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Deater M, Lloyd RE. TDRD3 functions as a selective autophagy receptor with dual roles in autophagy and modulation of stress granule stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.22.614367. [PMID: 39345463 PMCID: PMC11430058 DOI: 10.1101/2024.09.22.614367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Tudor Domain Containing 3 (TDRD3) is a methylarginine-reader protein that functions as a scaffold in the nucleus facilitating transcription, however TDRD3 is also recruited to stress granules (SGs) during the Integrated Stress Response (ISR) although its function therein remains largely unknown. We previously showed that TDRD3 is a novel antiviral restriction factor that is cleaved by virus 2A protease, and plays complex modulatory roles in both interferon and inflammatory signaling during stress and enterovirus infections. Here we have found that TDRD3 contains structural motifs similar to known selective autophagy receptors such as p62/SQSTM1, sharing ubiquitin associated domains (UBA) and LC3 interacting regions (LIR) that anchor cargo destined for autophagosomes to activated LC3 protein coating autophagosome membranes. This is of interest since enteroviruses hijack autophagy machinery to facilitate formation of viral replication factories, virus assembly and egress from the infected cell. Here we explored possible roles of TDRD3 in autophagy, hypothesizing that TDRD3 may function as a specialized selective autophagy receptor. We found that KO of TDRD3 in HeLa cells significantly reduces starvation induced autophagy, while its reintroduction restores it in a dose-dependent manner. Autophagy receptors are degraded during autophagy and expression levels decrease during this time. We found that TDRD3 levels decrease to the same extent as the autophagy receptor p62/SQSTM1 during autophagy, indicating autophagy-targeted turnover in that role. Knockout of TDRD3 or G3BP1 did not make significant changes in overall cell localization of LC3B or p62/SQSTM1, but did result in greater concentration of Lamp2 phagosome marker for phagosomes and phagolysosomes. To test the potential roles of TDRD3 in autophagic processes, we created a series of deletion mutants of TDRD3 lacking either UBA domain or the various LIR motifs that are predicted to interact with LC3B. Microscopic examination of starved cells expressing these variants of TDRD3 showed ΔLIR-TDRD3 had defects in colocalization with LC3B or Lamp2. Further, super resolution microscopy revealed ring structures with TDRD3 interfacing with p62/SQSTM1. In examination of arsenite induced stress granules we found recruitment of TDRD3 variants disrupted normally tight SG condensation, altered the decay rate of SGs upon release from stress and the kinetics of SG formation. We found evidence that the LIR3 motif on TDRD3 is involved in TDRD3 interaction with LC3B in coIP experiments, colocalization studies, and that this motif plays a key role in TDRD3 recruitment to SGs and SG resolution. Overall, these data support a functional role of TDRD3 in selective autophagy in a mode similar to p62/SQSTM1, with specific roles in SG stability and turnover. Enterovirus cleavage of TDRD3 likely affects both antiviral and autophagic responses that the virus controls for replication.
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Chen X, Fansler MM, Janjoš U, Ule J, Mayr C. The FXR1 network acts as signaling scaffold for actomyosin remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.05.565677. [PMID: 37961296 PMCID: PMC10635158 DOI: 10.1101/2023.11.05.565677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the FXR1 network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause Fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. These findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as organizer of signaling reactions.
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Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M. Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Urška Janjoš
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- UK Dementia Research Institute at King’s College London, London, SE5 9NU, UK
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
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Fan WW, Xu T, Gao J, Zhang HY, Li Y, Hu DD, Gao S, Zhang JH, Liu X, Liu D, Li PL, Wong CCL, Yao XB, Shi YY, Yang ZY, Wang XS, Ruan K. A bivalent inhibitor against TDRD3 to suppress phase separation of methylated G3BP1. Chem Commun (Camb) 2024; 60:762-765. [PMID: 38126399 DOI: 10.1039/d3cc04654k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The formation of membrane-less organelles is driven by multivalent weak interactions while mediation of such interactions by small molecules remains an unparalleled challenge. Here, we uncovered a bivalent inhibitor that blocked the recruitment of TDRD3 by the two methylated arginines of G3BP1. Relative to the monovalent inhibitor, this bivalent inhibitor demonstrated an enhanced binding affinity to TDRD3 and capability to suppress the phase separation of methylated G3BP1, TDRD3, and RNAs, and in turn inhibit the stress granule growth in cells. Our result paves a new path to mediate multivalent interactions involved in SG assembly for potential combinational chemotherapy by bivalent inhibitors.
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Affiliation(s)
- Wei-Wei Fan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Tian Xu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Jia Gao
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Han-Yu Zhang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Yan Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Duo-Duo Hu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Shuaixin Gao
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Peking University First Hospital; School of Basic Medical Sciences, Peking University Health Science Center; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jia-Hai Zhang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Xing Liu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Dan Liu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Pi-Long Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Peking University First Hospital; School of Basic Medical Sciences, Peking University Health Science Center; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xue-Biao Yao
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Yun-Yu Shi
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Zhen-Ye Yang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Xi-Sheng Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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Saha S, Huang SYN, Yang X, Saha LK, Sun Y, Khandagale P, Jenkins LM, Pommier Y. The TDRD3-USP9X complex and MIB1 regulate TOP3B homeostasis and prevent deleterious TOP3B cleavage complexes. Nat Commun 2023; 14:7524. [PMID: 37980342 PMCID: PMC10657456 DOI: 10.1038/s41467-023-43151-z] [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: 03/02/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023] Open
Abstract
TOP3B is stabilized by TDRD3. Hypothesizing that TDRD3 recruits a deubiquitinase, we find that TOP3B interacts with USP9X via TDRD3. Inactivation of USP9X destabilizes TOP3B, and depletion of both TDRD3 and USP9X does not promote further TOP3B ubiquitylation. Additionally, we observe that MIB1 mediates the ubiquitylation and proteasomal degradation of TOP3B by directly interacting with TOP3B independently of TDRD3. Combined depletion of USP9X, TDRD3 and MIB1 causes no additional increase in TOP3B levels compared to MIB1 knockdown alone indicating that the TDRD3-USP9X complex works downstream of MIB1. To comprehend why cells degrade TOP3B in the absence of TDRD3, we measured TOP3Bccs. Lack of TDRD3 increases TOP3Bccs in DNA and RNA, and induced R-loops, γH2AX and growth defect. Biochemical experiments confirm that TDRD3 increases the turnover of TOP3B. Our work provides molecular insights into the mechanisms by which TDRD3 protect cells from deleterious TOP3Bccs which are otherwise removed by TRIM41.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Prashant Khandagale
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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5
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Rosa IR, Barbosa CP, Ferrandez CA, Sonoda BDB, Christofolini DM, Trevisan CM, Laganà AS, Peluso C, Bianco B. Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study. JBRA Assist Reprod 2023; 27:428-435. [PMID: 37417852 PMCID: PMC10712833 DOI: 10.5935/1518-0557.20220074] [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: 06/21/2022] [Accepted: 12/26/2022] [Indexed: 07/08/2023] Open
Abstract
OBJECTIVE Single nucleotide variants have been implicated in the response to fertility treatment and a pharmacogenomic approach may help to customize therapy based on patient genome. We aimed to evaluate the effect, individual and combined, of SYCP2L (rs2153157:G>A) and TDRD3 (rs4886238:G>A) variants on ovarian reserve, response to controlled ovarian stimulation (COS) and reproductive outcomes of women undergoing in vitro fertilization (IVF) treatment. METHODS This cross-sectional study included 149 normoovulatory women undergoing IVF. Genotyping was performed using the TaqMan real-time polymerase chain reaction method. Clinical parameters and reproductive outcomes were compared according to the genotypes of the variants studied. RESULTS Considering ovarian reserve, there were no significant differences among SYCP2L or TDRD3 genotypes in terms of FSH levels or AFC; however, AMH levels were significantly different in carriers of both variants. Regarding the SYCP2L rs2153157:G>A variant, lower AMH levels were observed in women carrying an AA genotype compared to women carrying a heterozygous genotype (p=0.01). Considering the TDRD3 rs4886238:G>A variant, women carrying an AA genotype presented higher AMH levels than carriers of GG and GA genotypes (p=0.025). Nevertheless, no difference was found regarding response to COS or reproductive outcomes. Considering the combined effect of the variants, women carrying the heterozygous genotype of both variants presented statistically increased AMH levels compared to SYCP2L rs2153157 AA genotype carriers and TDRD3 rs4886238 GG genotype carriers (p=0.042). CONCLUSIONS Individually and combined, the SYCP2L rs2153157 and TDRD3 rs4886238 variants have an effect on AMH level.
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Affiliation(s)
- Iasmim Ribeiro Rosa
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
| | - Caio Parente Barbosa
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
- Instituto Ideia Fértil, Santo André, Brazil
| | - Caroline Awoki Ferrandez
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
| | - Bianca Del Bel Sonoda
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
| | - Denise Maria Christofolini
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
- Instituto Ideia Fértil, Santo André, Brazil
| | - Camila Martins Trevisan
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
| | - Antonio Simone Laganà
- Unit of Gynecologic Oncology, ARNAS “Civico - Di Cristina -
Benfratelli”, Department of Health Promotion, Mother and Child Care, Internal
Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Carla Peluso
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
| | - Bianca Bianco
- Discipline of Sexual and Reproductive Health and Populational
Genetics, Department of Collective Health, Faculdade de Medicina do ABC/Centro
Universitário Saúde ABC, FMABC, Santo André, São Paulo,
Brazil
- Instituto Ideia Fértil, Santo André, Brazil
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Chen M, Wang Z, Li W, Chen Y, Xiao Q, Shang X, Huang X, Wei Z, Ji X, Liu Y. Crystal structure of Tudor domain of TDRD3 in complex with a small molecule antagonist. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194962. [PMID: 37499935 DOI: 10.1016/j.bbagrm.2023.194962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Tudor domain-containing protein 3 (TDRD3) is involved in regulating transcription and translation, promoting breast cancer progression, and modulating neurodevelopment and mental health, making it a promising therapeutic target for associated diseases. The Tudor domain of TDRD3 is essential for its biological functions, and targeting this domain with potent and selective chemical probes may modulate its engagement with chromatin and related functions. Here we reported a study of TDRD3 antagonist following on our earlier work on the development of the SMN antagonist, Compound 1, and demonstrated that TDRD3 can bind effectively to Compound 2, a triple-ring analog of Compound 1. Our structural analysis suggested that the triple-ring compound bound better to TDRD3 due to its smaller side chain at Y566 compared to W102 in SMN. We also revealed that adding a small hydrophobic group to the N-methyl site of Compound 1 can improve binding. These findings provide a path for identifying antagonists for single canonical Tudor domain-containing proteins such as TDRD3 and SMN.
