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Lu Y, Fu W, Xing W, Wu H, Zhang C, Xu D. Transcriptional regulation mechanism of PARP1 and its application in disease treatment. Epigenetics Chromatin 2024; 17:26. [PMID: 39118189 PMCID: PMC11308664 DOI: 10.1186/s13072-024-00550-w] [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: 04/08/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a multifunctional nuclear enzyme that catalyzes poly-ADP ribosylation in eukaryotic cells. In addition to maintaining genomic integrity, this nuclear enzyme is also involved in transcriptional regulation. PARP1 can trigger and maintain changes in the chromatin structure and directly recruit transcription factors. PARP1 also prevents DNA methylation. However, most previous reviews on PARP1 have focused on its involvement in maintaining genome integrity, with less focus on its transcriptional regulatory function. This article comprehensively reviews the transcriptional regulatory function of PARP1 and its application in disease treatment, providing new ideas for targeting PARP1 for the treatment of diseases other than cancer.
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Affiliation(s)
- Yu Lu
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China
- Hebei University, Baoding, Hebei, P.R. China
| | - Wenliang Fu
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China
| | - Weiwei Xing
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China
| | - Haowei Wu
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China
| | - Chao Zhang
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China.
| | - Donggang Xu
- Beijing Institute of Basic Medical Sciences, No. 27 Taiping Road, Beijing, 100850, P.R. China.
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2
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Eleazer R, Fondufe‐Mittendorf YN. The multifaceted role of PARP1 in RNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1617. [PMID: 32656996 PMCID: PMC7856298 DOI: 10.1002/wrna.1617] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are abundant nuclear proteins that synthesize ADP ribose polymers (pADPr) and catalyze the addition of (p)ADPr to target biomolecules. PARP1, the most abundant and well-studied PARP, is a multifunctional enzyme that participates in numerous critical cellular processes. A considerable amount of PARP research has focused on PARP1's role in DNA damage. However, an increasing body of evidence outlines more routine roles for PARP and PARylation in nearly every step of RNA biogenesis and metabolism. PARP1's involvement in these RNA processes is pleiotropic and has been ascribed to PARP1's unique flexible domain structures. PARP1 domains are modular self-arranged enabling it to recognize structurally diverse substrates and to act simultaneously through multiple discrete mechanisms. These mechanisms include direct PARP1-protein binding, PARP1-nucleic acid binding, covalent PARylation of target molecules, covalent autoPARylation, and induction of noncovalent interactions with PAR molecules. A combination of these mechanisms has been implicated in PARP1's context-specific regulation of RNA biogenesis and metabolism. We examine the mechanisms of PARP1 regulation in transcription initiation, elongation and termination, co-transcriptional splicing, RNA export, and post-transcriptional RNA processing. Finally, we consider promising new investigative avenues for PARP1 involvement in these processes with an emphasis on PARP1 regulation of subcellular condensates. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Yvonne N. Fondufe‐Mittendorf
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
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3
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Tian YN, Chen HD, Tian CQ, Wang YQ, Miao ZH. Polymerase independent repression of FoxO1 transcription by sequence-specific PARP1 binding to FoxO1 promoter. Cell Death Dis 2020; 11:71. [PMID: 31992690 PMCID: PMC6987093 DOI: 10.1038/s41419-020-2265-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/14/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) regulates gene transcription in addition to functioning as a DNA repair factor. Forkhead box O1 (FoxO1) is a transcription factor involved in extensive biological processes. Here, we report that PARP1 binds to two separate motifs on the FoxO1 promoter and represses its transcription in a polymerase-independent manner. Using PARP1-knock out (KO) cells, wild-type-PARP1-complemented cells and catalytic mutant PARP1E988K-reconstituted cells, we investigated transcriptional regulation by PARP1. PARP1 loss led to reduced DNA damage response and ~362-fold resistance to five PARP inhibitors (PARPis) in Ewing sarcoma cells. RNA sequencing showed 492 differentially expressed genes in a PARP1-KO subline, in which the FoxO1 mRNA levels increased up to more than five times. The change in the FoxO1 expression was confirmed at both mRNA and protein levels in different PARP1-KO and complemented cells. Moreover, exogenous PARP1 overexpression reduced the endogenous FoxO1 protein in RD-ES cells. Competitive EMSA and ChIP assays revealed that PARP1 specifically bound to the FoxO1 promoter. DNase I footprinting, mutation analyses, and DNA pulldown FREP assays showed that PARP1 bound to two particular nucleotide sequences separately located at −813 to −826 bp and −1805 to −1828 bp regions on the FoxO1 promoter. Either the PARPi olaparib or the PARP1 catalytic mutation (E988K) did not impair the repression of PARP1 on the FoxO1 expression. Exogenous FoxO1 overexpression did not impair cellular PARPi sensitivity. These findings demonstrate a new PARP1-gene promoter binding mode and a new transcriptional FoxO1 gene repressor.
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Affiliation(s)
- Yu-Nan Tian
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Hua-Dong Chen
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Chang-Qing Tian
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Ying-Qing Wang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
| | - Ze-Hong Miao
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. .,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
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Diastereomeric Recognition of 5',8-cyclo-2'-Deoxyadenosine Lesions by Human Poly(ADP-ribose) Polymerase 1 in a Biomimetic Model. Cells 2019; 8:cells8020116. [PMID: 30717407 PMCID: PMC6406461 DOI: 10.3390/cells8020116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/20/2019] [Accepted: 02/01/2019] [Indexed: 12/21/2022] Open
Abstract
5’,8-Cyclo-2’-deoxyadenosine (cdA), in the 5’R and 5’Sdiastereomeric forms, are typical non strand-break oxidative DNA lesions, induced by hydroxyl radicals, with emerging importance as a molecular marker. These lesions are exclusively repaired by the nucleotide excision repair (NER) mechanism with a low efficiency, thus readily accumulating in the genome. Poly(ADP-ribose) polymerase1 (PARP1) acts as an early responder to DNA damage and plays a key role as a nick sensor in the maintenance of the integrity of the genome by recognizing nicked DNA. So far, it was unknown whether the two diastereomeric cdA lesions could induce specific PARP1 binding. Here, we provide the first evidence of PARP1 to selectively recognize the diastereomeric lesions of 5’S-cdA and 5’R-cdA in vitro as compared to deoxyadenosine in model DNA substrates (23-mers) by using circular dichroism, fluorescence spectroscopy, immunoblotting analysis, and gel mobility shift assay. Several features of the recognition of the damaged and undamaged oligonucleotides by PARP1 were characterized. Remarkably, PARP1 exhibits different affinities in binding to a double strand (ds) oligonucleotide, which incorporates cdA lesions in R and S diastereomeric form. In particular, PARP1 proved to bind oligonucleotides, including a 5’S-cdA, with a higher affinity constant for the 5’S lesion in a model of ds DNA than 5’R-cdA, showing different recognition patterns, also compared with undamaged dA. This new finding highlights the ability of PARP1 to recognize and differentiate the distorted DNA backbone in a biomimetic system caused by different diastereomeric forms of a cdA lesion.
