1
|
Anitha A, Banerjee M, Thanseem I, Prakash A, Melempatt N, Sumitha PS, Iype M, Thomas SV. Rare Pathogenic Variants Identified in Whole Exome Sequencing of Monozygotic Twins With Autism Spectrum Disorder. Pediatr Neurol 2024; 158:113-123. [PMID: 39038432 DOI: 10.1016/j.pediatrneurol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a childhood-onset complex neurodevelopmental disorder characterized by problems with communication and social interaction and restricted, repetitive, stereotyped behavior. The prevalence of ASD is one in 36 children. The genetic architecture of ASD is complex in spite of its high heritability. To identify the potential candidate genes of ASD, we carried out a comprehensive genetic study of monozygotic (MZ) twins concordant or discordant for ASD. METHODS Five MZ twins and their parents were recruited for the study. Four of the twins were concordant, whereas one was discordant for ASD. Whole exome sequencing was conducted for the twins and their parents. The exome DNA was enriched using Twist Human Customized Core Exome Kit, and paired-end sequencing was performed on HiSeq system. RESULTS We identified several rare and pathogenic variants (homozygous recessive, compound heterozygous, de novo) in ASD-affected individuals. CONCLUSION We report novel variants in individuals diagnosed with ASD. Several of these genes are involved in brain-related functions and not previously reported in ASD. Intriguingly, some of the variants were observed in the genes involved in sensory perception (auditory [MYO15A, PLEC, CDH23, UBR3, GPSM2], olfactory [OR9K2], gustatory [TAS2R31], and visual [CDH23, UBR3]). This is the first comprehensive genetic study of MZ twins in an Indian population. Further validation is required to determine whether these variants are associated with ASD.
Collapse
Affiliation(s)
- Ayyappan Anitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India.
| | - Moinak Banerjee
- Department of Neurobiology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Ismail Thanseem
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Anil Prakash
- Department of Neurobiology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Nisha Melempatt
- Department of Audiology and Speech Language Pathology (ASLP), ICCONS, Palakkad, Kerala, India
| | - P S Sumitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Palakkad, Kerala, India
| | - Mary Iype
- Department of Neurology, ICCONS, Thiruvananthapuram, Kerala, India; Department of Neurology, ICCONS, Shoranur, Kerala, India; Department of Pediatric Neurology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Sanjeev V Thomas
- Department of Neurology, ICCONS, Thiruvananthapuram, Kerala, India; Department of Neurology, ICCONS, Shoranur, Kerala, India
| |
Collapse
|
2
|
Zou D, Li K, Su L, Liu J, Lu Y, Huang R, Li M, Mang X, Geng Q, Li P, Tang J, Yu Z, Zhang Z, Chen D, Miao S, Yu J, Yan W, Song W. DDX20 is required for cell-cycle reentry of prospermatogonia and establishment of spermatogonial stem cell pool during testicular development in mice. Dev Cell 2024; 59:1707-1723.e8. [PMID: 38657611 DOI: 10.1016/j.devcel.2024.04.002] [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: 05/11/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
RNA-binding proteins (RBPs), as key regulators of mRNA fate, are abundantly expressed in the testis. However, RBPs associated with human male infertility remain largely unknown. Through bioinformatic analyses, we identified 62 such RBPs, including an evolutionarily conserved RBP, DEAD-box helicase 20 (DDX20). Male germ-cell-specific inactivation of Ddx20 at E15.5 caused T1-propsermatogonia (T1-ProSG) to fail to reenter cell cycle during the first week of testicular development in mice. Consequently, neither the foundational spermatogonial stem cell (SSC) pool nor progenitor spermatogonia were ever formed in the knockout testes. Mechanistically, DDX20 functions to control the translation of its target mRNAs, many of which encode cell-cycle-related regulators, by interacting with key components of the translational machinery in prospermatogonia. Our data demonstrate a previously unreported function of DDX20 as a translational regulator of critical cell-cycle-related genes, which is essential for cell-cycle reentry of T1-ProSG and formation of the SSC pool.