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Affiliation(s)
- Meixia Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhuowen Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Weiguo Li
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Suzhou, Jiangsu 215021, PR China
| | - Xinyue Ji
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China.
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China.
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7
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Asano-Inami E, Yokoi A, Sugiyama M, Hyodo T, Hamaguchi T, Kajiyama H. The association of UBAP2L and G3BP1 mediated by small nucleolar RNA is essential for stress granule formation. Commun Biol 2023; 6:415. [PMID: 37059803 PMCID: PMC10104854 DOI: 10.1038/s42003-023-04754-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
Stress granules (SGs) are dynamic, non-membranous structures composed of non-translating mRNAs and various proteins and play critical roles in cell survival under stressed conditions. Extensive proteomics analyses have been performed to identify proteins in SGs; however, the molecular functions of these components in SG formation remain unclear. In this report, we show that ubiquitin-associated protein 2-like (UBAP2L) is a crucial component of SGs. UBAP2L localized to SGs in response to various stresses, and its depletion significantly suppressed SG organization. Proteomics and RNA sequencing analyses found that UBAP2L formed a protein-RNA complex with Ras-GTP-activating protein SH3 domain binding protein 1 (G3BP1) and small nucleolar RNAs (snoRNAs). In vitro binding analysis demonstrated that snoRNAs were required for UBAP2L association with G3BP1. In addition, decreased expression of snoRNAs reduced the interaction between UBAP2L and G3BP1 and suppressed SG formation. Our results reveal a critical role of SG component, the UBAP2L/snoRNA/G3BP1 protein-RNA complex, and provide new insights into the regulation of SG assembly.
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Affiliation(s)
- Eri Asano-Inami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Mai Sugiyama
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi, 480-1195, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
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8
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Binda O, Juillard F, Ducassou JN, Kleijwegt C, Paris G, Didillon A, Baklouti F, Corpet A, Couté Y, Côté J, Lomonte P. SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members. Life Sci Alliance 2022; 6:6/1/e202201429. [PMID: 36375840 PMCID: PMC9684302 DOI: 10.26508/lsa.202201429] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Although recent advances in gene therapy provide hope for spinal muscular atrophy (SMA) patients, the pathology remains the leading genetic cause of infant mortality. SMA is a monogenic pathology that originates from the loss of the SMN1 gene in most cases or mutations in rare cases. Interestingly, several SMN1 mutations occur within the TUDOR methylarginine reader domain of SMN. We hypothesized that in SMN1 mutant cases, SMA may emerge from aberrant protein-protein interactions between SMN and key neuronal factors. Using a BioID proteomic approach, we have identified and validated a number of SMN-interacting proteins, including fragile X mental retardation protein (FMRP) family members (FMRFM). Importantly, SMA-linked SMNTUDOR mutant forms (SMNST) failed to interact with FMRFM In agreement with the recent work, we define biochemically that SMN forms droplets in vitro and these droplets are stabilized by RNA, suggesting that SMN could be involved in the formation of membraneless organelles, such as Cajal nuclear bodies. Finally, we found that SMN and FMRP co-fractionate with polysomes, in an RNA-dependent manner, suggesting a potential role in localized translation in motor neurons.
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Affiliation(s)
- Olivier Binda
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France .,University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Franceline Juillard
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Julia Novion Ducassou
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Constance Kleijwegt
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France,Université de Montpellier, CNRS UMR 9002, Institut de Génétique Humaine, Montpellier, France
| | - Geneviève Paris
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Andréanne Didillon
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Faouzi Baklouti
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Armelle Corpet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Jocelyn Côté
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Patrick Lomonte
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
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9
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Basu DS, Bhavsar R, Gulami I, Chavda S, Lingamallu SM, Muddashetty R, Veeranna C, Chattarji S, Thimmulappa R, Bhattacharya A, Guha A. FMRP protects the lung from xenobiotic stress by facilitating the Integrated Stress Response. J Cell Sci 2022; 135:275343. [DOI: 10.1242/jcs.258652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
Stress response pathways protect the lung from the damaging effects of environmental toxicants. Here we investigate the role of the Fragile X Mental Retardation Protein (FMRP), a multifunctional protein implicated in stress responses, in the lung. We report that FMRP is expressed in murine and human lungs, in the airways and more broadly. Analysis of airway stress responses in mice and in a murine cell line ex vivo, using the well-established Naphthalene (Nap) injury model, reveals that FMRP-deficient cells exhibit increased expression of markers of oxidative and genotoxic stress and increased cell death. Further inquiry shows that FMRP-deficient cells fail to actuate the Integrated Stress Response Pathway (ISR) and upregulate the transcription factor ATF4. Knockdown of ATF4 expression phenocopies the loss of FMRP. We extend our analysis of the role of FMRP to human bronchial BEAS-2B cells, using a 9, 10-Phenanthrenequinone air pollutant model, to find FMRP-deficient BEAS-2B also fail to actuate the ISR and exhibit greater susceptibility. Taken together, our data suggest that FMRP has a conserved role in protecting the airways by facilitating the ISR.
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Affiliation(s)
- Deblina Sain Basu
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
- Trans Disciplinary University, Yelahanka, Bangalore -560064, India
| | - Rital Bhavsar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
| | - Imtiyaz Gulami
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
- Trans Disciplinary University, Yelahanka, Bangalore -560064, India
| | - Saraswati Chavda
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
| | - Sai Manoz Lingamallu
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal-576104, India
| | - Ravi Muddashetty
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
| | | | - Sumantra Chattarji
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
- Brain Development and Disease Mechanisms (BDDM), inStem, GKVK Campus, Bangalore -560065, India
- National Centre for Biological Sciences, GKVK Campus, Bangalore- 560065, India
| | - Rajesh Thimmulappa
- JSS Medical College, JSS Academy of Higher Education & Research, Mysore- 570015, India
| | - Aditi Bhattacharya
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
- Brain Development and Disease Mechanisms (BDDM), inStem, GKVK Campus, Bangalore -560065, India
| | - Arjun Guha
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Campus, Bangalore -560065, India
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10
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Deater M, Tamhankar M, Lloyd RE. TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1. PLoS Pathog 2022; 18:e1010249. [PMID: 35085371 PMCID: PMC8824378 DOI: 10.1371/journal.ppat.1010249] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/08/2022] [Accepted: 01/05/2022] [Indexed: 12/19/2022] Open
Abstract
Stress granules (SGs) are highly dynamic cytoplasmic foci that form in response to activation of the integrated stress response (ISR) that results in eIF2α phosphorylation and global translation shutdown. Stress granules, which are largely nucleated by G3BP1, serve as hubs for mRNA triage, but there is mounting evidence that they also perform cell signaling functions that are vital to cell survival, particularly during viral infection. We previously showed that SG formation leads to NFκB activation and JNK signaling and that this association may be due in part to G3BP1-dependent recruitment of PKR to SGs. Others have reported close associations between G3BP1 and various innate immune PRRs of the type 1 interferon signaling system, including RIG-I. We also reported SG assembly dynamics is dependent on the arginine-methylation status of G3BP1. Another protein that rapidly localizes to SGs, TDRD3, is a methyl reader protein that performs transcriptional activation and adaptor functions within the nucleus, but neither the mechanism nor its function in SGs is clear. Here, we present evidence that TDRD3 localizes to SGs partly based upon methylation potential of G3BP1. We also characterize granules that TDRD3 forms during overexpression and show that these granules can form in the absence of G3BP but also contain translation components found in canonical SGs. We also show for the first time that SGs recruit additional interferon effectors IRF3, IRF7, TBK1, and Sting, and provide evidence that TDRD3 may play a role in recruitment of these factors. We also present evidence that TDRD3 is a novel antiviral protein that is cleaved by enteroviral 2A proteinase. G3BP1 and TDRD3 knockdown in cells results in altered transcriptional regulation of numerous IFN effectors in complex modulatory patterns that are distinctive for G3BP1 and TDRD3. Overall, we describe a novel role of TDRD3 in innate immunity in which G3BP1 and TDRD3 may coordinate to play important roles in regulation of innate antiviral defenses. When cells are exposed to environmental stresses, such as oxidative stress and viral infection, it induces a cellular response leading to the formation of Stress Granules (SGs) composed of stalled translation initiation complexes (RNA-binding proteins and mRNA) and many other cellular proteins. SGs are also considered to be antiviral structures when they form during viral infection, but viruses can block SG formation to facilitate their survival, often by targeting the essential SG protein G3BP1. Here, we show that a methyl reader protein, TDRD3, localizes to SGs partly based on the methylation potential of G3BP1, and may play a role in the recruitment of innate immune factors to SGs. Further, when overexpressed, TDRD3 can also form SG-like structures independently of G3BP1. We also present evidence that TDRD3 is a novel antiviral protein. Virus replication is enhanced in the absence of both TDRD3 and G3BP1, and virus infection leads to cleavage of TDRD3 by the enterovirus proteinase 2A. Finally, we also show that depletion of TDRD3 and G3BP1 together in cells leads to restriction of transcriptional activation of numerous IFN effectors in response to dsRNA. The patterns of transcriptional activation are distinctive for G3BP1 and TDRD3. We conclude that TDRD3 may play a novel and important role in the regulation of the host antiviral response.
