at the N-terminal end of CSN1 (CSN1NN) were essential for this interaction. In silico structure modeling demonstrated that CSN1NN could swing out towards SAP130 to dock onto its Helical Insertion protruding from the structure. These results support our model that CSN1 embeds itself within CSN protein complex through its C-terminal half and reaches out to targets through its N-terminal portion of the protein. Taken together, this is the first report to document the identical loss-of-function phenotypes of CSN1 and SAP130 during male gametogenesis. Thus, we propose that SAP130 and CSN1 coordinately regulate development of male reproductive organs.
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Affiliation(s)
- Shiori S Aki
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, 513 Tsurumaki, Waseda, Shinjuku, Tokyo, 162-0041, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
- Center for Interdisciplinary AI and Data Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Takashi Aoyama
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Tsuge
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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32
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Goh CJH, Wong JH, El Farran C, Tan BX, Coffill CR, Loh YH, Lane D, Arumugam P. Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen. G3 (BETHESDA, MD.) 2021; 11:jkaa069. [PMID: 33604667 PMCID: PMC8022920 DOI: 10.1093/g3journal/jkaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Vemurafenib is a BRAF kinase inhibitor (BRAFi) that is used to treat melanoma patients harboring the constitutively active BRAF-V600E mutation. However, after a few months of treatment patients often develop resistance to vemurafenib leading to disease progression. Sequence analysis of drug-resistant tumor cells and functional genomic screens has identified several genes that regulate vemurafenib resistance. Reactivation of mitogen-activated protein kinase (MAPK) pathway is a recurrent feature of cells that develop resistance to vemurafenib. We performed a genome-scale CRISPR-based knockout screen to identify modulators of vemurafenib resistance in melanoma cells with a highly improved CRISPR sgRNA library called Brunello. We identified 33 genes that regulate resistance to vemurafenib out of which 14 genes have not been reported before. Gene ontology enrichment analysis showed that the hit genes regulate histone modification, transcription and cell cycle. We discuss how inactivation of hit genes might confer resistance to vemurafenib and provide a framework for follow-up investigations.
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Affiliation(s)
| | - Jin Huei Wong
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
| | - Chadi El Farran
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Ban Xiong Tan
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore
| | | | - Yuin-Hain Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - David Lane
- p53Lab, A*STAR, Singapore 138648, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
- Singapore Institute for Food and Biotechnology Innovation, Singapore 138632, Singapore
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33
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Maiuri T, Hung CL, Suart C, Begeja N, Barba-Bazan C, Peng Y, Savic N, Wong T, Truant R. DNA Repair in Huntington's Disease and Spinocerebellar Ataxias: Somatic Instability and Alternative Hypotheses. J Huntingtons Dis 2021; 10:165-173. [PMID: 33579859 PMCID: PMC7990435 DOI: 10.3233/jhd-200414] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of genome wide association studies (GWAS) in Huntington's disease (HD) research, driven by unbiased human data analysis, has transformed the focus of new targets that could affect age at onset. While there is a significant depth of information on DNA damage repair, with many drugs and drug targets, most of this development has taken place in the context of cancer therapy. DNA damage repair in neurons does not rely on DNA replication correction mechanisms. However, there is a strong connection between DNA repair and neuronal metabolism, mediated by nucleotide salvaging and the poly ADP-ribose (PAR) response, and this connection has been implicated in other age-onset neurodegenerative diseases. Validation of leads including the mismatch repair protein MSH3, and interstrand cross-link repair protein FAN1, suggest the mechanism is driven by somatic CAG instability, which is supported by the protective effect of CAA substitutions in the CAG tract. We currently do not understand: how somatic instability is triggered; the state of DNA damage within expanding alleles in the brain; whether this damage induces mismatch repair and interstrand cross-link pathways; whether instability mediates toxicity, and how this relates to human ageing. We discuss DNA damage pathways uncovered by HD GWAS, known roles of other polyglutamine disease proteins in DNA damage repair, and a panel of hypotheses for pathogenic mechanisms.