Collapse
Affiliation(s)
- Dingfeng Zou
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Luying Su
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jun Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Mengzhen Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Xinyu Mang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Qi Geng
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Pengyu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jielin Tang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Zhixin Yu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Zexuan Zhang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Dingyao Chen
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China; The Institute of Blood Transfusion, Chinese Academy of Medical Sciences, and Peking Union Medical College, Chengdu 610052, China.
| | - Wei Yan
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing 100005, China.
| |
Collapse
|
3
|
Wang D, Zhang J, Zhao Y, Cao R, Wang Y, Guo I, Peng C, Song Y, Zhang S. Single nucleotide polymorphisms of GEMIN3 modify the risk of primary Sjögren's syndrome in female patients. Am J Med Sci 2024:S0002-9629(24)01336-3. [PMID: 38969288 DOI: 10.1016/j.amjms.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND MicroRNA (miRNA)-processing machinery may modify the risk of primary Sjögren's syndrome (pSS) by altering miRNA expression profiles. Inflammatory cytokines and reactive oxygen species (ROS) are also involved in pSS; however, the role of altered miRNAs expression in its pathogenesis is still unclear. We aimed to evaluate the relationship between single-nucleotide polymorphisms (SNPs) in miRNA processing machinery genes, including XPO5 (rs11077), RAN (rs14035), Dicer (rs3742330), TNRC6B (rs9623117), GEMIN3 (rs197412), and GEMIN4 (rs2740348), and the risk of pSS in female patients. The potential associations of cytokines and ROS with pSS-susceptible SNPs were also evaluated. MATERIALS AND METHODS The SNPs confirmed by polymerase chain reaction ligase detection reaction were genotyped in 74 female patients with pSS and 77 controls. The relationship was analyzed by Student's t-test, Wilcoxon rank-sum test, chi-square test, Pearson's correlation test, and binary logistic regression analysis. RESULTS For rs197412 of the GEMIN3 gene, the genotype TT carrier was associated with a 2.172-fold increased risk for pSS when compared with that of CT+CC carrier (odds ratio: 2.172, 95% CI, 1.133-4.166, p=0.019). Simultaneously, the pSS-susceptible TT carriers were associated with increased interferon-γ (IFN-γ) (P < 0.001) and tumor necrosis factor-α (TNF-α) (P = 0.003) levels when compared with that of CT+CC genotype carriers in female patients with pSS. The subsequent analysis also showed a weak positive correlation between IFN-γ and TNF-α levels (r=0.271, P = 0.019). CONCLUSION The predictors of GEMIN3 SNPs might modify pSS development in females by mediating the expression of miRNAs and therefore regulate the levels of IFN-γ and TNF-α.
Collapse
Affiliation(s)
- Dong Wang
- Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China
| | - Jingjing Zhang
- Department of Immunology and Rheumatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China
| | - Yufei Zhao
- Department of Immunology and Rheumatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China
| | - Ruijie Cao
- Department of Immunology and Rheumatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China
| | - Yingnan Wang
- Department of Gastroenterology and Hepatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China
| | - Iren Guo
- Emma Willard School, 285 Pawling Avenue, Troy, NY 12180, United States
| | - Chenxing Peng
- Department of Immunology and Rheumatology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, PR China
| | - Yanrong Song
- Department of Medical Technology, Xingtai Medical College, No. 618, Iron North Road, Xindu District, Xingtai City, Hebei, PR China
| | - Shasha Zhang
- Department of Immunology and Rheumatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, PR China.
| |
Collapse
|
4
|
Jacques F, Tichopád T, Demko M, Bystrý V, Křížová KC, Seifertová M, Voříšková K, Fuad MMH, Vetešník L, Šimková A. Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction. BMC Genomics 2024; 25:548. [PMID: 38824502 PMCID: PMC11144346 DOI: 10.1186/s12864-024-10462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.