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Affiliation(s)
- Matthew Deater
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Manasi Tamhankar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard E. Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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11
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Yuan W, Al-Hadid Q, Wang Z, Shen L, Cho H, Wu X, Yang Y. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution. Nucleic Acids Res 2021; 49:8573-8591. [PMID: 34329467 PMCID: PMC8421139 DOI: 10.1093/nar/gkab642] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/14/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.
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Affiliation(s)
- Wei Yuan
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Qais Al-Hadid
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Hyejin Cho
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope National Cancer Center, Duarte, CA 91010, USA
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12
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Cai T, Yu Z, Wang Z, Liang C, Richard S. Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. J Biol Chem 2021; 297:100821. [PMID: 34029587 PMCID: PMC8141346 DOI: 10.1016/j.jbc.2021.100821] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) necessary for the viral life cycle, but it remains unknown whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins are methylated. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG motifs, preferred PRMT target sequences. We confirmed arginine methylation of N protein by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated from cell culture. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5'-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. We also defined the N protein interactome in HEK293 cells, which identified PRMT1 and many of its RGG/RG substrates, including the known interacting protein G3BP1 as well as other components of stress granules (SGs), which are part of the host antiviral response. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. Also, the coexpression of methylarginine reader Tudor domain-containing protein 3 quenched N protein-mediated suppression of SGs in a dose-dependent manner. Finally, pretreatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. Because type I PRMT inhibitors are already undergoing clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may represent an additional therapeutic application of these drugs.
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Affiliation(s)
- Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhen Wang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada.
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13
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Moreira F, Arenas M, Videira A, Pereira F. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. J Mol Evol 2021; 89:384-395. [PMID: 33999213 DOI: 10.1007/s00239-021-10011-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
DNA topoisomerase III beta (TOP3B) is unique by operating on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, its precise cellular functions and evolutionary history remain poorly understood. Here, we show that TOP3B is conserved across main metazoan groups and evolved under strong purifying selection. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation of the protein. On the contrary, subdomain II is the less conserved, possibly because it is the most structurally flexible region of all TOP3B regions. Interestingly, TOP3B residue at position 472, previously associated with schizophrenia, is highly variable across animals, suggesting a more specific role in humans and related species. Finally, we show that all TOP3B CXXC zinc finger motifs previously identified at the protein C-terminal region are retained across metazoans. We also found that the two major methylation sites known to regulate TOP3B activity are located in the most conserved region of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout animals. Overall, our results provide a better understanding of the evolution and functional roles of TOP3B.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal. .,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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14
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McKie SJ, Neuman KC, Maxwell A. DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 2021; 43:e2000286. [PMID: 33480441 PMCID: PMC7614492 DOI: 10.1002/bies.202000286] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.
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Affiliation(s)
- Shannon J. McKie
- Department Biological Chemistry, John Innes Centre, Norwich, UK
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich, UK
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15
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Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1. Biomolecules 2020; 10:biom10060872. [PMID: 32517187 PMCID: PMC7356810 DOI: 10.3390/biom10060872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/31/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells determine the protein output of their genetic program by regulating mRNA transcription, localization, translation and turnover rates. This regulation is accomplished by an ensemble of RNA-binding proteins (RBPs) that bind to any given mRNA, thus forming mRNPs. Poly(A) binding proteins (PABPs) are prominent members of virtually all mRNPs that possess poly(A) tails. They serve as multifunctional scaffolds, allowing the recruitment of diverse factors containing a poly(A)-interacting motif (PAM) into mRNPs. We present the crystal structure of the variant PAM motif (termed PAM2w) in the N-terminal part of the positive translation factor LARP4B, which binds to the MLLE domain of the poly(A) binding protein C1 cytoplasmic 1 (PABPC1). The structural analysis, along with mutational studies in vitro and in vivo, uncovered a new mode of interaction between PAM2 motifs and MLLE domains.
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16
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Roles of Topoisomerases in Heterochromatin, Aging, and Diseases. Genes (Basel) 2019; 10:genes10110884. [PMID: 31683993 PMCID: PMC6896002 DOI: 10.3390/genes10110884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/23/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Heterochromatin is a transcriptionally repressive chromatin architecture that has a low abundance of genes but an enrichment of transposons. Defects in heterochromatin can cause the de-repression of genes and transposons, leading to deleterious physiological changes such as aging, cancer, and neurological disorders. While the roles of topoisomerases in many DNA-based processes have been investigated and reviewed, their roles in heterochromatin formation and function are only beginning to be understood. In this review, we discuss recent findings on how topoisomerases can promote heterochromatin organization and impact the transcription of genes and transposons. We will focus on two topoisomerases: Top2α, which catenates and decatenates double-stranded DNA, and Top3β, which can change the topology of not only DNA, but also RNA. Both enzymes are required for normal heterochromatin formation and function, as the inactivation of either protein by genetic mutations or chemical inhibitors can result in defective heterochromatin formation and the de-silencing of transposons. These defects may contribute to the shortened lifespan and neurological disorders observed in individuals carrying mutations of Top3β. We propose that topological stress may be generated in both DNA and RNA during heterochromatin formation and function, which depend on multiple topoisomerases to resolve.
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17
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Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. Gigascience 2019; 8:giy160. [PMID: 30535196 PMCID: PMC6381762 DOI: 10.1093/gigascience/giy160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. FINDINGS Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. CONCLUSION The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
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Affiliation(s)
- Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Amin Saffari
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Maria Beatriz Walter Costa
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Embrapa Agroenergia, Parque Estacaeo Biologica (PqEB), Asa Norte, Brasilia/DF, 70770-901, Brazil
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
- Max Planck Institute for Physics of Complex Systems, Noethnitzerstrasse 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01397 Dresden, Germany
| | - Manjusha Chintalapati
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Gero Doose
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Jörg Overmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Christoph Bleidorn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, Potsdam, 14476, Germany
| | - Klaus Henle
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Katja Nowick
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Rui Faria
- Department of Animal and Plant Sciences, Alfred Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, Leipzig, 04107, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
- Fraunhofer Institut Für Zelltherapie Und Immunologie, Perlickstrasse 1, Leipzig, 04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger strasse 17, Wien, 1090, Austria
- Center for non-Coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, Frederiksberg C, 1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, 87501, USA
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
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18
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Lee SK, Xue Y, Shen W, Zhang Y, Joo Y, Ahmad M, Chinen M, Ding Y, Ku WL, De S, Lehrmann E, Becker KG, Lei EP, Zhao K, Zou S, Sharov A, Wang W. Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila. Nat Commun 2018; 9:4946. [PMID: 30470739 PMCID: PMC6251927 DOI: 10.1038/s41467-018-07101-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3β represents a family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3β interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3β and RISC mutants are similarly defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay. Moreover, both Top3β and AGO2 mutants exhibit reduced levels of heterochromatin protein HP1 in heterochromatin. Furthermore, expression of several genes and transposable elements in heterochromatin is increased in the Top3β mutant. Notably, Top3β mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of transposable elements. Our data suggest that Top3β may act as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing. Topoisomerases solve topological problems during DNA metabolism, but their role in RNA metabolism remains unclear. Here the authors provide evidence that in Drosophila, Topoisomerase 3β interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) to promote heterochromatin formation and transcriptional silencing.
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Affiliation(s)
- Seung Kyu Lee
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yutong Xue
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weiping Shen
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yongqing Zhang
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yuyoung Joo
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Muzammil Ahmad
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Madoka Chinen
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive Kidney Diseases, Bethesda, MD, 20892, USA
| | - Yi Ding
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Supriyo De
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elin Lehrmann
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Kevin G Becker
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elissa P Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive Kidney Diseases, Bethesda, MD, 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Alexei Sharov
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weidong Wang
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.
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19
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Handling FMRP and its molecular partners: Structural insights into Fragile X Syndrome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 141:3-14. [PMID: 30905341 DOI: 10.1016/j.pbiomolbio.2018.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/01/2018] [Indexed: 12/29/2022]
Abstract
Fragile X Mental Retardation Protein (FMRP) is a RNA-binding protein (RBP) known to control different steps of mRNA metabolism, even though its complete function is not fully understood yet. Lack or mutations of FMRP lead to Fragile X Syndrome (FXS), the most common form of inherited intellectual disability and a leading monogenic cause of autism spectrum disorder (ASD). It is well established that FMRP has a multi-domain architecture, a feature that allows this RBP to be engaged in a large interaction network with numerous proteins and mRNAs or non-coding RNAs. Insights into the three-dimensional (3D) structure of parts of its three domains (N-terminus, central domain and C-terminus) were obtained using Nuclear Magnetic Resonance and X-ray diffraction, but the complete 3D arrangement of each domain with respect to the others is still missing. Here, we review the structural features of FMRP and of the network of its protein and RNA interactions. Understanding these aspects is the first necessary step towards the design of novel compounds for new therapeutic interventions in FXS.