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Affiliation(s)
- Tamara Maiuri
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Claudia L.K. Hung
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Celeste Suart
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Nola Begeja
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Carlos Barba-Bazan
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Yi Peng
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Natasha Savic
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Timothy Wong
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
| | - Ray Truant
- McMaster University, Department of Biochemistry and Biomedical Sciences, Hamilton, Ontario, Canada
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Grant PA, Winston F, Berger SL. The biochemical and genetic discovery of the SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194669. [PMID: 33338653 DOI: 10.1016/j.bbagrm.2020.194669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
One of the major advances in our understanding of gene regulation in eukaryotes was the discovery of factors that regulate transcription by controlling chromatin structure. Prominent among these discoveries was the demonstration that Gcn5 is a histone acetyltransferase, establishing a direct connection between transcriptional activation and histone acetylation. This breakthrough was soon followed by the purification of a protein complex that contains Gcn5, the SAGA complex. In this article, we review the early genetic and biochemical experiments that led to the discovery of SAGA and the elucidation of its multiple activities.
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Affiliation(s)
- Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, United States of America
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States of America.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Department of Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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Antisense Transcription across Nucleotide Repeat Expansions in Neurodegenerative and Neuromuscular Diseases: Progress and Mysteries. Genes (Basel) 2020; 11:genes11121418. [PMID: 33261024 PMCID: PMC7760973 DOI: 10.3390/genes11121418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Unstable repeat expansions and insertions cause more than 30 neurodegenerative and neuromuscular diseases. Remarkably, bidirectional transcription of repeat expansions has been identified in at least 14 of these diseases. More remarkably, a growing number of studies has been showing that both sense and antisense repeat RNAs are able to dysregulate important cellular pathways, contributing together to the observed clinical phenotype. Notably, antisense repeat RNAs from spinocerebellar ataxia type 7, myotonic dystrophy type 1, Huntington's disease and frontotemporal dementia/amyotrophic lateral sclerosis associated genes have been implicated in transcriptional regulation of sense gene expression, acting either at a transcriptional or posttranscriptional level. The recent evidence that antisense repeat RNAs could modulate gene expression broadens our understanding of the pathogenic pathways and adds more complexity to the development of therapeutic strategies for these disorders. In this review, we cover the amazing progress made in the understanding of the pathogenic mechanisms associated with repeat expansion neurodegenerative and neuromuscular diseases with a focus on the impact of antisense repeat transcription in the development of efficient therapies.
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Arede L, Pina C. Buffering noise: KAT2A modular contributions to stabilization of transcription and cell identity in cancer and development. Exp Hematol 2020; 93:25-37. [PMID: 33223444 DOI: 10.1016/j.exphem.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
KAT2A is a histone acetyltransferase recently identified as a vulnerability in at least some forms of Acute Myeloid Leukemia (AML). Its loss or inhibition prompts leukemia stem cells out of self-renewal and into differentiation with ultimate exhaustion of the leukemia pool. We have recently linked the Kat2a requirement in AML to control of transcriptional noise, reflecting an evolutionary-conserved role of Kat2a in promoting burst-like promoter activity and stabilizing gene expression. We suggest that through this role, Kat2a contributes to preservation of cell identity. KAT2A exerts its acetyltransferase activity in the context of two macromolecular complexes, Spt-Ada-Gcn5-Acetyltransferase (SAGA) and Ada-Two-A-Containing (ATAC), but the specific contribution of each complex to stabilization of gene expression is currently unknown. By reviewing specific gene targets and requirements of the two complexes in cancer and development, we suggest that SAGA regulates lineage-specific programs, and ATAC maintains biosynthetic activity through control of ribosomal protein and translation-associated genes, on which cells may be differentially dependent. While our data suggest that KAT2A-mediated regulation of transcriptional noise in AML may be exerted through ATAC, we discuss potential caveats and probe general vs. complex-specific contributions of KAT2A to transcriptional stability, with implications for control and perturbation of cell identity.