Collapse
Affiliation(s)
- Florian Jacques
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic.
| | - Tomáš Tichopád
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CAS, Liběchov, 277 21, Czech Republic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, Vodňany, 389 25, Czech Republic
| | - Martin Demko
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Vojtěch Bystrý
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Kristína Civáňová Křížová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Kristýna Voříšková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Md Mehedi Hasan Fuad
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Lukáš Vetešník
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Science, Květná 8, Brno, 603 65, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| |
Collapse
|
5
|
Chen Z, Zhang J, Feng T, Wang X, Zhou S, Pan W, Chen Z, Yan Y, Dai J. DDX20 positively regulates the interferon pathway to inhibit viral infection. Antiviral Res 2024; 225:105875. [PMID: 38552910 DOI: 10.1016/j.antiviral.2024.105875] [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: 12/18/2023] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
The DEAD-box (DDX) family comprises RNA helicases characterized by the conserved sequence D(Asp)-E(Glu)-A(Ala)-D(Asp), participating in various RNA metabolism processes. Some DDX family members have been identified for their crucial roles in viral infections. In this study, RNAi library screening of the DDX family unveiled the antiviral activity of DDX20. Knockdown of DDX20 enhanced the replication of viruses such as vesicular stomatitis virus (VSV) and herpes simplex virus type I (HSV-1), while overexpression of DDX20 significantly diminished the replication level of these viruses. Mechanistically, DDX20 elevated the phosphorylation level of IRF3 induced by external stimuli by facilitating the interaction between TBK1 and IRF3, thereby promoting the expression of IFN-β. The increased IFN-β production, in turn, upregulated the expression of interferon-stimulated genes (ISGs), including Cig5 and IFIT1, thereby exerting the antiviral effect. Finally, in an in vivo infection study, Ddx20 gene-deficient mice exhibited increased susceptibility to viral infection. This study provides new evidence that DDX20 positively modulates the interferon pathway and restricts viral infection.
Collapse
Affiliation(s)
- Zhiqiang Chen
- Department of Nuclear Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| | - Jinyu Zhang
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| | - Tingting Feng
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China; Central Laboratory, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Xiujuan Wang
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| | - Shimeng Zhou
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| | - Wen Pan
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| | - Zhengrong Chen
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, China.
| | - Yongdong Yan
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, China.
| | - Jianfeng Dai
- Institute of Biology and Medical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.
| |
Collapse
|
6
|
He L, Yang J, Hao Y, Yang X, Shi X, Zhang D, Zhao D, Yan W, Bie X, Chen L, Chen G, Zhao S, Liu X, Zheng H, Zhang K. DDX20: A Multifunctional Complex Protein. Molecules 2023; 28:7198. [PMID: 37894677 PMCID: PMC10608988 DOI: 10.3390/molecules28207198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
DEAD-box decapping enzyme 20 (DDX20) is a putative RNA-decapping enzyme that can be identified by the conserved motif Asp-Glu-Ala-Asp (DEAD). Cellular processes involve numerous RNA secondary structure alterations, including translation initiation, nuclear and mitochondrial splicing, and assembly of ribosomes and spliceosomes. DDX20 reportedly plays an important role in cellular transcription and post-transcriptional modifications. On the one hand, DDX20 can interact with various transcription factors and repress the transcriptional process. On the other hand, DDX20 forms the survival motor neuron complex and participates in the assembly of snRNP, ultimately affecting the RNA splicing process. Finally, DDX20 can potentially rely on its RNA-unwinding enzyme function to participate in microRNA (miRNA) maturation and act as a component of the RNA-induced silencing complex. In addition, although DDX20 is not a key component in the innate immune system signaling pathway, it can affect the nuclear factor kappa B (NF-κB) and p53 signaling pathways. In particular, DDX20 plays different roles in tumorigenesis development through the NF-κB signaling pathway. This process is regulated by various factors such as miRNA. DDX20 can influence processes such as viral replication in cells by interacting with two proteins in Epstein-Barr virus and can regulate the replication process of several viruses through the innate immune system, indicating that DDX20 plays an important role in the innate immune system. Herein, we review the effects of DDX20 on the innate immune system and its role in transcriptional and post-transcriptional modification processes, based on which we provide an outlook on the future of DDX20 research in innate immunity and viral infections.