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20
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Bai H, Sun Y, Liu N, Xue F, Li Y, Xu S, Ye J, Zhang L, Chen Y, Chen J. Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays. BMC Genomics 2018; 19:501. [PMID: 29954329 PMCID: PMC6022433 DOI: 10.1186/s12864-018-4882-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood. Results In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), respectively. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. Conclusions Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization. Electronic supplementary material The online version of this article (10.1186/s12864-018-4882-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Bai
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanyan Sun
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Nian Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fuguang Xue
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunlei Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Songshan Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianhua Ye
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Zhang
- CapitalBio Corporation, Beijing, 102206, China
| | - Yu Chen
- Beijing General Station of Animal Husbandry Service, Beijing, 102200, China
| | - Jilan Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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21
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ZFAND1 Recruits p97 and the 26S Proteasome to Promote the Clearance of Arsenite-Induced Stress Granules. Mol Cell 2018; 70:906-919.e7. [PMID: 29804830 DOI: 10.1016/j.molcel.2018.04.021] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 01/10/2023]
Abstract
Stress granules (SGs) are cytoplasmic assemblies of mRNPs stalled in translation initiation. They are induced by various stress conditions, including exposure to the environmental toxin and carcinogen arsenic. While perturbed SG turnover is linked to the pathogenesis of neurodegenerative diseases, the molecular mechanisms underlying SG formation and turnover are still poorly understood. Here, we show that ZFAND1 is an evolutionarily conserved regulator of SG clearance. ZFAND1 interacts with two key factors of protein degradation, the 26S proteasome and the ubiquitin-selective segregase p97, and recruits them to arsenite-induced SGs. In the absence of ZFAND1, SGs lack the 26S proteasome and p97, accumulate defective ribosomal products, and persist after arsenite removal, indicating their transformation into aberrant, disease-linked SGs. Accordingly, ZFAND1 depletion is epistatic to the expression of pathogenic mutant p97 with respect to SG clearance, suggesting that ZFAND1 function is relevant to the multisystem degenerative disorder IBMPFD/ALS.
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22
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Liu J, Zhang S, Liu M, Liu Y, Nshogoza G, Gao J, Ma R, Yang Y, Wu J, Zhang J, Li F, Ruan K. Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. FEBS J 2018; 285:2091-2103. [DOI: 10.1111/febs.14469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Jiuyang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Shuya Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Mingqing Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yaqian Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jia Gao
- Center of Medical Physics and Technology Hefei Institute of Physical Science Chinese Academy of Science Hefei China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yang Yang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
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23
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Ahmad M, Shen W, Li W, Xue Y, Zou S, Xu D, Wang W. Topoisomerase 3β is the major topoisomerase for mRNAs and linked to neurodevelopment and mental dysfunction. Nucleic Acids Res 2017; 45:2704-2713. [PMID: 28039324 PMCID: PMC5389537 DOI: 10.1093/nar/gkw1293] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022] Open
Abstract
Human cells contain five topoisomerases in the nucleus and cytoplasm, but which one is the major topoisomerase for mRNAs is unclear. To date, Top3β is the only known topoisomerase that possesses RNA topoisomerase activity, binds mRNA translation machinery and interacts with an RNA-binding protein, FMRP, to promote synapse formation; and Top3β gene deletion has been linked to schizophrenia. Here, we show that Top3β is also the most abundant mRNA-binding topoisomerase in cells. Top3β, but not other topoisomerases, contains a distinctive RNA-binding domain; and deletion of this domain diminishes the amount of Top3β that associates with mRNAs, indicating that Top3β is specifically targeted to mRNAs by its RNA binding domain. Moreover, Top3β mutants lacking either its RNA-binding domain or catalytic residue fail to promote synapse formation, suggesting that Top3β requires both its mRNA-binding and catalytic activity to facilitate neurodevelopment. Notably, Top3β proteins bearing point mutations from schizophrenia and autism individuals are defective in association with FMRP; whereas one of the mutants is also deficient in binding mRNAs, catalyzing RNA topoisomerase reaction, and promoting synapse formation. Our data suggest that Top3β is the major topoisomerase for mRNAs, and requires both RNA binding and catalytic activity to promote neurodevelopment and prevent mental dysfunction.
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Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yutong Xue
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weidong Wang
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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24
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Ayoubian H, Fröhlich T, Pogodski D, Flatley A, Kremmer E, Schepers A, Feederle R, Arnold GJ, Grässer FA. Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein-Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation. J Gen Virol 2017; 98:2128-2142. [PMID: 28758620 DOI: 10.1099/jgv.0.000870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Epstein-Barr virus is a human herpes virus with oncogenic potential. The virus-encoded nuclear antigen 2 (EBNA2) is a key mediator of viral tumorigenesis. EBNA2 features an arginine-glycine (RG) repeat at amino acids (aa)339-354 that is essential for the transformation of lymphocytes and contains symmetrically (SDMA) and asymmetrically (ADMA) di-methylated arginine residues. The SDMA-modified EBNA2 binds the survival motor neuron protein (SMN), thus mimicking SMD3, a cellular SDMA-containing protein that interacts with SMN. Accordingly, a monoclonal antibody (mAb) specific for the SDMA-modified RG repeat of EBNA2 also binds to SMD3. With the novel mAb 19D4 we now show that EBNA2 contains mono-methylated arginine (MMA) residues within the RG repeat. Using 19D4, we immune-precipitated and analysed by mass spectrometry cellular proteins in EBV-transformed B-cells that feature MMA motifs that are similar to the one in EBNA2. Among the cellular proteins identified, we confirmed by immunoprecipitation and/or Western blot analyses Aly/REF, Coilin, DDX5, FXR1, HNRNPK, LSM4, MRE11, NRIP, nucleolin, PRPF8, RBM26, SMD1 (SNRDP1) and THRAP3 proteins that are either known to contain MMA residues or feature RG repeat sequences that probably serve as methylation substrates. The identified proteins are involved in splicing, tumorigenesis, transcriptional activation, DNA stability and RNA processing or export. Furthermore, we found that several proteins involved in energy metabolism are associated with MMA-modified proteins. Interestingly, the viral EBNA1 protein that features methylated RG repeat motifs also reacted with the antibodies. Our results indicate that the region between aa 34-52 of EBNA1 contains ADMA or SDMA residues, while the region between aa 328-377 mainly contains MMA residues.
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Affiliation(s)
- Hiresh Ayoubian
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Dagmar Pogodski
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
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25
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Tudor Domain Containing Protein 3 Promotes Tumorigenesis and Invasive Capacity of Breast Cancer Cells. Sci Rep 2017; 7:5153. [PMID: 28698590 PMCID: PMC5506013 DOI: 10.1038/s41598-017-04955-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
Tudor domain containing protein 3 (TDRD3) is a modular protein identified based on its ability to recognize methylated arginine motifs through its Tudor domain. We have previously shown that TDRD3 localizes to cytoplasmic stress granules, a structure shown to promote survival upon treatment with chemotherapeutic drugs in cancer cells. Here, we report TDRD3 as a novel regulator of cell proliferation and invasion in breast cancer cells. Our study also demonstrates that TDRD3 depletion inhibits tumor formation and metastasis to the lung in vivo. Furthermore, we show that TDRD3 regulates the expression of a number of key genes associated with promotion of breast cancer tumorigenesis and disease progression. Strikingly, we report that TDRD3 regulates some of these key targets at the level of translation. These findings provide the first experimental demonstration of a functional role for TDRD3 in promoting breast cancer development and progression, and identify TDRD3 as a potential new therapeutic target for breast cancer.
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26
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Chen F, Luo M, Lai F, Yu C, Cheng H, Zhou R. Biased Duplications and Loss of Members in Tdrd Family in Teleost Fish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:727-736. [DOI: 10.1002/jez.b.22757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/29/2017] [Accepted: 06/02/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Feng Chen
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
| | - Majing Luo
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
| | - Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
| | - Chunlai Yu
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis; Laboratory of Molecular and Developmental Genetics; College of Life Sciences; Wuhan University; Wuhan P. R. China
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27
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Ahmad M, Xu D, Wang W. Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life. RNA Biol 2017; 14:854-864. [PMID: 28534707 DOI: 10.1080/15476286.2017.1330741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Topoisomerases solve critical topological problems in DNA metabolism and have long been regarded as the "magicians" of the DNA world. Here we present views from 2 of our recent studies indicating that Type IA topoisomerases from all domains of life often possess dual topoisomerase activities for both DNA and RNA. In animals, one of the 2 Type IA topoisomerases, Top3β, contains an RNA-binding domain, possesses RNA topoisomerase activity, binds mRNAs, interacts with mRNA-binding proteins, and associates with active mRNA translation machinery. The RNA-binding domain is required for Top3β to bind mRNAs and promote normal neurodevelopment. Top3β forms a highly conserved complex with Tudor-domain-containing 3 (TDRD3), a protein known to interact with translation factors, histones, RNA polymerase II, single stranded DNA and RNA. Top3β requires TDRD3 for its association with the mRNA translation machinery. We suggest that Type IA topoisomerases can be "magicians" for not only DNA, but also RNA; and they may solve topological problems for both nucleic acids in all domains of life. In animals, Top3β-TDRD3 is a dual-activity topoisomerase complex that can act on DNA to stimulate transcription, and on mRNA to promote translation.
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Affiliation(s)
- Muzammil Ahmad
- a Genome Instability and Chromatin-Remodeling Section , National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Dongyi Xu
- b State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing , China
| | - Weidong Wang
- a Genome Instability and Chromatin-Remodeling Section , National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
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28
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Singh RN, Howell MD, Ottesen EW, Singh NN. Diverse role of survival motor neuron protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:299-315. [PMID: 28095296 PMCID: PMC5325804 DOI: 10.1016/j.bbagrm.2016.12.008] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023]
Abstract
The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance. The tissue-specific requirement of SMN is dictated by the variety and the abundance of its interacting partners. Reduced expression of SMN causes spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA displays a broad spectrum ranging from embryonic lethality to an adult onset. Aberrant expression and/or localization of SMN has also been associated with male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. This review provides a summary of various SMN functions with implications to a better understanding of SMA and other pathological conditions.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States.
| | - Matthew D Howell
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
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29
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Goto-Ito S, Yamagata A, Takahashi TS, Sato Y, Fukai S. Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor. Sci Rep 2017; 7:42123. [PMID: 28176834 PMCID: PMC5296760 DOI: 10.1038/srep42123] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767–OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)–RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.