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Li G, Cunin P, Wu D, Diogo D, Yang Y, Okada Y, Plenge RM, Nigrovic PA. The Rheumatoid Arthritis Risk Variant CCR6DNP Regulates CCR6 via PARP-1. PLoS Genet 2016; 12:e1006292. [PMID: 27626929 PMCID: PMC5023119 DOI: 10.1371/journal.pgen.1006292] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/10/2016] [Indexed: 12/29/2022] Open
Abstract
Understanding the implications of genome-wide association studies (GWAS) for disease biology requires both identification of causal variants and definition of how these variants alter gene function. The non-coding triallelic dinucleotide polymorphism CCR6DNP is associated with risk for rheumatoid arthritis, and is considered likely causal because allelic variation correlates with expression of the chemokine receptor CCR6. Using transcription activator-like effector nuclease (TALEN) gene editing, we confirmed that CCR6DNP regulates CCR6. To identify the associated transcription factor, we applied a novel assay, Flanking Restriction Enhanced Pulldown (FREP), to identify specific association of poly (ADP-ribose) polymerase 1 (PARP-1) with CCR6DNP consistent with the established allelic risk hierarchy. Correspondingly, manipulation of PARP-1 expression or activity impaired CCR6 expression in several lineages. These findings show that CCR6DNP is a causal variant through which PARP-1 regulates CCR6, and introduce a highly efficient approach to interrogate non-coding genetic polymorphisms associated with human disease. Genome-wide association studies (GWAS) identify loci associated with human disease risk, but bridging the gap between locus and mechanism has proven particularly difficult in cases where associated variants do not alter coding. We aimed to develop a generalizable approach to this problem. Previously, a dual nucleotide polymorphism within the first intron of CCR6 (termed the CCR6DNP) had been associated with risk for rheumatoid arthritis, but the pathway by which this variant altered gene expression could not be determined. Here, we employed sequence perturbation to confirm a regulatory role for the CCR6DNP. Next, using a new technique termed Flanking Restriction Enhanced Pulldown (FREP), we identified PARP-1 as the protein that regulates CCR6 expression through allelic association with the CCR6DNP, a finding confirmed by chromatin immunoprecipitation and functional assays. These findings reveal an unexpected regulatory pathway for CCR6 implicated in rheumatoid arthritis and other disease by human genetics, and more generally introduce a novel approach to identifying regulatory protein-DNA interactions.
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Affiliation(s)
- Gang Li
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- * E-mail: (GL); (PAN)
| | - Pierre Cunin
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Di Wu
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Dorothée Diogo
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yu Yang
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Robert M. Plenge
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Peter A. Nigrovic
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Immunology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- * E-mail: (GL); (PAN)
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6
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Maluchenko NV, Kulaeva OI, Kotova EY, Chupyrkina AA, Nikitin DV, Kirpichnikov MP, Studitsky VM. Molecular mechanisms of transcriptional regulation by Poly(ADP-ribose) polymerase 1. Mol Biol 2015. [DOI: 10.1134/s0026893315010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae. SCIENCE CHINA-LIFE SCIENCES 2013; 57:52-8. [PMID: 24369357 DOI: 10.1007/s11427-013-4597-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
Abstract
Recent studies have found many antisense non-coding transcripts at the opposite strand of some protein-coding genes. In yeast, it was reported that such antisense transcripts play regulatory roles for their partner genes by forming a feedback loop with the protein-coding genes. Since not all coding genes have accompanying antisense transcripts, it would be interesting to know whether there are sequence signatures in a coding gene that are decisive or associated with the existence of such antisense partners. We collected all the annotated antisense transcripts in the yeast Saccharomyces cerevisiae, analyzed sequence motifs around the genes with antisense partners, and classified genes with and without accompanying antisense transcripts by using machine learning methods. Some weak but statistically significant sequence features are detected, which indicates that there are sequence signatures around the protein-coding genes that may be decisive or indicative for the existence of accompanying antisense transcripts.
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8
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Pelham C, Jimenez T, Rodova M, Rudolph A, Chipps E, Islam MR. Regulation of HFE expression by poly(ADP-ribose) polymerase-1 (PARP1) through an inverted repeat DNA sequence in the distal promoter. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1257-1265. [PMID: 24184271 DOI: 10.1016/j.bbagrm.2013.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/28/2013] [Accepted: 10/22/2013] [Indexed: 02/08/2023]
Abstract
Hereditary hemochromatosis (HH) is a common autosomal recessive disorder of iron overload among Caucasians of northern European descent. Over 85% of all cases with HH are due to mutations in the hemochromatosis protein (HFE) involved in iron metabolism. Although the importance in iron homeostasis is well recognized, the mechanism of sensing and regulating iron absorption by HFE, especially in the absence of iron response element in its gene, is not fully understood. In this report, we have identified an inverted repeat sequence (ATGGTcttACCTA) within 1700bp (-1675/+35) of the HFE promoter capable to form cruciform structure that binds PARP1 and strongly represses HFE promoter. Knockdown of PARP1 increases HFE mRNA and protein. Similarly, hemin or FeCl3 treatments resulted in increase in HFE expression by reducing nuclear PARP1 pool via its apoptosis induced cleavage, leading to upregulation of the iron regulatory hormone hepcidin mRNA. Thus, PARP1 binding to the inverted repeat sequence on the HFE promoter may serve as a novel iron sensing mechanism as increased iron level can trigger PARP1 cleavage and relief of HFE transcriptional repression.