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Affiliation(s)
- Liliana Arede
- Departments of Haematology; Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- College of Health, Medicine and Life Sciences - Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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Shao W, Ding Z, Zheng ZZ, Shen JJ, Shen YX, Pu J, Fan YJ, Query CC, Xu YZ. Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription. Nucleic Acids Res 2020; 48:5799-5813. [PMID: 32399566 PMCID: PMC7293005 DOI: 10.1093/nar/gkaa311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 04/08/2020] [Accepted: 05/03/2020] [Indexed: 01/23/2023] Open
Abstract
Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome assembly and splicing proofreading at the branch-point region. From an open UV mutagenesis screen for genetic suppressors of prp5 defects and subsequent targeted testing, we identify components of the TBP-binding module of the Spt–Ada–Gcn5 Acetyltransferase (SAGA) complex, Spt8p and Spt3p. Spt8Δ and spt3Δ rescue the cold-sensitivity of prp5-GAR allele, and prp5 mutants restore growth of spt8Δ and spt3Δ strains on 6-azauracil. By chromatin immunoprecipitation (ChIP), we find that prp5 alleles decrease recruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Δ. Further ChIP-seq reveals that global effects on Pol II-binding are mutually rescued by prp5-GAR and spt8Δ. Inhibited splicing caused by prp5-GAR is also restored by spt8Δ. In vitro assays indicate that Prp5p directly interacts with Spt8p, but not Spt3p. We demonstrate that Prp5p's splicing proofreading is modulated by Spt8p and Spt3p. Therefore, this study reveals that interactions between the TBP-binding module of SAGA and the spliceosomal ATPase Prp5p mediate a balance between transcription initiation/elongation and pre-spliceosome assembly.
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Affiliation(s)
- Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhan Ding
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zeng-Zhang Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ji-Jia Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yu-Xian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jia Pu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Jie Fan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Yong-Zhen Xu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
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Torres-Zelada EF, Weake VM. The Gcn5 complexes in Drosophila as a model for metazoa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194610. [PMID: 32735945 DOI: 10.1016/j.bbagrm.2020.194610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/14/2023]
Abstract
The histone acetyltransferase Gcn5 is conserved throughout eukaryotes where it functions as part of large multi-subunit transcriptional coactivator complexes that stimulate gene expression. Here, we describe how studies in the model insect Drosophila melanogaster have provided insight into the essential roles played by Gcn5 in the development of multicellular organisms. We outline the composition and activity of the four different Gcn5 complexes in Drosophila: the Spt-Ada-Gcn5 Acetyltransferase (SAGA), Ada2a-containing (ATAC), Ada2/Gcn5/Ada3 transcription activator (ADA), and Chiffon Histone Acetyltransferase (CHAT) complexes. Whereas the SAGA and ADA complexes are also present in the yeast Saccharomyces cerevisiae, ATAC has only been identified in other metazoa such as humans, and the CHAT complex appears to be unique to insects. Each of these Gcn5 complexes is nucleated by unique Ada2 homologs or splice isoforms that share conserved N-terminal domains, and differ only in their C-terminal domains. We describe the common and specialized developmental functions of each Gcn5 complex based on phenotypic analysis of mutant flies. In addition, we outline how gene expression studies in mutant flies have shed light on the different biological roles of each complex. Together, these studies highlight the key role that Drosophila has played in understanding the expanded biological function of Gcn5 in multicellular eukaryotes.