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Affiliation(s)
- Sakurako Goto-Ito
- Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,CREST, JST, Saitama 332-0012, Japan
| | - Atsushi Yamagata
- Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,CREST, JST, Saitama 332-0012, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8501, Japan
| | - Tomio S Takahashi
- Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,CREST, JST, Saitama 332-0012, Japan
| | - Yusuke Sato
- Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,CREST, JST, Saitama 332-0012, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8501, Japan
| | - Shuya Fukai
- Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,CREST, JST, Saitama 332-0012, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8501, Japan
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30
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Narayanan N, Wang Z, Li L, Yang Y. Arginine methylation of USP9X promotes its interaction with TDRD3 and its anti-apoptotic activities in breast cancer cells. Cell Discov 2017; 3:16048. [PMID: 28101374 PMCID: PMC5206711 DOI: 10.1038/celldisc.2016.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/20/2016] [Indexed: 12/23/2022] Open
Abstract
The Tudor domain-containing proteins are characterized by their specific interactions with methylated protein motifs, including methyl-arginines and methyl-lysines. The Tudor domain-containing protein 3 (TDRD3) is one of the major methyl-arginine effector molecules that recognizes methylated arginine residues on histones and the C-terminal domain of RNA polymerase II, and activates transcription. However, majority of the cellular TDRD3 localizes to the cytoplasm and its functions there are still elusive. Here, we have identified ubiquitin-specific protease 9 X-linked (USP9X) as a TDRD3-interacting protein by GST (glutathione S-transferase) pull-down and co-immunoprecipitation. Detailed characterization suggests that the interaction between TDRD3 and USP9X is mediated through the Tudor domain of TDRD3 and the arginine methylation of USP9X. This interaction plays a critical role in TDRD3 protein stability, as knockdown of USP9X expression leads to increased TDRD3 ubiquitination. We also found that USP9X co-localizes with TDRD3 in cytoplasmic stress granules and this localization is diminished in Tdrd3-null mouse embryonic fibroblast cells, suggesting that TDRD3 is essential for USP9X stress granule localization. Furthermore, we found that one of the USP9X de-ubiquitination targets, myeloid cell leukemia protein 1, is regulated by TDRD3, indicating that TDRD3 potentially regulates USP9X de-ubiquitinase activity. Finally, we show that knockdown of TDRD3 expression sensitizes breast cancer cells to chemotherapeutic drug-induced apoptosis, likely due to its regulation of USP9X. This study provides a novel candidate strategy for targeting apoptosis pathways in cancer therapy.
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Affiliation(s)
- Nithya Narayanan
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Ling Li
- Division of Hematopoietic Stem Cell and Leukemia Research, Department of Hematology and HCT, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
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31
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Rosario R, Filis P, Tessyman V, Kinnell H, Childs AJ, Gray NK, Anderson RA. FMRP Associates with Cytoplasmic Granules at the Onset of Meiosis in the Human Oocyte. PLoS One 2016; 11:e0163987. [PMID: 27695106 PMCID: PMC5047637 DOI: 10.1371/journal.pone.0163987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/16/2016] [Indexed: 01/09/2023] Open
Abstract
Germ cell development and primordial follicle formation during fetal life is critical in establishing the pool of oocytes that subsequently determines the reproductive lifespan of women. Fragile X-associated primary ovarian insufficiency (FXPOI) is caused by inheritance of the FMR1 premutation allele and approximately 20% of women with the premutation allele develop ovarian dysfunction and premature ovarian insufficiency. However, the underlying disease mechanism remains obscure, and a potential role of FMRP in human ovarian development has not been explored. We have characterised the expression of FMR1 and FMRP in the human fetal ovary at the time of germ cell entry into meiosis through to primordial follicle formation. FMRP expression is exclusively in germ cells in the human fetal ovary. Increased FMRP expression in germ cells coincides with the loss of pluripotency-associated protein expression, and entry into meiosis is associated with FMRP granulation. In addition, we have uncovered FMRP association with components of P-bodies and stress granules, suggesting it may have a role in mRNA metabolism at the time of onset of meiosis. Therefore, this data support the hypothesis that FMRP plays a role regulating mRNAs during pivotal maturational processes in fetal germ cells, and ovarian dysfunction resulting from FMR1 premutation may have its origins during these stages of oocyte development.
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Affiliation(s)
- Roseanne Rosario
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Panagiotis Filis
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Victoria Tessyman
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Hazel Kinnell
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Andrew J. Childs
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Nicola K. Gray
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Richard A. Anderson
- MRC Centre for Reproductive Health, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
- * E-mail:
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32
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Tsai WC, Gayatri S, Reineke LC, Sbardella G, Bedford MT, Lloyd RE. Arginine Demethylation of G3BP1 Promotes Stress Granule Assembly. J Biol Chem 2016; 291:22671-22685. [PMID: 27601476 DOI: 10.1074/jbc.m116.739573] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic condensates of stalled messenger ribonucleoprotein complexes (mRNPs) that form when eukaryotic cells encounter environmental stress. RNA-binding proteins are enriched for arginine methylation and facilitate SG assembly through interactions involving regions of low amino acid complexity. How methylation of specific RNA-binding proteins regulates RNA granule assembly has not been characterized. Here, we examined the potent SG-nucleating protein Ras-GAP SH3-binding protein 1 (G3BP1), and found that G3BP1 is differentially methylated on specific arginine residues by protein arginine methyltransferase (PRMT) 1 and PRMT5 in its RGG domain. Several genetic and biochemical interventions that increased methylation repressed SG assembly, whereas interventions that decreased methylation promoted SG assembly. Arsenite stress quickly and reversibly decreased asymmetric arginine methylation on G3BP1. These data indicate that arginine methylation in the RGG domain prevents large SG assembly and rapid demethylation is a novel signal that regulates SG formation.
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Affiliation(s)
- Wei-Chih Tsai
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Sitaram Gayatri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Science Park, Smithville, Texas 78957, and
| | - Lucas C Reineke
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Gianluca Sbardella
- Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Science Park, Smithville, Texas 78957, and
| | - Richard E Lloyd
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030,
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33
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DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3. Proc Natl Acad Sci U S A 2016; 113:E5544-51. [PMID: 27582462 DOI: 10.1073/pnas.1605517113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and directing it to cellular compartments critical for gene expression, the biochemical mechanism of how TDRD3 can affect the functions of Top3β is not known. We report here sensitive biochemical assays for the activities of Top3β on DNA and RNA substrates in resolving topological entanglements and for the analysis of TDRD3 functions. TDRD3 stimulates the relaxation activity of Top3β on hypernegatively supercoiled DNA and changes the reaction from a distributive to a processive mode. Both supercoil retention assays and binding measurement by fluorescence anisotropy reveal a heretofore unknown preference for binding single-stranded nucleic acids over duplex. Whereas TDRD3 has a structure-specific binding preference, it does not discriminate between DNA and RNA. This unique property for binding with nucleic acids can have an important function in serving as a hub to form nucleoprotein complexes on DNA and RNA. To gain insight into the roles of Top3β on RNA metabolism, we designed an assay by annealing two single-stranded RNA circles with complementary sequences. Top3β is capable of converting two such single-stranded RNA circles into a double-stranded RNA circle, and this strand-annealing activity is enhanced by TDRD3. These results demonstrate that TDRD3 can enhance the biochemical activities of Top3β on both DNA and RNA substrates, in addition to its function of targeting Top3β to critical sites in subcellular compartments.