Collapse
Affiliation(s)
- Lu He
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Jinke Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Yu Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xing Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xijuan Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Dajun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Dengshuai Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Wenqian Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xintian Bie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Lingling Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Guohui Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Siyue Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Xiangtao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Keshan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| |
Collapse
|
7
|
Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun 2023; 14:6580. [PMID: 37852981 PMCID: PMC10584915 DOI: 10.1038/s41467-023-42324-0] [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: 06/11/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Spliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3'-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
Collapse
Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Nenad Radivojević
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sýkora
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nicholas Huston
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
- Department of Chemistry, Yale University, New Haven, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic.
| |
Collapse
|
8
|
Gong Y, Liang Y, Liu J, Wei J, Zhang S, Chen F, Zhang Q, Wang L, Lan H, Wu L, Ge W, Li S, Wang L, Shan H, He H. DDX24 Is Essential for Cell Cycle Regulation in Vascular Smooth Muscle Cells During Vascular Development via Binding to FANCA mRNA. Arterioscler Thromb Vasc Biol 2023; 43:1653-1667. [PMID: 37470182 DOI: 10.1161/atvbaha.123.319505] [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: 05/04/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND The DEAD-box family is essential for tumorigenesis and embryogenesis. Previously, we linked the malfunction of DDX (DEAD-box RNA helicase)-24 to a special type of vascular malformation. Here, we aim to investigate the function of DDX24 in vascular smooth muscle cells (VSMCs) and embryonic vascular development. METHODS Cardiomyocyte (CMC) and VSMC-specific Ddx24 knockout mice were generated by crossing Tagln-Cre mice with Ddx24flox/flox transgenic mice. The development of blood vessels was explored by stereomicroscope photography and immunofluorescence staining. Flow cytometry and cell proliferation assays were used to verify the regulation of DDX24 on the function of VSMCs. RNA sequencing and RNA immunoprecipitation coupled with quantitative real-time polymerase chain reaction were combined to investigate DDX24 downstream regulatory molecules. RNA pull-down and RNA stability experiments were performed to explore the regulation mechanism of DDX24. RESULTS CMC/VSMC-specific Ddx24 knockout mice died before embryonic day 13.5 with defects in vessel formation and abnormal vascular remodeling in extraembryonic tissues. Ddx24 knockdown suppressed VSMC proliferation via cell cycle arrest, likely due to increased DNA damage. DDX24 protein bound to and stabilized the mRNA of FANCA (FA complementation group A) that responded to DNA damage. Consistent with the function of DDX24, depletion of FANCA also impacted cell cycle and DNA repair of VSMCs. Overexpression of FANCA was able to rescue the alterations caused by DDX24 deficiency. CONCLUSIONS Our study unveiled a critical role of DDX24 in VSMC-mediated vascular development, highlighting a potential therapeutic target for VSMC-related pathological conditions.
Collapse
Affiliation(s)
- Yujiao Gong
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yan Liang
- Department of Obstetrics and Gynecology, Perinatal Medical Center (Y.L., J.L., Li Wang), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Perinatal Medical Center (Y.L., J.L., Li Wang), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jiaxing Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- Department of Interventional Medicine and Center for Interventional Medicine (J.W., H.S.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Shushan Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Fangbin Chen
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Qianqian Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Lijie Wang
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huimin Lan
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Lily Wu
- Departments of Molecular and Medical Pharmacology (L. Wu), Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles
- Urology (L. Wu), Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles
- Pediatrics (L. Wu), Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles
| | - Wei Ge
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, China (W.G.)