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Affiliation(s)
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J. (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A. Int J Mol Sci 2020; 21:ijms21155234. [PMID: 32718059 PMCID: PMC7432364 DOI: 10.3390/ijms21155234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
DNA mismatch repair-deficient colorectal cancers (CRCs) accumulate numerous frameshift mutations at repetitive sequences recognized as microsatellite instability (MSI). When coding mononucleotide repeats (cMNRs) are affected, tumors accumulate frameshift mutations and premature termination codons (PTC) potentially leading to truncated proteins. Nonsense-mediated RNA decay (NMD) can degrade PTC-containing transcripts and protect from such faulty proteins. As it also regulates normal transcripts and cellular physiology, we tested whether NMD genes themselves are targets of MSI frameshift mutations. A high frequency of cMNR frameshift mutations in the UPF3A gene was found in MSI CRC cell lines (67.7%), MSI colorectal adenomas (55%) and carcinomas (63%). In normal colonic crypts, UPF3A expression was restricted to single chromogranin A-positive cells. SILAC-based proteomic analysis of KM12 CRC cells revealed UPF3A-dependent down-regulation of several enzymes involved in cholesterol biosynthesis. Furthermore, reconstituted UPF3A expression caused alterations of 85 phosphosites in 52 phosphoproteins. Most of them (38/52, 73%) reside in nuclear phosphoproteins involved in regulation of gene expression and RNA splicing. Since UPF3A mutations can modulate the (phospho)proteomic signature and expression of enzymes involved in cholesterol metabolism in CRC cells, UPF3A may influence other processes than NMD and loss of UPF3A expression might provide a growth advantage to MSI CRC cells.
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Affiliation(s)
- Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Eva-Maria Katzenmaier
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
| | - Nina Roeckel
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
| | - Stefan M. Woerner
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Internal Medicine I, Endocrinology and Metabolism, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Vera Fuchs
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, DKFZ (German Cancer Research Center), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Yan P. Yuan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Peer Bork
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany;
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Andreas Kulozik
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Department of Pediatric Oncology, Hematology and Immunology, Children’s Hospital, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.M.); (E.-M.K.); (N.R.); (V.F.); (M.v.K.D.); (M.K.); (J.K.)
- Molecular Medicine Partnership Unit, Medical Faculty of the University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; (S.M.W.); (P.B.); (G.N.-Y.); (A.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-564223
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40
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Nuño-Cabanes C, Rodríguez-Navarro S. The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194607. [PMID: 32712338 DOI: 10.1016/j.bbagrm.2020.194607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Gene expression, the decoding of DNA information into accessible instructions for protein synthesis, is a complex process in which multiple steps, including transcription, mRNA processing and mRNA export, are regulated by different factors. One of the first steps in this process involves chemical and structural changes in chromatin to allow transcription. For such changes to occur, histone tail and DNA epigenetic modifications foster the binding of transcription factors to promoter regions. The SAGA coactivator complex plays a crucial role in this process by mediating histone acetylation through Gcn5, and histone deubiquitination through Ubp8 enzymes. However, most SAGA subunits interact physically with other proteins beyond the SAGA complex. These interactions could represent SAGA-independent functions or a mechanism to widen SAGA multifunctionality. Among the different mechanisms to perform more than one function, protein moonlighting defines unrelated molecular activities for the same polypeptide sequence. Unlike pleiotropy, where a single gene can affect different phenotypes, moonlighting necessarily involves separate functions of a protein at the molecular level. In this review we describe in detail some of the alternative physical interactions of several SAGA subunits. In some cases, the alternative role constitutes a clear moonlighting function, whereas in most of them the lack of molecular evidence means that we can only define these interactions as promiscuous that require further work to verify if these are moonlighting functions.
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig, 11, E-46010 Valencia, Spain.