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34
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Ahmad M, Xue Y, Lee SK, Martindale JL, Shen W, Li W, Zou S, Ciaramella M, Debat H, Nadal M, Leng F, Zhang H, Wang Q, Siaw GEL, Niu H, Pommier Y, Gorospe M, Hsieh TS, Tse-Dinh YC, Xu D, Wang W. RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res 2016; 44:6335-49. [PMID: 27257063 PMCID: PMC4994864 DOI: 10.1093/nar/gkw508] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
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Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Yutong Xue
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Naples 80131, Italy
| | - Hélène Debat
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Marc Nadal
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Fenfei Leng
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Quan Wang
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Grace Ee-Lu Siaw
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Myriam Gorospe
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Tao-Shih Hsieh
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan Department of Biochemistry, Duke University Medical Center, Durham, NC 73532, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Weidong Wang
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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35
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Day FR, Ruth KS, Thompson DJ, Lunetta KL, Pervjakova N, Chasman DI, Stolk L, Finucane HK, Sulem P, Bulik-Sullivan B, Esko T, Johnson AD, Elks CE, Franceschini N, He C, Altmaier E, Brody JA, Franke LL, Huffman JE, Keller MF, McArdle PF, Nutile T, Porcu E, Robino A, Rose LM, Schick UM, Smith JA, Teumer A, Traglia M, Vuckovic D, Yao J, Zhao W, Albrecht E, Amin N, Corre T, Hottenga JJ, Mangino M, Smith AV, Tanaka T, Abecasis G, Andrulis IL, Anton-Culver H, Antoniou AC, Arndt V, Arnold AM, Barbieri C, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bernstein L, Bielinski SJ, Blomqvist C, Boerwinkle E, Bogdanova NV, Bojesen SE, Bolla MK, Borresen-Dale AL, Boutin TS, Brauch H, Brenner H, Brüning T, Burwinkel B, Campbell A, Campbell H, Chanock SJ, Chapman JR, Chen YDI, Chenevix-Trench G, Couch FJ, Coviello AD, Cox A, Czene K, Darabi H, De Vivo I, Demerath EW, Dennis J, Devilee P, Dörk T, dos-Santos-Silva I, Dunning AM, Eicher JD, Fasching PA, Faul JD, Figueroa J, Flesch-Janys D, Gandin I, Garcia ME, García-Closas M, Giles GG, Girotto GG, Goldberg MS, González-Neira A, Goodarzi MO, Grove ML, Gudbjartsson DF, Guénel P, Guo X, Haiman CA, Hall P, Hamann U, Henderson BE, Hocking LJ, Hofman A, Homuth G, Hooning MJ, Hopper JL, Hu FB, Huang J, Humphreys K, Hunter DJ, Jakubowska A, Jones SE, Kabisch M, Karasik D, Knight JA, Kolcic I, Kooperberg C, Kosma VM, Kriebel J, Kristensen V, Lambrechts D, Langenberg C, Li J, Li X, Lindström S, Liu Y, Luan J, Lubinski J, Mägi R, Mannermaa A, Manz J, Margolin S, Marten J, Martin NG, Masciullo C, Meindl A, Michailidou K, Mihailov E, Milani L, Milne RL, Müller-Nurasyid M, Nalls M, Neale BM, Nevanlinna H, Neven P, Newman AB, Nordestgaard BG, Olson JE, Padmanabhan S, Peterlongo P, Peters U, Petersmann A, Peto J, Pharoah PD, Pirastu NN, Pirie A, Pistis G, Polasek O, Porteous D, Psaty BM, Pylkäs K, Radice P, Raffel LJ, Rivadeneira F, Rudan I, Rudolph A, Ruggiero D, Sala CF, Sanna S, Sawyer EJ, Schlessinger D, Schmidt MK, Schmidt F, Schmutzler RK, Schoemaker MJ, Scott RA, Seynaeve CM, Simard J, Sorice R, Southey MC, Stöckl D, Strauch K, Swerdlow A, Taylor KD, Thorsteinsdottir U, Toland AE, Tomlinson I, Truong T, Tryggvadottir L, Turner ST, Vozzi D, Wang Q, Wellons M, Willemsen G, Wilson JF, Winqvist R, Wolffenbuttel BB, Wright AF, Yannoukakos D, Zemunik T, Zheng W, Zygmunt M, Bergmann S, Boomsma DI, Buring JE, Ferrucci L, Montgomery GW, Gudnason V, Spector TD, van Duijn CM, Alizadeh BZ, Ciullo M, Crisponi L, Easton DF, Gasparini PP, Gieger C, Harris TB, Hayward C, Kardia SL, Kraft P, McKnight B, Metspalu A, Morrison AC, Reiner AP, Ridker PM, Rotter JI, Toniolo D, Uitterlinden AG, Ulivi S, Völzke H, Wareham NJ, Weir DR, Yerges-Armstrong LM, Price AL, Stefansson K, Visser JA, Ong KK, Chang-Claude J, Murabito JM, Perry JR, Murray A. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. Nat Genet 2015; 47:1294-1303. [PMID: 26414677 PMCID: PMC4661791 DOI: 10.1038/ng.3412] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/02/2015] [Indexed: 02/02/2023]
Abstract
Menopause timing has a substantial impact on infertility and risk of disease, including breast cancer, but the underlying mechanisms are poorly understood. We report a dual strategy in ∼70,000 women to identify common and low-frequency protein-coding variation associated with age at natural menopause (ANM). We identified 44 regions with common variants, including two regions harboring additional rare missense alleles of large effect. We found enrichment of signals in or near genes involved in delayed puberty, highlighting the first molecular links between the onset and end of reproductive lifespan. Pathway analyses identified major association with DNA damage response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomization analyses supported a causal effect of later ANM on breast cancer risk (∼6% increase in risk per year; P = 3 × 10(-14)), likely mediated by prolonged sex hormone exposure rather than DDR mechanisms.
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Affiliation(s)
- Felix R. Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Katherine S. Ruth
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Deborah J. Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Kathryn L. Lunetta
- Boston University School of Public Health, Department of Biostatistics. Boston, Massachusetts 02118, USA
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
| | - Natalia Pervjakova
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115, USA
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus MC, 3015GE Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, 2300 RC Leiden, the Netherlands
| | - Hilary K. Finucane
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
| | - Brendan Bulik-Sullivan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, US
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
| | - Andrew D. Johnson
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
| | - Cathy E. Elks
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chunyan He
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle Washington 98101 USA
| | - Lude L. Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Jennifer E. Huffman
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Margaux F. Keller
- Merck Pharmaceuticals, 33 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Patrick F. McArdle
- Program in Personalized Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | - Teresa Nutile
- Institute of Genetics and Biophysics - CNR, via Pietro Castellino 111, 80131, Naples, Italy
| | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, 09042 Sardinia, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, 07100 Sassari, Italy
- Center for Statistical Genetics, Ann Arbor, University of Michigan, Michigan 48109-2029, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
| | - Ursula M. Schick
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109-1024, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Dragana Vuckovic
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, 34149 Trieste, Italy
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Najaf Amin
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, 3015 GE, Rotterdam, the Netherlands
| | - Tanguy Corre
- Department of Medical Genetics, University of Lausanne, CH-1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London, UK
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland 21224, United States of America
| | - Goncalo Abecasis
- Center for Statistical Genetics, Ann Arbor, University of Michigan, Michigan 48109-2029, USA
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alice M. Arnold
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Caterina Barbieri
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Matthias W. Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | | | - Suzette J. Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Anne-Lise Borresen-Dale
- Department of Genetics, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Barbara Burwinkel
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Archie Campbell
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Harry Campbell
- Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - J. Ross Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | | | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrea D. Coviello
- Boston University School of Medicine, Department of Medicine, Sections of Preventive Medicine and Endocrinology, Boston, MA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ellen W. Demerath
- Division of Epidemiology & Community Health, University of Minnesotta, Minneapolis MN 55455
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel dos-Santos-Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - John D. Eicher
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ilaria Gandin
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, 34149 Trieste, Italy
| | - Melissa E. Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Graham G. Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Giorgia G. Girotto
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, 34149 Trieste, Italy
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Canada
| | - Anna González-Neira
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Megan L. Grove
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Daniel F. Gudbjartsson
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101 Reykjavik, Iceland
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lynne J. Hocking
- Musculoskeletal Research Programme, Division of Applied Medicine, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Albert Hofman
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, 3015 GE, Rotterdam, the Netherlands
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Frank B. Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics,Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - David J. Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Samuel E. Jones
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - David Karasik
- Harvard Medical School, Boston, MA 02115, USA
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, 02131, USA
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Split, Croatia
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109-1024, USA
| | - Veli-Matti Kosma
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Xin Li
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sara Lindström
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Arto Mannermaa
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nicholas G. Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Corrado Masciullo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Roger L. Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Medicine I, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Michael Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Ben M. Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, US
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Patrick Neven
- KULeuven (University of Leuven), Department of Oncology, Multidisciplinary Breast Center, University Hospitals Leuven, Belgium
| | - Anne B. Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Børge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Janet E. Olson
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Ulrike Peters
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109-1024, USA
| | - Astrid Petersmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Nicola N. Pirastu
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, 34149 Trieste, Italy
| | - Ailith Pirie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Giorgio Pistis
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, 09042 Sardinia, Italy
- University of Sassari, Department of Biomedical Sciences, Sassari, 07100 Sassari, Italy
- Center for Statistical Genetics, Ann Arbor, University of Michigan, Michigan 48109-2029, USA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - David Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle Washington 98101 USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98101, USA
- Department of Health Services, University of Washington, Seattle, Washington 98101, USA
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Leslie J. Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- UCLA Clinical & Translational Science Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, 3015GE Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, 2300 RC Leiden, the Netherlands
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, 3015 GE, Rotterdam, the Netherlands
| | - Igor Rudan
- Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics - CNR, via Pietro Castellino 111, 80131, Naples, Italy
| | - Cinzia F. Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milano, Italy
| | - Serena Sanna
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, 09042 Sardinia, Italy
| | - Elinor J. Sawyer
- Research Oncology, Guy’s Hospital, King’s College London, London, UK
| | - David Schlessinger
- National Institute on Aging, Intramural Research Program, Baltimore, MD 20892, USA
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | - Minouk J. Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Caroline M. Seynaeve
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Canada
| | - Rossella Sorice
- Institute of Genetics and Biophysics - CNR, via Pietro Castellino 111, 80131, Naples, Italy
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Doris Stöckl
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Amanda E. Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Thérèse Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | | | - Stephen T. Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Diego Vozzi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
| | - Melissa Wellons
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37203, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - James F. Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - Bruce B.H.R. Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- LifeLines Cohort Study and Biobank, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research “Demokritos“, Athens, Greece
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Marek Zygmunt
- Department of Obstetrics and Gynecology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, CH-1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Julie E. Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland 21224, United States of America
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, 3015 GE, Rotterdam, the Netherlands
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marina Ciullo
- Institute of Genetics and Biophysics - CNR, via Pietro Castellino 111, 80131, Naples, Italy
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, 09042 Sardinia, Italy
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paolo P. Gasparini
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, 34149 Trieste, Italy
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milano, Italy
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus MC, 3015GE Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, 2300 RC Leiden, the Netherlands
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, 3015 GE, Rotterdam, the Netherlands
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, 34137 Trieste, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Laura M. Yerges-Armstrong
- Program in Personalized Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | | | | | - AOCS Investigators
- Peter MacCallum Cancer Centre, The University of Melbourne, Melbourne, Australia
| | - Generation Scotland
- A Collaboration between the University Medical Schools and NHS in Aberdeen, Dundee, Edinburgh and Glasgow, UK
| | | | | | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101 Reykjavik, Iceland
| | - Jenny A. Visser
- Department of Internal Medicine, Erasmus MC, 3015GE Rotterdam, the Netherlands
| | - Ken K. Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department of Paediatrics,University of Cambridge,Cambridge, CB2 0QQ, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joanne M. Murabito
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, Massachusetts 01702-5827, USA
- Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA 02118, USA
| | - John R.B. Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
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Abstract
Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
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Affiliation(s)
- J Ross Buchan
- a Department of Molecular and Cellular Biology ; University of Arizona ; Tucson , AZ USA
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Laisk-Podar T, Kaart T, Peters M, Salumets A. Genetic variants associated with female reproductive ageing – potential markers for assessing ovarian function and ovarian stimulation outcome. Reprod Biomed Online 2015; 31:199-209. [DOI: 10.1016/j.rbmo.2015.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 02/19/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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Weisz ED, Monyak RE, Jongens TA. Deciphering discord: How Drosophila research has enhanced our understanding of the importance of FMRP in different spatial and temporal contexts. Exp Neurol 2015; 274:14-24. [PMID: 26026973 DOI: 10.1016/j.expneurol.2015.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 01/06/2023]
Abstract
Fragile X Syndrome (FXS) is the most common heritable form of intellectual impairment as well as the leading monogenetic cause of autism. In addition to its canonical definition as a neurodevelopmental disease, recent findings in the clinic suggest that FXS is a systemic disorder that is characterized by a variety of heterogeneous phenotypes. Efforts to study FXS pathogenesis have been aided by the development and characterization of animal models of the disease. Research efforts in Drosophila melanogaster have revealed key insights into the mechanistic underpinnings of FXS. While much remains unknown, it is increasingly apparent that FXS involves a myriad of spatially and temporally specific alterations in cellular function. Consequently, the literature is filled with numerous discordant findings. Researchers and clinicians alike must be cognizant of this dissonance, as it will likely be important for the design of preclinical studies to assess the efficacy of therapeutic strategies to improve the lives of FXS patients.