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Affiliation(s)
- Christopher Pelham
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
| | - Tamara Jimenez
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
| | - Marianna Rodova
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
| | - Angela Rudolph
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
| | - Elizabeth Chipps
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
| | - M Rafiq Islam
- Biochemistry Laboratory, Northwest Missouri State University, Maryville, MO 64468
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9
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Ali AAE, Timinszky G, Arribas-Bosacoma R, Kozlowski M, Hassa PO, Hassler M, Ladurner AG, Pearl LH, Oliver AW. The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks. Nat Struct Mol Biol 2012; 19:685-692. [PMID: 22683995 PMCID: PMC4826610 DOI: 10.1038/nsmb.2335] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/29/2012] [Indexed: 12/22/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a primary DNA damage sensor whose (ADP-ribose) polymerase activity is acutely regulated by interaction with DNA breaks. Upon activation at sites of DNA damage, PARP1 modifies itself and other proteins by covalent addition of long, branched polymers of ADP-ribose, which in turn recruit downstream DNA repair and chromatin remodeling factors. PARP1 recognizes DNA damage through its N-terminal DNA-binding domain (DBD), which consists of a tandem repeat of an unusual zinc-finger (ZnF) domain. We have determined the crystal structure of the human PARP1-DBD bound to a DNA break. Along with functional analysis of PARP1 recruitment to sites of DNA damage in vivo, the structure reveals a dimeric assembly whereby ZnF1 and ZnF2 domains from separate PARP1 molecules form a strand-break recognition module that helps activate PARP1 by facilitating its dimerization and consequent trans-automodification.
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Affiliation(s)
- Ammar A E Ali
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN7 9QR, UK
| | - Gyula Timinszky
- Genome Biology Unit, Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Physiological Chemistry, Adolf Butenandt Institute, University of Munich, Butenandt Street 5, 81377 Munich, Germany
| | - Raquel Arribas-Bosacoma
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN7 9QR, UK
| | - Marek Kozlowski
- Genome Biology Unit, Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Physiological Chemistry, Adolf Butenandt Institute, University of Munich, Butenandt Street 5, 81377 Munich, Germany
| | - Paul O Hassa
- Genome Biology Unit, Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Hassler
- Genome Biology Unit, Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Physiological Chemistry, Adolf Butenandt Institute, University of Munich, Butenandt Street 5, 81377 Munich, Germany
| | - Andreas G Ladurner
- Genome Biology Unit, Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Physiological Chemistry, Adolf Butenandt Institute, University of Munich, Butenandt Street 5, 81377 Munich, Germany
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN7 9QR, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN7 9QR, UK
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Kobayashi T. Suppression of matrix metalloproteinase-9 expression in undifferentiated, non-apoptotic keratinocytes is abrogated by the cleavage of poly(ADP-ribose) polymerase-1. Apoptosis 2012; 16:1205-16. [PMID: 21915713 DOI: 10.1007/s10495-011-0650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Matrix metalloproteinase (MMP)-9, an enzyme that degrades the extracellular matrix, has been implicated as a key enzyme in the process of tissue remodeling. This study demonstrates the regulation of MMP-9 transcription through a gene regulatory element in its promoter (the KRE-M9 element). The KRE-M9-binding protein was purified and identified as poly(ADP-ribose) polymerase-1 (PARP-1), which inhibits the transcription of MMP-9 similar to involucrin. This regulation occurs in non-apoptotic keratinocytes using the distinctive culture conditions of high and low Ca(2+) levels. PARP cleavage, which occurs during apoptosis, results in de-repression of MMP-9 promoter activity. These data clarify a new role of PARP-1 and suggest a physiologically relevant connection between caspase activation and MMP-9 expression.
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Affiliation(s)
- Takashi Kobayashi
- Department of Dermatology, National Defense Medical College, Tokorozawa, Saitama, Japan.
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Jiang YC, Wu HM, Cheng KH, Sunny Sun H. Menstrual cycle-dependent febrile episode mediated by sequence-specific repression of poly(ADP-ribose) polymerase-1 on the transcription of the human serotonin receptor 1A gene. Hum Mutat 2011; 33:209-17. [DOI: 10.1002/humu.21622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/16/2011] [Indexed: 01/22/2023]
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12
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Ko HL, Ren EC. Novel poly (ADP-ribose) polymerase 1 binding motif in hepatitis B virus core promoter impairs DNA damage repair. Hepatology 2011; 54:1190-8. [PMID: 21721027 DOI: 10.1002/hep.24502] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 06/06/2011] [Indexed: 12/12/2022]
Abstract
UNLABELLED It is well-established that hepatitis B virus (HBV) infection is associated with the development of hepatocellular carcinoma (HCC), but patients with high viral DNA load have significantly higher risk. As host factors are required for efficient viral replication and may, therefore, contribute to high viral DNA load, we screened for host factors that can transcriptionally activate the HBV core promoter (HBVCP). We report here that poly (ADP-ribose) polymerase 1 (PARP1), which is known for its DNA repair activity, binds prominently to an octamer motif in the HBVCP and increases transcriptional efficiency. By utilizing a series of single base substitutions at each nucleotide position of the octamer, the PARP1 binding motif can be defined as "RNNWCAAA." Intriguingly, introduction of a vector construct bearing tandem repeats of the octamer motif was able to impair the DNA repair function of PARP1. This finding suggests that HBV viral DNA contains specific sequence motifs that may play a role in disrupting the DNA repair pathways of infected hepatocytes. CONCLUSION This study has identified a novel octamer motif in the HBVCP that binds PARP1, and this interaction increases the replication efficiency of HBV. The presence of this octamer motif in hepatocytes was shown to inhibit the DNA repair capacity of PARP1, potentially contributing to the development of HCC.