| | - Shuai Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Li Wang
- Department of Obstetrics and Gynecology, Perinatal Medical Center (Y.L., J.L., Li Wang), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hong Shan
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- Department of Interventional Medicine and Center for Interventional Medicine (J.W., H.S.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huanhuan He
- Guangdong Provincial Engineering Research Center of Molecular Imaging (Y.G., J.W., S.Z., F.C., Q.Z., Lijie Wang, H.L., S.L., H.S., H.H.), The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| |
Collapse
|
9
|
Yao C, Sun Y, Zhang Z, Jia X, Zou P, Wang Y. Integration of RNAi and RNA-seq uncovers the regulation mechanism of DDX20 on vitellogenin expression in Scylla paramamosain. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101028. [PMID: 36244220 DOI: 10.1016/j.cbd.2022.101028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
Vitellogenesis in crustaceans is controlled by several steroid hormones. In humans, the expression of SF-1, a gene that regulates gonadal development and the synthesis of steroid hormones, is affected by DDX20. However, how the homologous gene FTZ-F1 is regulated by DDX20 and its association with vitellogenesis remains unknown in the mud crab Scylla paramamosain. In this study, SpDDX20 and SpFTZ-F1 were identified in the transcriptome of mature ovarian tissue from the mud crab. qRT-PCR results revealed that the expression levels of SpFTZ-F1 and SpVTG in the ovaries of crab in the experimental group injected with dsDDX20 (EO) were significantly higher (P < 0.05) than those in the negative control group injected with dsEGFP (NO) and the blank control group injected with SPSS (BO). The differentially expressed genes (DEGs) identified by comparative transcriptome analysis of the EO group and NO group were enriched into five pathways related to ovarian steroidogenesis. The expression of CYP17, CYP3A4, CYP1A1 and 3β-HSD were up-regulated in pathways related to steroid hormone production and biosynthesis. The expression of the INSR, IRS and PI3K genes in the insulin signaling pathway were significantly increased (P < 0.05). The expression level of the TGF-β gene was up-regulated (P < 0.05) in the transforming growth factor pathway, whereas the expression level of the Smad2 gene was down-regulated (P < 0.05). The expression of GnRHR, GS, AC and PKA genes in the gonadotropin-releasing hormone signaling pathway were up-regulated. Our data provide a foundation for investigating the relationship between DDX20 and FTZ-F1 in the regulation of vitellogenin expression in S. paramamosain.
Collapse
Affiliation(s)
- Chengjie Yao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Yulong Sun
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiwei Jia
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Pengfei Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China.
| |
Collapse
|
10
|
Wang Y, Yasmin L, Li L, Gao P, Xu X, Sun X, Godbout R. DDX1 vesicles control calcium-dependent mitochondrial activity in mouse embryos. Nat Commun 2022; 13:3794. [PMID: 35778392 PMCID: PMC9249788 DOI: 10.1038/s41467-022-31497-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
The DEAD box protein DDX1, previously associated with 3'-end RNA processing and DNA repair, forms large aggregates in the cytoplasm of early mouse embryos. Ddx1 knockout causes stalling of embryos at the 2-4 cell stages. Here, we identify a DDX1-containing membrane-bound calcium-containing organelle with a nucleic acid core. We show that aggregates of these organelles form ring-like structures in early-stage embryos which we have named Membrane Associated RNA-containing Vesicles. We present evidence that DDX1 is required for the formation of Membrane Associated RNA-containing Vesicles which in turn regulate the spatial distribution of calcium in embryos. We find that Ddx1 knockout in early embryos disrupts calcium distribution, and increases mitochondria membrane potential, mitochondrial activity, and reactive oxygen species. Sequencing analysis of embryos from Ddx1 heterozygote crosses reveals downregulation of a subset of RNAs involved in developmental and mitochondrial processes in the embryos with low Ddx1 RNA. We propose a role for Membrane Associated RNA-containing Vesicles in calcium-controlled mitochondrial functions that are essential for embryonic development.
Collapse
Affiliation(s)
- Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Lubna Yasmin
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Pinzhang Gao
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Xia Xu
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Xuejun Sun
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada.
| |
Collapse
|
11
|
Bizen N, Bepari AK, Zhou L, Abe M, Sakimura K, Ono K, Takebayashi H. Ddx20, an Olig2 binding factor, governs the survival of neural and oligodendrocyte progenitor cells via proper Mdm2 splicing and p53 suppression. Cell Death Differ 2022; 29:1028-1041. [PMID: 34974536 PMCID: PMC9090832 DOI: 10.1038/s41418-021-00915-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/05/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Olig2 is indispensable for motoneuron and oligodendrocyte fate-specification in the pMN domain of embryonic spinal cords, and also involved in the proliferation and differentiation of several cell types in the nervous system, including neural progenitor cells (NPCs) and oligodendrocytes. However, how Olig2 controls these diverse biological processes remains unclear. Here, we demonstrated that a novel Olig2-binding protein, DEAD-box helicase 20 (Ddx20), is indispensable for the survival of NPCs and oligodendrocyte progenitor cells (OPCs). A central nervous system (CNS)-specific Ddx20 conditional knockout (cKO) demonstrated apoptosis and cell cycle arrest in NPCs and OPCs, through the potentiation of the p53 pathway in DNA damage-dependent and independent manners, including SMN complex disruption and the abnormal splicing of Mdm2 mRNA. Analyzes of Olig2 null NPCs showed that Olig2 contributed to NPC proliferation through Ddx20 protein stabilization. Our findings provide novel mechanisms underlying the Olig2-mediated proliferation of NPCs, via the Ddx20-p53 axis, in the embryonic CNS.