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Affiliation(s)
- Eliana D Weisz
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Rachel E Monyak
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States
| | - Thomas A Jongens
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States.
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39
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Linder B, Hirmer A, Gal A, Rüther K, Bolz HJ, Winkler C, Laggerbauer B, Fischer U. Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 tri-snRNP integration and is associated with retinitis pigmentosa. PLoS One 2014; 9:e111754. [PMID: 25383878 PMCID: PMC4226509 DOI: 10.1371/journal.pone.0111754] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/30/2014] [Indexed: 12/19/2022] Open
Abstract
Pre-mRNA splicing by the spliceosome is an essential step in the maturation of nearly all human mRNAs. Mutations in six spliceosomal proteins, PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, cause retinitis pigmentosa (RP), a disease characterized by progressive photoreceptor degeneration. All splicing factors linked to RP are constituents of the U4/U6.U5 tri-snRNP subunit of the spliceosome, suggesting that the compromised function of this particle may lead to RP. Here, we report the identification of the p.R192H variant of the tri-snRNP factor PRPF4 in a patient with RP. The mutation affects a highly conserved arginine residue that is crucial for PRPF4 function. Introduction of a corresponding mutation into the zebrafish homolog of PRPF4 resulted in a complete loss of function in vivo. A series of biochemical experiments suggested that p.R192H disrupts the binding interface between PRPF4 and its interactor PRPF3. This interferes with the ability of PRPF4 to integrate into the tri-snRNP, as shown in a human cell line and in zebrafish embryos. These data suggest that the p.R192H variant of PRPF4 represents a functional null allele. The resulting haploinsufficiency of PRPF4 compromises the function of the tri-snRNP, reinforcing the notion that this spliceosomal particle is of crucial importance in the physiology of the retina.
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Affiliation(s)
- Bastian Linder
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Anja Hirmer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Andreas Gal
- Department of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Rüther
- Department of Ophthalmology, Sankt Gertrauden-Krankenhaus, Berlin, Germany
| | - Hanno Jörn Bolz
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Christoph Winkler
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
- * E-mail:
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40
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Gayatri S, Bedford MT. Readers of histone methylarginine marks. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:702-10. [PMID: 24583552 PMCID: PMC4099268 DOI: 10.1016/j.bbagrm.2014.02.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/31/2014] [Accepted: 02/14/2014] [Indexed: 11/15/2022]
Abstract
Arginine methylation is a common posttranslational modification (PTM) that alters roughly 0.5% of all arginine residues in the cells. There are three types of arginine methylation: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). These three PTMs are enriched on RNA-binding proteins and on histones, and also impact signal transduction cascades. To date, over thirty arginine methylation sites have been cataloged on the different core histones. These modifications alter protein structure, impact interactions with DNA, and also generate docking sites for effector molecules. The primary "readers" of methylarginine marks are Tudor domain-containing proteins. The complete family of thirty-six Tudor domain-containing proteins has yet to be fully characterized, but at least ten bind methyllysine motifs and eight bind methylarginine motifs. In this review, we will highlight the biological roles of the Tudor domains that interact with arginine methylated motifs, and also address other types of interactions that are regulated by these particular PTMs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Sitaram Gayatri
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
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41
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Cong P, Li A, Ji Q, Chen Y, Mo D. Molecular analysis of porcine TDRD10 gene: a novel member of the TDRD family. Gene 2014; 548:190-7. [PMID: 25017056 DOI: 10.1016/j.gene.2014.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/03/2014] [Accepted: 07/09/2014] [Indexed: 12/01/2022]
Abstract
Tudor domain-containing proteins (TDRDs) are characterized by various numbers of Tudor domains, which are known to recognize and bind to symmetric methylated arginine residues. These proteins affect a wide variety of processes, including differentiation, genome stability and gametogenesis. In mammals, there are 12 members (TDRD1-TDRD12) in the TDRD protein family. Among them, the information about TDRD10 is less known. Here, we analyzed the sequence and structure properties of porcine TDRD10 gene, and examined its expression profile and subcellular distribution. Our data show that porcine TDRD10 has an opening reading frame (ORF) of 1068 bp, which encodes 355 amino acids. It localizes to chromosome 4. The gene product of porcine TDRD10 contains a Tudor domain and a RNA recognition motif (RRM). Serial deletion shows that the 5'-flanking sequence of porcine TDRD10 contains several negative and positive regulatory elements and identifies a 670-bp TATA-less region as an optimal promoter. Site-directed mutagenesis reveals that the nucleotides from -451 to -445 relative to the transcriptional start site forms one of the very important positive regulatory elements. Real time PCR detects the highest expression level of porcine TDRD10 gene in heart among 12 tissues. In PK15 cells, it mainly distributed in the cell nucleus, but also exhibited localization to the cytoplasm. These results increase our knowledge of TDRD10 gene, and provide basis for further investigation of its function.
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Affiliation(s)
- Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Qianqian Ji
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China.
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42
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Georgieva D, Dimitrov R, Kitanova M, Genova G. New X-chromosomal interactors of dFMRP regulate axonal and synaptic morphology of brain neurons in Drosophila melanogaster. BIOTECHNOL BIOTEC EQ 2014; 28:697-709. [PMID: 26740770 PMCID: PMC4684054 DOI: 10.1080/13102818.2014.937897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/21/2014] [Indexed: 11/12/2022] Open
Abstract
Fragile X syndrome is a neuro-developmental disease caused by transcriptional inactivation of the gene FMR1 (fragile X mental retardation 1) and loss of its protein product FMRP. FMRP has multiple neuronal functions which are implemented together with other proteins. To better understand these functions, the aim of this study was to reveal new protein interactors of dFMRP. In a forward genetic screen, we isolated ethyl-metanesulphonate-induced X-chromosomal modifier mutations of dfmr1. Four of them were identified and belong to the genes: peb/hindsight, rok, shaggy and ras. They are dominant suppressors of the dfmr1 overexpression wing phenotype ‘notched wings’. These mutations dominantly affected the axonal and synaptic morphology of the lateral ventral neurons (LNv's) in adult Drosophila brains. Heterozygotes for each of them displayed effects in the axonal growth, pathfinding, branching and in the synapse formation of these neurons. Double heterozygotes for both dfmr1-null mutation and for each of the suppressor mutations showed robust genetic interactions in the fly central nervous system. The mutations displayed severe defects in the axonal growth and synapse formation of the LNv's in adult brains. Our biochemical studies showed that neither of the proteins – Rok, Shaggy, Peb/Hnt or Ras – encoded by the four mutated genes regulates the protein level of dFMRP, but dFMRP negatively regulates the protein expression level of Rok in the brain. Altogether, these data suggest that Rok, Shaggy, Peb/Hnt and Ras are functional partners of dFMRP, which are required for correct wing development and for neuronal connectivity in Drosophila brain.
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Affiliation(s)
- Dimitrina Georgieva
- Faculty of Biology, Sofia University 'St. Kliment Ohridski' , Sofia , Bulgaria
| | - Roumen Dimitrov
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences , Sofia , Bulgaria
| | - Meglena Kitanova
- Faculty of Biology, Sofia University 'St. Kliment Ohridski' , Sofia , Bulgaria
| | - Ginka Genova
- Faculty of Biology, Sofia University 'St. Kliment Ohridski' , Sofia , Bulgaria
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43
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Jedrusik-Bode M. C. elegans sirtuin SIR-2.4 and its mammalian homolog SIRT6 in stress response. WORM 2014; 3:e29102. [PMID: 26442197 DOI: 10.4161/worm.29102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/26/2014] [Accepted: 05/02/2014] [Indexed: 01/09/2023]
Abstract
Stress is a significant life event. The immediate response to stress is critical for survival. In organisms ranging from the unicellular Saccharomyces cerevisiae to protozoa (Trypanosoma brucei) and metazoan (such as Caenorhabditis elegans, Homo sapiens) stress response leads to the formation of cytoplasmic RNA-protein complexes referred to as stress granules (SGs). SGs regulate cell survival during stress by the sequestration of the signaling molecules implicated in apoptosis. They are a transient place of messenger ribonucleoproteins (mRNPs) remodeling for storage, degradation, or reinitiation of translation during stress and recovery from stress. Recently, we have identified chromatin factor, the sirtuin C. elegans SIR-2.4 variant and its mammalian homolog SIRT6 as a regulator of SGs formation. SIRT6 is highly conserved NAD(+)-dependent lysine deacetylase and ADP-ribosyltransferase impacting longevity, metabolism, and cancer. We observed that the cellular formation of SGs by SIRT6 or SIR-2.4 was linked with the cell viability or C. elegans survival and was dependent on SIRT6 enzymatic activity. Here, we discuss how SIR-2.4/SIRT6 influences SGs formation and stress response. We suggest possible mechanisms for such an unanticipated function of a chromatin regulatory factor SIRT6 in assembly of stress granules and cellular stress resistance.