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Affiliation(s)
- Hui-Ling Ko
- Singapore Immunology Network, A*STAR, Immunos, Singapore
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Zhou X, Sun X, Cooper KL, Wang F, Liu KJ, Hudson LG. Arsenite interacts selectively with zinc finger proteins containing C3H1 or C4 motifs. J Biol Chem 2011; 286:22855-63. [PMID: 21550982 DOI: 10.1074/jbc.m111.232926] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Arsenic inhibits DNA repair and enhances the genotoxicity of DNA-damaging agents such as benzo[a]pyrene and ultraviolet radiation. Arsenic interaction with DNA repair proteins containing functional zinc finger motifs is one proposed mechanism to account for these observations. Here, we report that arsenite binds to both CCHC DNA-binding zinc fingers of the DNA repair protein PARP-1 (poly(ADP-ribose) polymerase-1). Furthermore, trivalent arsenite coordinated with all three cysteine residues as demonstrated by MS/MS. MALDI-TOF-MS analysis of peptides harboring site-directed substitutions of cysteine with histidine residues within the PARP-1 zinc finger revealed that arsenite bound to peptides containing three or four cysteine residues, but not to peptides with two cysteines, demonstrating arsenite binding selectivity. This finding was not unique to PARP-1; arsenite did not bind to a peptide representing the CCHH zinc finger of the DNA repair protein aprataxin, but did bind to an aprataxin peptide mutated to a CCHC zinc finger. To investigate the impact of arsenite on PARP-1 zinc finger function, we measured the zinc content and DNA-binding capacity of PARP-1 immunoprecipitated from arsenite-exposed cells. PARP-1 zinc content and DNA binding were decreased by 76 and 80%, respectively, compared with protein isolated from untreated cells. We observed comparable decreases in zinc content for XPA (xeroderma pigmentosum group A) protein (CCCC zinc finger), but not SP-1 (specificity protein-1) or aprataxin (CCHH zinc finger). These findings demonstrate that PARP-1 is a direct molecular target of arsenite and that arsenite interacts selectively with zinc finger motifs containing three or more cysteine residues.
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Affiliation(s)
- Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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The DNA-binding domain of human PARP-1 interacts with DNA single-strand breaks as a monomer through its second zinc finger. J Mol Biol 2011; 407:149-70. [PMID: 21262234 PMCID: PMC3094755 DOI: 10.1016/j.jmb.2011.01.034] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/16/2010] [Accepted: 01/14/2011] [Indexed: 01/10/2023]
Abstract
Poly(ADP-ribose)polymerase-1 (PARP-1) is a highly abundant chromatin-associated enzyme present in all higher eukaryotic cell nuclei, where it plays key roles in the maintenance of genomic integrity, chromatin remodeling and transcriptional control. It binds to DNA single- and double-strand breaks through an N-terminal region containing two zinc fingers, F1 and F2, following which its C-terminal catalytic domain becomes activated via an unknown mechanism, causing formation and addition of polyadenosine-ribose (PAR) to acceptor proteins including PARP-1 itself. Here, we report a biophysical and structural characterization of the F1 and F2 fingers of human PARP-1, both as independent fragments and in the context of the 24-kDa DNA-binding domain (F1 + F2). We show that the fingers are structurally independent in the absence of DNA and share a highly similar structural fold and dynamics. The F1 + F2 fragment recognizes DNA single-strand breaks as a monomer and in a single orientation. Using a combination of NMR spectroscopy and other biophysical techniques, we show that recognition is primarily achieved by F2, which binds the DNA in an essentially identical manner whether present in isolation or in the two-finger fragment. F2 interacts much more strongly with nicked or gapped DNA ligands than does F1, and we present a mutational study that suggests origins of this difference. Our data suggest that different DNA lesions are recognized by the DNA-binding domain of PARP-1 in a highly similar conformation, helping to rationalize how the full-length protein participates in multiple steps of DNA single-strand breakage and base excision repair.
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15
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Aker M, Bomsztyk K, Emery DW. Poly(ADP-ribose) polymerase-1 (PARP-1) contributes to the barrier function of a vertebrate chromatin insulator. J Biol Chem 2010; 285:37589-97. [PMID: 20876582 DOI: 10.1074/jbc.m110.174532] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The prototypic chromatin insulator cHS4 has proven effective in reducing silencing chromosomal position effects in a variety of settings. Most of this barrier insulator activity has been mapped to a 250-bp core region, as well as to several proteins that bind this region. However, recent studies from our laboratory demonstrated that an extended 400-bp core region of the cHS4 element is necessary to achieve full barrier insulator activity when used as a single copy in the context of recombinant gammaretroviral and lentiviral vectors. In this study, electrophoretic gel mobility shift assays revealed specific DNA-protein binding activities associated with the distal portion of this extended core region. Affinity purification and tandem mass spectrometry studies led to the identification of one of these proteins as poly(ADP-ribose) polymerase-1 (PARP-1). The identity of this binding activity as PARP-1 was subsequently verified by a variety of biochemical studies in vitro and by chromatin immunoprecipitation studies in vivo. Functional studies with gammaretroviral reporter vectors in cell lines and primary mouse bone marrow progenitor cultures showed that cHS4 barrier activity was abrogated upon mutation of the putative PARP-1-binding site or upon treatment with a PARP inhibitor, respectively. The barrier activity of the cHS4 element was also found to be abrogated in studies using bone marrow from Parp1-null mice. Taken together, this study demonstrates that binding of PARP-1 plays a key functional role in the barrier activity of the extended cHS4 insulator core element.
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Affiliation(s)
- Mari Aker
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
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16
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Chen J, Sun Y, Mao X, Liu Q, Wu H, Chen Y. RANKL up-regulates brain-type creatine kinase via poly(ADP-ribose) polymerase-1 during osteoclastogenesis. J Biol Chem 2010; 285:36315-21. [PMID: 20837480 DOI: 10.1074/jbc.m110.157743] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Receptor activator of nuclear factor κB ligand (RANKL) is the key regulator for osteoclast formation and function. During osteoclastogenesis, RANKL-stimulated signals differentially modulate expression of a large number of proteins. Using proteomics approaches, we identified that brain-type cytoplasmic creatine kinase (Ckb) was greatly induced in mature osteoclasts. Ckb has been shown to contribute to osteoclast function. However, the mechanisms of Ckb regulation and the contribution of other isoforms of creatine kinase during RANKL-induced osteoclastogenesis are unknown. We found that Ckb was the predominant isoform of creatine kinase during osteoclastogenesis. Real-time PCR confirmed that RANKL induced ckb mRNA expression by over 40-fold in primary mouse bone marrow macrophages and Raw 264.7 cells. The RANKL-responsive region was identified within the -0.4- to -0.2-kb 5'-flanking region of the ckb gene. Affinity binding purification followed by mass spectrometry analysis revealed that poly(ADP-ribose) polymerase-1 (PARP-1) bound to the -0.4/-0.2-kb fragment that negatively regulated expression of ckb in response to RANKL stimulation. Electrophoretic mobility shift assays with PARP-1-specific antibody located the binding site of PARP-1 to the TTCCCA consensus sequence. The expression of PARP-1 was reduced during RANKL-induced osteoclastogenesis, concurrently with increased expression of Ckb. Consistently, knockdown of PARP-1 by lentivirus-delivered shRNA enhanced ckb mRNA expression. The activity of PARP-1 was determined to be required for its inhibitory effect on the ckb expression. In summary, we have demonstrated that PARP-1 is a negative regulator of the ckb expression. Down-regulation of PARP-1 is responsible for the up-regulation of ckb during RANKL-induced osteoclastogenesis.