Collapse
Affiliation(s)
- Norihisa Bizen
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Asim K Bepari
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Li Zhou
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Center for Coordination of Research Facilities (CCRF), Niigata University, Niigata, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan. .,Center for Coordination of Research Facilities (CCRF), Niigata University, Niigata, Japan.
| |
Collapse
|
12
|
Identification and Characterization of MicroRNAs Involving in Initial Sex Differentiation of Chlamys farreri Gonads. BIOLOGY 2022; 11:biology11030456. [PMID: 35336829 PMCID: PMC8945268 DOI: 10.3390/biology11030456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Sex formation of gonads encompasses two ancient and highly conserved biological processes, sex determination and sex differentiation. The processes are strictly regulated by a complex of gene networks. There is increasing evidence that miRNAs play key roles in many biological processes. however, information is limited in their contribution to sex differentiation in animals. In the present study, we identified the novel miRNAs involved in sex-related genes regulation and explored the miRNA–mRNA networks underlying the posttranscriptional regulation during the initial sex differentiation in Zhikong scallop, Chlamys farreri. Our findings provide an important basis for studying the sex differentiation mechanisms, as well as developing sex control techniques in bivalves. Abstract Research on expressional regulation of genes at the initial sex differentiation of gonads will help to elucidate the mechanisms of sex determination and differentiation in animals. However, information on initial sex differentiation of gonads is limited in bivalves. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that can regulate the target gene expression at the posttranscription level by degrading the mRNA or repressing the mRNA translation. In the present study, we investigated the small RNAs transcriptome using the testes and ovaries of Zhikong scallop Chlamys farreri juveniles with a shell height of 5.0 mm, a critical stage of initial sex differentiation of gonads. A total of 75 known mature miRNAs and 103 novel miRNAs were identified. By comparing the expression of miRNAs between the ovary and testis, 11 miRNAs were determined to be differentially expressed. GO annotations and KEGG analyses indicated that many putative target genes that matched to these differentially expressed miRNAs participated in the regulation of sex differentiation. Furthermore, two selected miRNAs, cfa-novel_miR65 and cfa-miR-87a-3p_1, were confirmed to downregulate expressions of Foxl2 (a female-critical gene) and Klf4 (a male-critical gene), respectively, using a dual-luciferase reporter analysis. Our findings provided new insights into the initial sex differentiation of gonads regulated by miRNAs in bivalves.
Collapse
|
13
|
Aldhalaan H, AlBakheet A, AlRuways S, AlMutairi N, AlNakiyah M, AlGhofaili R, Cardona-Londoño KJ, Alahmadi KO, AlQudairy H, AlRasheed MM, Colak D, Arold ST, Kaya N. A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. Genes (Basel) 2021; 13:genes13010092. [PMID: 35052432 PMCID: PMC8774908 DOI: 10.3390/genes13010092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022] Open
Abstract
Pathogenic variants in GEMIN4 contribute to a hereditary disorder characterized by neurodevelopmental features, microcephaly, cataracts, and renal abnormalities (known as NEDMCR). To date, only two homoallelic variations have been linked to the disease. Moreover, clinical features associated with the variants have not been fully elucidated yet. Here, we identified a novel variant in GEMIN4 (NM_015721:exon2:c.440A>G:p.His147Arg) in two siblings from a consanguineous Saudi family by using whole exome sequencing followed by Sanger sequence verification. We comprehensively investigated the patients’ clinical features, including brain imaging and electroencephalogram findings, and compared their phenotypic characteristics with those of previously reported cases. In silico prediction and structural modeling support that the p.His147Arg variant is pathogenic.