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Strahl BD, Briggs SD. The SAGA continues: The rise of cis- and trans-histone crosstalk pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194600. [PMID: 32645359 DOI: 10.1016/j.bbagrm.2020.194600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 01/30/2023]
Abstract
Fueled by key technological innovations during the last several decades, chromatin-based research has greatly advanced our mechanistic understanding of how genes are regulated by epigenetic factors and their associated histone-modifying activities. Most notably, the landmark finding that linked histone acetylation by Gcn5 of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex to gene activation ushered in a new area of chromatin research and a realization that histone-modifying activities have integral genome functions. This review will discuss past and recent studies that have shaped our understanding of how the histone-modifying activities of SAGA are regulated by, and modulate the outcomes of, other histone modifications during gene transcription. Because much of our understanding of SAGA was established with budding yeast, we will focus on yeast as a model. We discuss the actions of cis- and trans-histone crosstalk pathways that involve the histone acetyltransferase, deubiquitylase, and reader domains of SAGA. We conclude by considering unanswered questions about SAGA and related complexes.
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Affiliation(s)
- Brian D Strahl
- Department of Biochemistry and Biophysics, 120 Mason Farm Rd, University of North Carolina at Chapel Hill, NC 27599, USA.
| | - Scott D Briggs
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, Hansen Life Science Research Building, 201S, University Street, West Lafayette, IN 47907; USA.
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Cheon Y, Kim H, Park K, Kim M, Lee D. Dynamic modules of the coactivator SAGA in eukaryotic transcription. Exp Mol Med 2020; 52:991-1003. [PMID: 32616828 PMCID: PMC8080568 DOI: 10.1038/s12276-020-0463-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) is a highly conserved transcriptional coactivator that consists of four functionally independent modules. Its two distinct enzymatic activities, histone acetylation and deubiquitylation, establish specific epigenetic patterns on chromatin and thereby regulate gene expression. Whereas earlier studies emphasized the importance of SAGA in regulating global transcription, more recent reports have indicated that SAGA is involved in other aspects of gene expression and thus plays a more comprehensive role in regulating the overall process. Here, we discuss recent structural and functional studies of each SAGA module and compare the subunit compositions of SAGA with related complexes in yeast and metazoans. We discuss the regulatory role of the SAGA deubiquitylating module (DUBm) in mRNA surveillance and export, and in transcription initiation and elongation. The findings suggest that SAGA plays numerous roles in multiple stages of transcription. Further, we describe how SAGA is related to human disease. Overall, in this report, we illustrate the newly revealed understanding of SAGA in transcription regulation and disease implications for fine-tuning gene expression. A protein that helps add epigenetic information to genome, SAGA, controls many aspects of gene activation, potentially making it a target for cancer therapies. To fit inside the tiny cell nucleus, the genome is tightly packaged, and genes must be unpacked before they can be activated. Known to be important in genome opening, SAGA has now been shown to also play many roles in gene activation. Daeyoup Lee at the KAIST, Daejeon, South Korea, and co-workers have reviewed recent discoveries about SAGA’s structure, function, and roles in disease. They report that SAGA’s complex (19 subunits organized into four modules) allows it to play so many roles, genome opening, initiating transcription, and efficiently exporting mRNAs. Its master role means that malfunction of SAGA may be linked to many diseases.
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Affiliation(s)
- Youngseo Cheon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Harim Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Kyubin Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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Novak J, Zamostna B, Vopalensky V, Buryskova M, Burysek L, Doleckova D, Pospisek M. Interleukin-1α associates with the tumor suppressor p53 following DNA damage. Sci Rep 2020; 10:6995. [PMID: 32332775 PMCID: PMC7181607 DOI: 10.1038/s41598-020-63779-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/06/2020] [Indexed: 01/07/2023] Open
Abstract
Interleukin-1α (IL-1α) is a dual-function proinflammatory mediator. In addition to its role in the canonical IL-1 signaling pathway, which employs membrane-bound receptors, a growing body of evidence shows that IL-1α has some additional intracellular functions. We identified the interaction of IL-1α with the tumor suppressor p53 in the nuclei and cytoplasm of both malignant and noncancerous mammalian cell lines using immunoprecipitation and the in situ proximity ligation assay (PLA). This interaction was enhanced by treatment with the antineoplastic drug etoposide, which suggests a role for the IL-1α•p53 interaction in genotoxic stress.