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Affiliation(s)
- Jianfeng Chen
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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17
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Zhu G, Chang P, Lippard SJ. Recognition of platinum-DNA damage by poly(ADP-ribose) polymerase-1. Biochemistry 2010; 49:6177-83. [PMID: 20550106 DOI: 10.1021/bi100775t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) was recently identified as a platinum-DNA damage response protein. To investigate the properties of binding of PARP-1 to different platinum-DNA adducts in greater detail, biotinylated DNA probes containing a site-specific cisplatin 1,2-d(GpG) or 1,3-d(GpTpG) intrastrand cross-link or a cisplatin 5'-GC/5'-GC interstrand cross-link (ICL) were utilized in binding assays with cell-free extracts (CFEs) in vitro. The activated state of PARP-1 was generated by treatment of cells with a DNA-damaging agent or by addition of NAD(+) to CFEs. PARP-1 binds with a higher affinity to cisplatin-damaged DNA than to undamaged DNA, and the amount of protein that binds to the most common cisplatin-DNA cross-link, 1,2-d(GpG), is greater than the amount that binds to other types of cisplatin-DNA cross-links. Both DNA damage-activated PARP-1 and unactivated PARP-1 bind to cisplatin-damaged DNA, and both automodified PARP-1 and cleaved PARP-1 bind to cisplatin-DNA lesions. The role of poly(ADP-ribose) (pADPr) in mediating binding of PARP-1 to platinum damage was further investigated. The extent of binding of PARP-1 to the cisplatin 1,2-d(GpG) cross-link decreases upon automodification, and overactivated PARP-1 loses its affinity for the cross-link. Elimination of pADPr facilitates binding of PARP-1 to the cisplatin 1,2-d(GpG) cross-link. PARP-1 also binds to DNA damaged by other platinum compounds, including oxaliplatin and pyriplatin, indicating protein affinity for the damage in an adduct-specific manner rather than recognition of distorted DNA. Our results reveal the unique binding properties for binding of PARP-1 to platinum-DNA damage, providing insights into, and a better understanding of, the cellular response to platinum-based anticancer drugs.
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Affiliation(s)
- Guangyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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18
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Yang N, Gong F, Sun L, Yang D, Han X, Ma C, Sun Y. Poly (ADP-ribose) polymerase-1 binds to BCL2 major breakpoint region and regulates BCL2 expression. J Cell Biochem 2010; 110:1208-18. [DOI: 10.1002/jcb.22635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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19
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Uncoupling of the transactivation and transrepression functions of PARP1 protein. Proc Natl Acad Sci U S A 2010; 107:6406-11. [PMID: 20371698 DOI: 10.1073/pnas.0914152107] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Poly(ADP ribose) polymerase 1 (PARP1) is a nuclear protein that regulates chromatin remodeling and transcription as well as DNA repair and genome stability pathways. Recent studies have revealed a paradoxical dual role of PARP1 protein in transcription. Specifically, although PARP1 controls transcriptional activation of a subset of genes that are heat shock- or hormone-dependent, it also directly inactivates transcription, establishes heterochromatin domains, and silences retrotransposable elements. However, the domains required for these disparate functions are currently unknown. In this paper, we report the discovery of a previously undescribed mutation in the Drosophila Parp locus. We show that the mutants express a deletion mutant of PARP1 protein with an altered DNA binding domain that carries only the second Zn-finger. We demonstrate that this alteration specifically excludes PARP1 protein from heterochromatin and makes PARP1 unable to maintain repression of retrotransposable elements. By characterizing the biological activity of this unique PARP1 mutant protein isoform, we have uncoupled the transactivation and transrepression functions of this protein.
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20
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Agarwal A, Mahfouz RZ, Sharma RK, Sarkar O, Mangrola D, Mathur PP. Potential biological role of poly (ADP-ribose) polymerase (PARP) in male gametes. Reprod Biol Endocrinol 2009; 7:143. [PMID: 19961617 PMCID: PMC2800114 DOI: 10.1186/1477-7827-7-143] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 12/05/2009] [Indexed: 12/13/2022] Open
Abstract
Maintaining the integrity of sperm DNA is vital to reproduction and male fertility. Sperm contain a number of molecules and pathways for the repair of base excision, base mismatches and DNA strand breaks. The presence of Poly (ADP-ribose) polymerase (PARP), a DNA repair enzyme, and its homologues has recently been shown in male germ cells, specifically during stage VII of spermatogenesis. High PARP expression has been reported in mature spermatozoa and in proven fertile men. Whenever there are strand breaks in sperm DNA due to oxidative stress, chromatin remodeling or cell death, PARP is activated. However, the cleavage of PARP by caspase-3 inactivates it and inhibits PARP's DNA-repairing abilities. Therefore, cleaved PARP (cPARP) may be considered a marker of apoptosis. The presence of higher levels of cPARP in sperm of infertile men adds a new proof for the correlation between apoptosis and male infertility. This review describes the possible biological significance of PARP in mammalian cells with the focus on male reproduction. The review elaborates on the role played by PARP during spermatogenesis, sperm maturation in ejaculated spermatozoa and the potential role of PARP as new marker of sperm damage. PARP could provide new strategies to preserve fertility in cancer patients subjected to genotoxic stresses and may be a key to better male reproductive health.