Collapse
Affiliation(s)
- Hesham Aldhalaan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Albandary AlBakheet
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
| | - Sarah AlRuways
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Nouf AlMutairi
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Maha AlNakiyah
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Reema AlGhofaili
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Kelly J. Cardona-Londoño
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.J.C.-L.); (S.T.A.)
| | - Khalid Omar Alahmadi
- Department of Radiology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Hanan AlQudairy
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
| | - Maha M. AlRasheed
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh 11211, Saudi Arabia;
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Stefan T. Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.J.C.-L.); (S.T.A.)
| | - Namik Kaya
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.); (N.A.); (M.A.); (R.A.); (H.A.)
- Correspondence: ; Tel.: +966-11-4647272 (ext. 39612)
| |
Collapse
|
14
|
Simankova A, Bizen N, Saitoh S, Shibata S, Ohno N, Abe M, Sakimura K, Takebayashi H. Ddx20, DEAD box helicase 20, is essential for the differentiation of oligodendrocyte and maintenance of myelin gene expression. Glia 2021; 69:2559-2574. [PMID: 34231259 DOI: 10.1002/glia.24058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Abstract
Oligodendrocytes form myelin sheaths that surround axons, contributing to saltatory conduction and proper central nervous system (CNS) function. Oligodendrocyte progenitor cells (OPCs) are generated during the embryonic stage and differentiate into myelinating oligodendrocytes postnatally. Ddx20 is a multifunctional, DEAD-box helicase involved in multiple cellular processes, including transcription, splicing, microRNA biogenesis, and translation. Although defects in each of these processes result in abnormal oligodendrocyte differentiation and myelination, the involvement of Ddx20 in oligodendrocyte terminal differentiation remains unknown. To address this question, we used Mbp-Cre mice to generate Ddx20 conditional knockout (cKO) mice to allow for the deletion of Ddx20 from mature oligodendrocytes. Mbp-Cre;Ddx20 cKO mice demonstrated small body sizes, behavioral abnormalities, muscle weakness, and short lifespans, with mortality by the age of 2 months old. Histological analyses demonstrated significant reductions in the number of mature oligodendrocytes and drastic reductions in the expression levels of myelin-associated mRNAs, such as Mbp and Plp at postnatal day 42. The number of OPCs did not change. A thin myelin layer was observed for large-diameter axons in Ddx20 cKO mice, based on electron microscopic analysis. A bromodeoxyuridine (BrdU) labeling experiment demonstrated that terminal differentiation was perturbed from ages 2 weeks to 7 weeks in the CNS of Mbp-Cre;Ddx20 cKO mice. The activation of mitogen-activated protein (MAP) kinase, which promotes myelination, was downregulated in the Ddx20 cKO mice based on immunohistochemical detection. These results indicate that Ddx20 is an essential factor for terminal differentiation of oligodendrocytes and maintenance of myelin gene expression.
Collapse
Affiliation(s)
- Anna Simankova
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Norihisa Bizen
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sei Saitoh
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Biomedical Molecular Sciences (Anatomy II), Fujita Health University School of Medicine, Toyoake, Japan
| | - Shinsuke Shibata
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan.,Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Center for Coordination of Research Facilities, Niigata University, Niigata, Japan
| |
Collapse
|
15
|
Cullen SM, Hassan N, Smith-Raska M. Effects of non-inherited ancestral genotypes on offspring phenotypes. Biol Reprod 2021; 105:747-760. [PMID: 34159361 DOI: 10.1093/biolre/ioab120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
It is well established that environmental exposures can modify the profile of heritable factors in an individual's germ cells, ultimately affecting the inheritance of phenotypes in descendants. Similar to exposures, an ancestor's genotype can also affect the inheritance of phenotypes across generations, sometimes in offspring who do not inherit the genetic aberration. This can occur via a variety of prenatal, in utero, or postnatal mechanisms. In this review, we discuss the evidence for this process in mammals, with a focus on examples that are potentially mediated through the germline, while also considering alternate routes of inheritance. Non-inherited ancestral genotypes may influence descendant's disease risk to a much greater extent than currently appreciated, and focused evaluation of this phenomenon may reveal novel mechanisms of inheritance.