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Affiliation(s)
- J Novak
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Zamostna
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - V Vopalensky
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M Buryskova
- Protean s.r.o., Dobra Voda u Ceskych Budejovic, Czech Republic
| | - L Burysek
- Protean s.r.o., Dobra Voda u Ceskych Budejovic, Czech Republic
| | - D Doleckova
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic.
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45
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Sun C. The SF3b complex: splicing and beyond. Cell Mol Life Sci 2020; 77:3583-3595. [PMID: 32140746 PMCID: PMC7452928 DOI: 10.1007/s00018-020-03493-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
The SF3b complex is an intrinsic component of the functional U2 small nuclear ribonucleoprotein (snRNP). As U2 snRNP enters nuclear pre-mRNA splicing, SF3b plays key roles in recognizing the branch point sequence (BPS) and facilitating spliceosome assembly and activation. Since the discovery of SF3b, substantial progress has been made in elucidating its molecular mechanism during splicing. In addition, numerous recent studies indicate that SF3b and its components are engaged in various molecular and cellular events that are beyond the canonical role in splicing. This review summarizes the current knowledge on the SF3b complex and highlights its multiple roles in splicing and beyond.
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Affiliation(s)
- Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500, China.
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46
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Abstract
Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.
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47
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Kwan SY, Sheel A, Song CQ, Zhang XO, Jiang T, Dang H, Cao Y, Ozata DM, Mou H, Yin H, Weng Z, Wang XW, Xue W. Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes. Hepatology 2020; 71:275-290. [PMID: 31188495 PMCID: PMC6906267 DOI: 10.1002/hep.30807] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/27/2019] [Indexed: 01/10/2023]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive subtype of liver cancer with few effective treatments, and the underlying mechanisms that drive HCC pathogenesis remain poorly characterized. Identifying genes and pathways essential for HCC cell growth will aid the development of new targeted therapies for HCC. Using a kinome CRISPR screen in three human HCC cell lines, we identified transformation/transcription domain-associated protein (TRRAP) as an essential gene for HCC cell proliferation. TRRAP has been implicated in oncogenic transformation, but how it functions in cancer cell proliferation is not established. Here, we show that depletion of TRRAP or its co-factor, histone acetyltransferase KAT5, inhibits HCC cell growth through induction of p53-independent and p21-independent senescence. Integrated cancer genomics analyses using patient data and RNA sequencing identified mitotic genes as key TRRAP/KAT5 targets in HCC, and subsequent cell cycle analyses revealed that TRRAP-depleted and KAT5-depleted cells are arrested at the G2/M phase. Depletion of topoisomerase II alpha (TOP2A), a mitotic gene and TRRAP/KAT5 target, was sufficient to recapitulate the senescent phenotype of TRRAP/KAT5 knockdown. Conclusion: Our results uncover a role for TRRAP/KAT5 in promoting HCC cell proliferation by activating mitotic genes. Targeting the TRRAP/KAT5 complex is a potential therapeutic strategy for HCC.
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Affiliation(s)
- Suet-Yan Kwan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ankur Sheel
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Tingting Jiang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Hien Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Yueying Cao
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Deniz M. Ozata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Hao Yin
- Medical research institute, Wuhan University, Wuhan, PR China
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605
- Program in Molecular Medicine, Department of Molecular, Cell and Cancer Biology, and Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605
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48
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Rechkunova NI, Maltseva EA, Lavrik OI. Post-translational Modifications of Nucleotide Excision Repair Proteins and Their Role in the DNA Repair. BIOCHEMISTRY (MOSCOW) 2019; 84:1008-1020. [PMID: 31693460 DOI: 10.1134/s0006297919090037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleotide excision repair (NER) is one of the major DNA repair pathways aimed at maintaining genome stability. Correction of DNA damage by the NER system is a multistage process that proceeds with the formation of multiple DNA-protein and protein-protein intermediate complexes and requires precise coordination and regulation. NER proteins undergo post-translational modifications, such as ubiquitination, sumoylation, phosphorylation, acetylation, and poly(ADP-ribosyl)ation. These modifications affect the interaction of NER factors with DNA and other proteins and thus regulate either their recruitment into the complexes or dissociation from these complexes at certain stages of DNA repair, as well as modulate the functional activity of NER proteins and control the process of DNA repair in general. Here, we review the data on the post-translational modifications of NER factors and their effects on DNA repair. Protein poly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerase 1 and its impact on NER are discussed in detail, since such analysis has not been done before.