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Affiliation(s)
- Ashok Agarwal
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Reda Z Mahfouz
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Rakesh K Sharma
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Oli Sarkar
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
- McGill University Health Center, Montreal, Canada
| | - Devna Mangrola
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Premendu P Mathur
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
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21
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Mahoney W, Hong JH, Yaffe M, Farrance I. The transcriptional co-activator TAZ interacts differentially with transcriptional enhancer factor-1 (TEF-1) family members. Biochem J 2009; 388:217-25. [PMID: 15628970 PMCID: PMC1186710 DOI: 10.1042/bj20041434] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Members of the highly related TEF-1 (transcriptional enhancer factor-1) family (also known as TEAD, for TEF-1, TEC1, ABAA domain) bind to MCAT (muscle C, A and T sites) and A/T-rich sites in promoters active in cardiac, skeletal and smooth muscle, placenta, and neural crest. TEF-1 activity is regulated by interactions with transcriptional co-factors [p160, TONDU (Vgl-1, Vestigial-like protein-1), Vgl-2 and YAP65 (Yes-associated protein 65 kDa)]. The strong transcriptional co-activator YAP65 interacts with all TEF-1 family members, and, since YAP65 is related to TAZ (transcriptional co-activator with PDZ-binding motif), we wanted to determine if TAZ also interacts with members of the TEF-1 family. In the present study, we show by GST (glutathione S-transferase) pull-down assays, by co-immunoprecipitation and by modified mammalian two-hybrid assays that TEF-1 interacts with TAZ in vitro and in vivo. Electrophoretic mobility-shift assays with purified TEF-1 and GST-TAZ fusion protein showed that TAZ interacts with TEF-1 bound to MCAT DNA. TAZ can interact with endogenous TEF-1 proteins, since exogenous TAZ activated MCAT-dependent reporter promoters. Like YAP65, TAZ interacted with all four TEF-1 family members. GST pull-down assays with increasing amounts of [35S]TEF-1 and [35S]RTEF-1 (related TEF-1) showed that TAZ interacts more efficiently with TEF-1 than with RTEF-1. This differential interaction also extended to the interaction of TEF-1 and RTEF-1 with TAZ in vivo, as assayed by a modified mammalian two-hybrid experiment. These data show that differential association of TEF-1 proteins with transcriptional co-activators may regulate the activity of TEF-1 family members.
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Affiliation(s)
- William M. Mahoney
- *Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, U.S.A
| | - Jeong-Ho Hong
- †Center for Cancer Research, E18-580, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, U.S.A
| | - Michael B. Yaffe
- †Center for Cancer Research, E18-580, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, U.S.A
| | - Iain K. G. Farrance
- *Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, U.S.A
- To whom correspondence should be addressed (email )
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22
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Vidaković M, Gluch A, Qiao J, Oumard A, Frisch M, Poznanović G, Bode J. PARP-1 expression in the mouse is controlled by an autoregulatory loop: PARP-1 binding to an upstream S/MAR element and to a novel recognition motif in its promoter suppresses transcription. J Mol Biol 2009; 388:730-50. [PMID: 19303024 DOI: 10.1016/j.jmb.2009.03.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/26/2009] [Accepted: 03/09/2009] [Indexed: 11/16/2022]
Abstract
This work identifies central components of a feedback mechanism for the expression of mouse poly(ADP-ribose) polymerase-1 (PARP-1). Using the stress-induced duplex destabilization algorithm, multiple base-unpairing regions (BURs) could be localized in the 5' region of the mouse PARP-1 gene (muPARP-1). Some of these could be identified as scaffold/matrix-attachment regions (S/MARs), suggesting an S/MAR-mediated transcriptional regulation. PARP-1 binding to the most proximal element, S/MAR 1, and to three consensus motifs, AGGCC, in its own promoter (basepairs -956 to +100), could be traced by electrophoretic mobility-shift assay. The AGGCC-complementary GGCCT motif was detected by cis-diammine-dichloro platinum cross-linking and functionally characterized by the effects of site-directed mutagenesis on its performance in wild type (PARP-1(+/+)) and PARP-1 knockout cells (PARP-1(-/-)). Mutation of the central AGGCC tract at basepairs -554 to -550 prevented PARP-1/promoter interactions, whereby muPARP-1 expression became up-regulated. Transfection of a series of reporter gene constructs with or without S/MAR 1 (basepairs -1523 to -1007) and the more distant S/MAR 2 (basepairs -8373 to -6880), into PARP-1(+/+) as well as PARP-1(-/-) cells, revealed an additional, major level of muPARP-1 promoter down-regulation, triggered by PARP-1 binding to S/MAR 1. We conclude that S/MAR 1 represents an upstream control element that acts in conjunction with the muPARP-1 promoter. These interactions are part of a negative autoregulatory loop.
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Affiliation(s)
- Melita Vidaković
- Helmholtz Centre for Infection Research, Epigenetic Regulation, Braunschweig, Germany
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23
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Kotova E, Jarnik M, Tulin AV. Poly (ADP-ribose) polymerase 1 is required for protein localization to Cajal body. PLoS Genet 2009; 5:e1000387. [PMID: 19229318 PMCID: PMC2637609 DOI: 10.1371/journal.pgen.1000387] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 01/20/2009] [Indexed: 11/19/2022] Open
Abstract
Recently, the nuclear protein known as Poly (ADP-ribose) Polymerase1 (PARP1) was shown to play a key role in regulating transcription of a number of genes and controlling the nuclear sub-organelle nucleolus. PARP1 enzyme is known to catalyze the transfer of ADP-ribose to a variety of nuclear proteins. At present, however, while we do know that the main acceptor for pADPr in vivo is PARP1 protein itself, by PARP1 automodification, the significance of PARP1 automodification for in vivo processes is not clear. Therefore, we investigated the roles of PARP1 auto ADP-ribosylation in dynamic nuclear processes during development. Specifically, we discovered that PARP1 automodification is required for shuttling key proteins into Cajal body (CB) by protein non-covalent interaction with pADPr in vivo. We hypothesize that PARP1 protein shuttling follows a chain of events whereby, first, most unmodified PARP1 protein molecules bind to chromatin and accumulate in nucleoli, but then, second, upon automodification with poly(ADP-ribose), PARP1 interacts non-covalently with a number of nuclear proteins such that the resulting protein-pADPr complex dissociates from chromatin into CB.
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Affiliation(s)
- Elena Kotova
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Michael Jarnik
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Alexei V. Tulin
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
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24
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Wang J, Bian C, Li J, Couch FJ, Wu K, Zhao RC. Poly(ADP-ribose) polymerase-1 down-regulates BRCA2 expression through the BRCA2 promoter. J Biol Chem 2008; 283:36249-56. [PMID: 18990703 PMCID: PMC2605989 DOI: 10.1074/jbc.m803693200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 11/05/2008] [Indexed: 01/05/2023] Open
Abstract
Expression of the BRCA2 tumor suppressor gene is tightly linked to its roles in DNA damage repair and maintenance of chromosomal stability and genomic integrity. Three transcription factors that activate (USF, NF-kappaB, and Elf1) and a single factor that represses (SLUG) BRCA2 promoter activity have been reported. In addition, a 67-bp region (-582 to -516) associated with inhibition of promoter activity has been identified. However, it remains unclear how the 67-bp region contributes to regulation of BRCA2 expression. Here, we describe the affinity purification of a 120-kDa protein that binds to a silencer-binding region within the 67-bp repression region of the BRCA2 promoter. Mass spectrometry revealed the identity of the protein as poly-(ADP-ribose) polymerase-1 (Parp-1). Gel shift, antibody super-shift, and chromatin immunoprecipitation (ChIP) assays demonstrated that Parp-1 is associated with the BRCA2 promoter both in vitro and in vivo. Furthermore, Parp-1 inhibitors (either 3-AB or NU1025) and Parp-1 gene specific siRNA resulted in increased levels of endogenous BRCA2 expression. Inhibition of Parp-1 activity (by 3-AB) reduced histone 3 lysine 9 acetylation and blocked Parp-1 binding to the BRCA2 promoter. These results indicate that Parp-1 down-regulates BRCA2 expression through an interaction with a repression region of the BRCA2 promoter.