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Affiliation(s)
- Monika Jedrusik-Bode
- Max Planck Institute for Biophysical Chemistry; Epigenetics in C elegans group; Göttingen, Germany
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44
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45
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Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell 2014; 53:484-97. [PMID: 24507716 DOI: 10.1016/j.molcel.2014.01.011] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/09/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022]
Abstract
Tudor domain-containing protein 3 (TDRD3) is a major methylarginine effector molecule that reads methyl-histone marks and facilitates gene transcription. However, the underlying mechanism by which TDRD3 functions as a transcriptional coactivator is unknown. We identified topoisomerase IIIB (TOP3B) as a component of the TDRD3 complex. TDRD3 serves as a molecular bridge between TOP3B and arginine-methylated histones. The TDRD3-TOP3B complex is recruited to the c-MYC gene promoter primarily by the H4R3me2a mark, and the complex promotes c-MYC gene expression. TOP3B relaxes negative supercoiled DNA and reduces transcription-generated R loops in vitro. TDRD3 knockdown in cells increases R loop formation at the c-MYC locus, and Tdrd3 null mice exhibit elevated R loop formation at this locus in B cells. Tdrd3 null mice show significantly increased c-Myc/Igh translocation, a process driven by R loop structures. By reducing negative supercoiling and resolving R loops, TOP3B promotes transcription, protects against DNA damage, and reduces the frequency of chromosomal translocations.
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Affiliation(s)
- Yanzhong Yang
- The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA
| | - Kevin M McBride
- The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA
| | - Sean Hensley
- The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA
| | - Yue Lu
- The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA
| | - Frederic Chedin
- Department of Molecular & Cellular Biology, The University of California at Davis, Davis, CA 95616, USA
| | - Mark T Bedford
- The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA.
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46
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Fernández E, Rajan N, Bagni C. The FMRP regulon: from targets to disease convergence. Front Neurosci 2013; 7:191. [PMID: 24167470 PMCID: PMC3807044 DOI: 10.3389/fnins.2013.00191] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/04/2013] [Indexed: 01/08/2023] Open
Abstract
The fragile X mental retardation protein (FMRP) is an RNA-binding protein that regulates mRNA metabolism. FMRP has been largely studied in the brain, where the absence of this protein leads to fragile X syndrome, the most frequent form of inherited intellectual disability. Since the identification of the FMRP gene in 1991, many studies have primarily focused on understanding the function/s of this protein. Hundreds of potential FMRP mRNA targets and several interacting proteins have been identified. Here, we report the identification of FMRP mRNA targets in the mammalian brain that support the key role of this protein during brain development and in regulating synaptic plasticity. We compared the genes from databases and genome-wide association studies with the brain FMRP transcriptome, and identified several FMRP mRNA targets associated with autism spectrum disorders, mood disorders and schizophrenia, showing a potential common pathway/s for these apparently different disorders.
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Affiliation(s)
- Esperanza Fernández
- Center for the Biology of Disease, Vlaams Institut voor Biotechnologie Leuven, Belgium ; Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven Leuven, Belgium
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47
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Bagni C, Oostra BA. Fragile X syndrome: From protein function to therapy. Am J Med Genet A 2013; 161A:2809-21. [PMID: 24115651 DOI: 10.1002/ajmg.a.36241] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/28/2013] [Indexed: 12/23/2022]
Abstract
Fragile X syndrome (FXS) is the leading monogenic cause of intellectual disability and autism. The FMR1 gene contains a CGG repeat present in the 5'-untranslated region which can be unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In patients with fragile X syndrome (FXS), a repeat length exceeding 200 CGGs generally leads to methylation of the repeat and the promoter region, which is accompanied by silencing of the FMR1 gene. The disease is a result of lack of expression of the fragile X mental retardation protein leading to severe symptoms, including intellectual disability, hyperactivity, and autistic-like behavior. The FMR1 protein (FMRP) has a number of functions. The translational dysregulation of a subset of mRNAs targeted by FMRP is probably the major contribution to FXS. FMRP is also involved in mRNA transport to synapses where protein synthesis occurs. For some FMRP-bound mRNAs, FMRP is a direct modulator of mRNA stability either by sustaining or preventing mRNA decay. Increased knowledge about the role of FMRP has led to the identification of potential treatments for fragile X syndrome that were often tested first in the different animal models. This review gives an overview about the present knowledge of the function of FMRP and the therapeutic strategies in mouse and man.
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Affiliation(s)
- Claudia Bagni
- VIB Center for the Biology of Disease, Catholic University of Leuven, Leuven, Belgium; Department of Biomedicine and Prevention, University of Rome, Tor Vergata, Italy
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48
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Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Nat Neurosci 2013; 16:1238-47. [PMID: 23912945 PMCID: PMC3853347 DOI: 10.1038/nn.3479] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/21/2013] [Indexed: 12/11/2022]
Abstract
Topoisomerases are crucial to solve DNA topological problems, but they have not been linked to RNA metabolism. Here we show that human topoisomerase 3β (Top3β) is an RNA topoisomerase that biochemically and genetically interacts with FMRP, a protein deficient in Fragile X syndrome and known to regulate translation of mRNAs important for neuronal function and autism. Notably, the FMRP-Top3β interaction is abolished by a disease-associated FMRP mutation, suggesting that Top3β may contribute to pathogenesis of mental disorders. Top3β binds multiple mRNAs encoded by genes with neuronal functions related to schizophrenia and autism. Expression of one such gene, ptk2/FAK, is reduced in neuromuscular junctions of Top3β mutant flies. Synapse formation is defective in Top3β mutant flies and mice, as observed in FMRP mutant animals. Our findings suggest that Top3β acts as an RNA topoisomerase and works with FMRP to promote expression of mRNAs critical for neurodevelopment and mental health.
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49
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Stoll G, Pietiläinen OPH, Linder B, Suvisaari J, Brosi C, Hennah W, Leppä V, Torniainen M, Ripatti S, Ala-Mello S, Plöttner O, Rehnström K, Tuulio-Henriksson A, Varilo T, Tallila J, Kristiansson K, Isohanni M, Kaprio J, Eriksson JG, Raitakari OT, Lehtimäki T, Jarvelin MR, Salomaa V, Hurles M, Stefansson H, Peltonen L, Sullivan PF, Paunio T, Lönnqvist J, Daly MJ, Fischer U, Freimer NB, Palotie A. Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders. Nat Neurosci 2013; 16:1228-1237. [PMID: 23912948 DOI: 10.1038/nn.3484] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/01/2013] [Indexed: 02/08/2023]
Abstract
Implicating particular genes in the generation of complex brain and behavior phenotypes requires multiple lines of evidence. The rarity of most high-impact genetic variants typically precludes the possibility of accruing statistical evidence that they are associated with a given trait. We found that the enrichment of a rare chromosome 22q11.22 deletion in a recently expanded Northern Finnish sub-isolate enabled the detection of association between TOP3B and both schizophrenia and cognitive impairment. Biochemical analysis of TOP3β revealed that this topoisomerase was a component of cytosolic messenger ribonucleoproteins (mRNPs) and was catalytically active on RNA. The recruitment of TOP3β to mRNPs was independent of RNA cis-elements and was coupled to the co-recruitment of FMRP, the disease gene product in fragile X mental retardation syndrome. Our results indicate a previously unknown role for TOP3β in mRNA metabolism and suggest that it is involved in neurodevelopmental disorders.
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Affiliation(s)
- Georg Stoll
- Department of Biochemistry, University of Würzburg, Germany
| | - Olli P H Pietiläinen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland
| | - Bastian Linder
- Department of Biochemistry, University of Würzburg, Germany
| | - Jaana Suvisaari
- National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Cornelia Brosi
- Department of Biochemistry, University of Würzburg, Germany
| | - William Hennah
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Virpi Leppä
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Minna Torniainen
- National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Sirpa Ala-Mello
- Helsinki University Central Hospital, Department of Clinical Genetics, Helsinki, Finland
| | - Oliver Plöttner
- Pharma Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany
| | | | - Annamari Tuulio-Henriksson
- National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Teppo Varilo
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland
| | - Jonna Tallila
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Matti Isohanni
- Department of Psychiatry, Institute of Clinical Medicine, University of Oulu, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Johan G Eriksson
- National Institute for Health and Welfare, Chronic Disease Epidemiology and Prevention, Helsinki, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, Finland.,Vasa Central Hospital, Finland.,Folkhälsan Research Centre, Helsinki, Finland.,Unit of General Practice, Helsinki University Central Hospital, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku and Turku University Central Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere and Tampere University Hospital, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom.,National Institute of Health and Welfare, Oulu, Finland.,Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Helsinki/Turku, Finland
| | | | | | - Leena Peltonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland.,University of Helsinki, Department of Medical Genetics, Helsinki, Finland
| | - Patrick F Sullivan
- Departments of Genetics, Psychiatry and Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tiina Paunio
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,National Institute for Health and Welfare, Public Health Genomics Unit, Helsinki, Finland.,University of Helsinki and Helsinki University Central Hospital, Department of Psychiatry, Helsinki, Finland
| | - Jouko Lönnqvist
- National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland.,Helsinki University Central Hospital, Department of Clinical Genetics, Helsinki, Finland
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Germany
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California, USA
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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50
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Abstract
There are nine protein arginine methyltransferases (PRMTs) encoded in mammalian genomes, the protein products of which catalyse three types of arginine methylation--monomethylation and two types of dimethylation. Protein arginine methylation is an abundant modification that has been implicated in signal transduction, gene transcription, DNA repair and mRNA splicing, among others. Studies have only recently linked this modification to carcinogenesis and metastasis. Sequencing studies have not generally found alterations to the PRMTs; however, overexpression of these enzymes is often associated with various cancers, which might make some of them viable targets for therapeutic strategies.
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Affiliation(s)
- Yanzhong Yang
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, P.O. BOX 389, Smithville, Texas 78957, USA
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