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Affiliation(s)
- N I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - E A Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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49
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Nardi IK, Stark JM, Larsen A, Salgia R, Raz DJ. USP22 Interacts with PALB2 and Promotes Chemotherapy Resistance via Homologous Recombination of DNA Double-Strand Breaks. Mol Cancer Res 2019; 18:424-435. [PMID: 31685642 PMCID: PMC9285637 DOI: 10.1158/1541-7786.mcr-19-0053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/15/2019] [Accepted: 10/29/2019] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is a highly conserved pathway that can facilitate the repair of DNA double-strand breaks (DSB). Several Deubiquitinases (DUB) have been implicated as key players in DNA damage repair (DDR) through HR. Here, we report USP22, a DUB that is highly overexpressed in multiple cancer types, is necessary for HR through a direct interaction with PALB2 through its C-terminal WD40 domain. This interaction stimulates USP22 catalytic activity in vitro. Furthermore, we show USP22 is necessary for BRCA2, PALB2, and Rad51 recruitment to DSBs and this is, in part, through USP22 stabilizing BRCA2 and PALB2 levels. Taken together, our results describe a role for USP22 in DNA repair. IMPLICATIONS: This research provides new and exciting mechanistic insights into how USP22 overexpression promotes chemoresistance in lung cancer. We believe this study, and others, will help aid in developing targeted drugs toward USP22 and known binding partners for lung cancer treatment.
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Affiliation(s)
- Isaac K Nardi
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California.
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center, Duarte, California
| | - Adrien Larsen
- Department of Computational Therapeutics, City of Hope National Medical Center, Duarte, California
| | - Ravi Salgia
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Dan J Raz
- Division of Thoracic Surgery, Baum Family Thoracic Oncology Laboratory, City of Hope National Medical Center, Duarte, California
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California
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50
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Zhang S, Xu L, Tang Z, Wang H, Gu J, Sun B, Zhang W, Niu D, Feng J. Overexpression of Alteration/Deficiency in Activation 3 correlates with poor prognosis in non-small cell lung cancer. Pathol Res Pract 2019; 215:152408. [PMID: 30954347 DOI: 10.1016/j.prp.2019.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/17/2019] [Accepted: 03/31/2019] [Indexed: 12/24/2022]
Abstract
Alteration/Deficiency in Activation 3 (ADA3), the human homologue of yeast ADA3, is involved in a variety of cell biological processes and plays an important role in tumorigenesis. Here, western blotting and reverse-transcription quantitative PCR (RT-qPCR) were conducted to explore the expression pattern of ADA3 in non-small cell lung cancer (NSCLC) patients. It was found that ADA3 protein expression in cancerous tissues was significantly higher than that in adjacent normal lung tissues, but there were no differences in mRNA levels. Tissue microarray immunohistochemical assay (TMA-IHC) was performed and we investigated the prognostic significance of ADA3 expression in 84 cases of NSCLC. Survival analyses showed that high expression of ADA3 was an independent prognostic factor for unfavorable overall survival (OS) in patients with NSCLC. In summary, the ADA3 expression level elevates in NSCLC and correlates with poor OS in NSCLC patients.
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Affiliation(s)
- Shuwen Zhang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Liqin Xu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Zhiyuan Tang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Haiying Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Jun Gu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Baier Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Weishuai Zhang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Donghua Niu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Jian Feng
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
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