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Affiliation(s)
- Jinhua Wang
- Institute of Basic Medical Sciences and School of Basic Medicine, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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25
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Ambrose HE, Willimott S, Beswick RW, Dantzer F, de Murcia JM, Yelamos J, Wagner SD. Poly(ADP-ribose) polymerase-1 (Parp-1)-deficient mice demonstrate abnormal antibody responses. Immunology 2008; 127:178-86. [PMID: 18778284 DOI: 10.1111/j.1365-2567.2008.02921.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Poly(ADP-ribosylation) of acceptor proteins is an epigenetic modification involved in DNA strand break repair, recombination and transcription. Here we provide evidence for the involvement of poly(ADP-ribose) polymerase-1 (Parp-1) in antibody responses. Parp-1(-/-) mice had increased numbers of T cells and normal numbers of total B cells. Marginal zone B cells were mildly reduced in number, and numbers of follicular B cells were preserved. There were abnormal levels of basal immunoglobulins, with reduced levels of immunoglobulin G2a (IgG2a) and increased levels of IgA and IgG2b. Analysis of specific antibody responses showed that T cell-independent responses were normal but T cell-dependent responses were markedly reduced. Germinal centres were normal in size and number. In vitro purified B cells from Parp-1(-/-) mice proliferated normally and showed normal IgM secretion, decreased switching to IgG2a but increased IgA secretion. Collectively our results demonstrate that Parp-1 has essential roles in normal T cell-dependent antibody responses and the regulation of isotype expression. We speculate that Parp-1 forms a component of the protein complex involved in resolving the DNA double-strand breaks that occur during class switch recombination.
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26
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Kraus WL. Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr Opin Cell Biol 2008; 20:294-302. [PMID: 18450439 DOI: 10.1016/j.ceb.2008.03.006] [Citation(s) in RCA: 342] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 03/11/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
Abstract
The regulation of gene expression requires a wide array of protein factors that can modulate chromatin structure, act at enhancers, function as transcriptional coregulators, or regulate insulator function. Poly(ADP-ribose) polymerase-1 (PARP-1), an abundant and ubiquitous nuclear enzyme that catalyzes the NAD(+)-dependent addition of ADP-ribose polymers on a variety of nuclear proteins, has been implicated in all of these functions. Recent biochemical, genomic, proteomic, and cell-based studies have highlighted the role of PARP-1 in each of these processes and provided new insights about the molecular mechanisms governing PARP-1-dependent regulation of gene expression. In addition, these studies have demonstrated how PARP-1 functions as an integral part of cellular signaling pathways that culminate in gene-regulatory outcomes.
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Affiliation(s)
- W Lee Kraus
- Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, United States.
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27
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Langelier MF, Servent KM, Rogers EE, Pascal JM. A third zinc-binding domain of human poly(ADP-ribose) polymerase-1 coordinates DNA-dependent enzyme activation. J Biol Chem 2007; 283:4105-14. [PMID: 18055453 DOI: 10.1074/jbc.m708558200] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a chromatin-associated enzyme with multiple cellular functions, including DNA repair, transcriptional regulation, and cell signaling. PARP-1 has a modular architecture with six independent domains comprising the 113-kDa polypeptide. Two zinc finger domains at the N terminus of PARP-1 bind to DNA and thereby activate the catalytic domain situated at the C terminus of the enzyme. The tight coupling of DNA binding and catalytic activities is critical to the cellular regulation of PARP-1 function; however, the mechanism for coordinating these activities remains an unsolved problem. Here, we demonstrate using spectroscopic and crystallographic analysis that human PARP-1 has a third zinc-binding domain. Biochemical mutagenesis and deletion analysis indicate that this region mediates interdomain contacts important for DNA-dependent enzyme activation. The crystal structure of the third zinc-binding domain reveals a zinc ribbon fold and suggests conserved residues that could form interdomain contacts. The new zinc-binding domain self-associates in the crystal lattice to form a homodimer with a head-totail arrangement. The structure of the homodimer provides a scaffold for assembling the activated state of PARP-1 and suggests a mechanism for coupling the DNA binding and catalytic functions of PARP-1.
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Affiliation(s)
- Marie-France Langelier
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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28
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Pinnola A, Naumova N, Shah M, Tulin AV. Nucleosomal Core Histones Mediate Dynamic Regulation of Poly(ADP-ribose) Polymerase 1 Protein Binding to Chromatin and Induction of Its Enzymatic Activity. J Biol Chem 2007; 282:32511-9. [PMID: 17827147 DOI: 10.1074/jbc.m705989200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 protein (PARP1) mediates chromatin loosening and activates the transcription of inducible genes, but the mechanism of PARP1 regulation in chromatin is poorly understood. We have found that PARP1 interaction with chromatin is dynamic and that PARP1 is exchanged continuously between chromatin and nucleoplasm, as well as between chromatin domains. Specifically, the PARP1 protein preferentially interacts with nucleosomal particles, and although the nucleosomal linker DNA is not necessary for this interaction, we have shown that the core histones, H3 and H4, are critical for PARP1 binding. We have also demonstrated that the histones H3 and H4 interact preferentially with the C-terminal portion of PARP1 protein and that the N-terminal domain of PARP1 negatively regulates these interactions. Finally, we have found that interaction with the N-terminal tail of the H4 histone triggers PARP1 enzymatic activity. Therefore, our data collectively suggests a model in which both the regulation of PARP1 protein binding to chromatin and the enzymatic activation of PARP1 protein depend on the dynamics of nucleosomal core histone mediation.
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Affiliation(s)
- Aaron Pinnola
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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29
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Ambrose HE, Papadopoulou V, Beswick RW, Wagner SD. Poly-(ADP-ribose) polymerase-1 (Parp-1) binds in a sequence-specific manner at the Bcl-6 locus and contributes to the regulation of Bcl-6 transcription. Oncogene 2007; 26:6244-52. [PMID: 17404575 DOI: 10.1038/sj.onc.1210434] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bcl-6 is a transcription factor that is normally expressed in germinal centre B cells. It is essential for the formation of germinal centres and the production of high-affinity antibodies. Transcriptional downregulation of Bcl-6 occurs on terminal differentiation to plasma cells. Bcl-6 is highly expressed in B-cell non-Hodgkin's lymphoma and, in a subset of cases of diffuse large cell lymphoma, the mechanism of Bcl-6 overexpression involves interruption of normal transcriptional controls. Transcriptional control of Bcl-6 is, therefore, important for normal antibody responses and lymphomagenesis, but little is known of the cis-acting control elements. This report focuses on a region of mouse/human sequence homology in the first intron of Bcl-6, which is a candidate site for such a control element. We demonstrate that poly-(ADP-ribose) polymerase-1 (Parp-1) binds in vitro and in vivo to specific sequences in this region. We further show that PARP inhibitors, and Parp-1 knockdown by siRNA induce Bcl-6 mRNA expression in Bcl-6 expressing cell lines. We speculate that Parp-1 activation plays a role in switching off Bcl-6 transcription and subsequent B-cell exit from the germinal centre.
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Affiliation(s)
- H E Ambrose
- Division of Investigative Sciences, Department of Haematology, Imperial College London, Hammersmith Hospital, London, UK
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30
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Beranger GE, Momier D, Rochet N, Quincey D, Guigonis JM, Samson M, Carle GF, Scimeca JC. RANKL treatment releases the negative regulation of the poly(ADP-ribose) polymerase-1 on Tcirg1 gene expression during osteoclastogenesis. J Bone Miner Res 2006; 21:1757-69. [PMID: 17002555 DOI: 10.1359/jbmr.060809] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
UNLABELLED The Tcirg1 gene encodes the osteoclast-specific a3 isoform of the V-ATPase a subunit. Using the mouse osteoclastic model RAW264.7 cells, we studied Tcirg1 gene expression, and we identified PARP-1 as a transcriptional repressor negatively regulated by RANKL during osteoclastogenesis. INTRODUCTION The TCIRG1 gene encodes the a3 isoform of the V-ATPase a subunit, and mutations at this locus account for approximately 60% of infantile malignant osteopetrosis cases. Using RAW264.7 cells as an osteoclastic differentiation model, we undertook a transcriptional study of the mouse Tcirg1 gene focused on the 4-kb region upstream of the transcription starting point. MATERIALS AND METHODS The promoter activity of serial-deletion fragments of the Tcirg1 gene promoter was monitored throughout the RAW264.7 cell differentiation process. We next performed EMSA, UV cross-linking, affinity purification, mass spectrometry analysis, gel supershift, and siRNA transfection experiments to identify the factor(s) interacting with the promoter. RESULTS The -3946/+113 region of the mouse Tcirg1 gene displayed a high basal promoter activity, which was enhanced by RANKL treatment of RAW264.7 cells. Constructs deleted up to -1589 retained this response to RANKL. A deletion up to -1402 induced a 3-fold enhancement of the basal activity, whereas RANKL response was not affected. EMSA experiments led us to identify within the -1589/-1402 region, a 10-nucleotide sequence, which bound a nuclear protein present in nondifferentiated RAW264.7 cells. This interaction was lost using nuclear extracts derived from RANKL-treated cells. Affinity purification followed by mass spectrometry analysis and gel supershift assay allowed the identification of poly(ADP-ribose) polymerase-1 (PARP-1) as this transcriptional repressor, whereas Western blot experiments revealed the cleavage of the DNA-binding domain of PARP-1 on RANKL treatment. Finally, both PARP-1 depletion after siRNA transfection and RAW264.7 cell treatment by an inhibitor of PARP-1 activity induced an increase of a3 mRNA expression. CONCLUSIONS We provide evidence that the basal transcription activity of the Tcirg1 gene is negatively regulated by the binding of PARP-1 protein to its promoter region in mouse pre-osteoclast. On RANKL treatment, PARP-1 protein is cleaved and loses its repression effect, allowing an increase of Tcirg1 gene expression that is critical for osteoclast function.
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Affiliation(s)
- Guillaume E Beranger
- GéPITOS-K2943 CNRS/UNSA, Faculté de Médecine de l'Université de Nice-Sophia Antipolis, Nice, France
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Amiri KI, Ha HC, Smulson ME, Richmond A. Differential regulation of CXC ligand 1 transcription in melanoma cell lines by poly(ADP-ribose) polymerase-1. Oncogene 2006; 25:7714-22. [PMID: 16799643 PMCID: PMC2665274 DOI: 10.1038/sj.onc.1209751] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The continuous production of the CXC ligand 1 (CXCL1) chemokine by melanoma cells is a major effector of tumor growth. We have previously shown that the constitutive expression of this chemokine is dependent upon transcription factors nuclear factor-kappa B (NF-kappaB), stimulating protein-1 (SP1), high-mobility group-I/Y (HMGI/Y), CAAT displacement protein (CDP) and poly(ADP-ribose) polymerase-1 (PARP-1). In this study, we demonstrate for the first time the mechanism of transcriptional regulation of CXCL1 through PARP-1 in melanoma cells. In its inactive state, PARP-1 binds to the CXCL1 promoter in a sequence-specific manner and prevents binding of NF-kappaB (p65/p50) to its element. However, activation of the PARP-1 enzymatic activity enhances CXCL1 expression, owing to the loss of PARP-1 binding to the CXCL1 promoter, accompanied by enhanced binding of p65 to the promoter. The delineation of the role of NF-kappaB-interacting factors in the putative CXCL1 enhanceosome will provide key information in developing strategies to block constitutive expression of this and other chemokines in cancer and to develop targeted therapy.
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Affiliation(s)
- KI Amiri
- Department of Veterans Affairs, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Microbiology, Meharry Medical College, Nashville, TN, USA
| | - HC Ha
- Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC, USA
| | - ME Smulson
- Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, Washington, DC, USA
| | - A Richmond
- Department of Veterans Affairs, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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