Collapse
Affiliation(s)
- Sean M Cullen
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, 413 East 69th Street, Room 1252D, New York, NY 10021
| | - Nora Hassan
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, 413 East 69th Street, Room 1252D, New York, NY 10021
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, 413 East 69th Street, Room 1252D, New York, NY 10021
| |
Collapse
|
16
|
Jia B, Xiang D, Fu X, Shao Q, Hong Q, Quan G, Wu G. Proteomic Changes of Porcine Oocytes After Vitrification and Subsequent in vitro Maturation: A Tandem Mass Tag-Based Quantitative Analysis. Front Cell Dev Biol 2020; 8:614577. [PMID: 33425922 PMCID: PMC7785821 DOI: 10.3389/fcell.2020.614577] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 01/01/2023] Open
Abstract
Cryopreservation of immature germinal vesicle (GV) oocytes is a promising strategy in pigs but still results in reduced oocyte quality due to inevitable cryodamages. Recently, there has been more focus on the molecular changes of oocytes after vitrification, but the alteration in the proteome level remains elusive. The aim of this study therefore was to decipher the proteomic characteristics of porcine GV oocytes following vitrification and in vitro maturation (IVM) by using tandem mass tag (TMT)-based quantitative approach and bioinformatics analysis. A total of 4,499 proteins were identified, out of which 153 presented significant difference. There were 94 up-regulated and 59 down-regulated proteins expressed differentially in the vitrified oocytes. Functional classification and enrichment analyses revealed that many of these proteins were involved in metabolism, signal transduction, response to stimulus, immune response, complement, coagulation cascades, and so on. Moreover, a parallel reaction monitoring technique validated the reliability of TMT data through quantitative analysis for 10 candidate proteins. In conclusion, our results provided a novel perspective of proteomics to comprehend the quality change in the vitrified porcine GV oocytes after IVM.
Collapse
Affiliation(s)
- Baoyu Jia
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Decai Xiang
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Xiangwei Fu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingyong Shao
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Guobo Quan
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Guoquan Wu
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| |
Collapse
|
17
|
Dubińska-Magiera M, Niedbalska-Tarnowska J, Migocka-Patrzałek M, Posyniak E, Daczewska M. Characterization of Hspb8 in Zebrafish. Cells 2020; 9:cells9061562. [PMID: 32604890 PMCID: PMC7348923 DOI: 10.3390/cells9061562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/13/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022] Open
Abstract
Hspb8 is a member of the small heat shock protein (sHSP) family. Its expression is known to be upregulated under heat shock. This protein interacts with different partners and can, therefore, be involved in various processes relevant to tissue integrity and functioning. In humans, mutations in the gene encoding Hspb8 can lead to the development of various diseases such as myopathies and neuropathies. In our study, we aimed to perform an in-depth characterization of zebrafish Hspb8 during zebrafish development. We applied techniques such as RT-qPCR, Western blot, immunofluorescence, co-immunoprecipitation, LC-MS, and morpholino-mediated knockdown. We broadened the knowledge regarding zebrafish hspb8 expression during development under normal and heat shock conditions as well as its tissue- and subcellular-specific localization. A co-IP analysis allowed us to conclude that zebrafish Hspb8 can interact with proteins such as Bag3 and Hsc70, which are crucial for formation of an autophagy-inducing complex. We also demonstrated that hspb8 morpholino-mediated knockdown has an impact on zebrafish embryos' morphology, muscle ultrastructure, and motility behavior. Our research provides a valuable resource for the potential use of the zebrafish as a model for studying pathological conditions associated with hspb8 disorders.
Collapse
Affiliation(s)
- Magda Dubińska-Magiera
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland; (J.N.-T.); (M.M.-P.); (E.P.)
- Correspondence: (M.D.-M.); (M.D.); Tel.: +48-71-375-4024 (M.D.-M.)
| | - Joanna Niedbalska-Tarnowska
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland; (J.N.-T.); (M.M.-P.); (E.P.)
- Hirszfeld Institute of Immunology and Experimental Therapy, the Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland
| | - Marta Migocka-Patrzałek
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland; (J.N.-T.); (M.M.-P.); (E.P.)
| | - Ewelina Posyniak
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland; (J.N.-T.); (M.M.-P.); (E.P.)
| | - Małgorzata Daczewska
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland; (J.N.-T.); (M.M.-P.); (E.P.)
- Correspondence: (M.D.-M.); (M.D.); Tel.: +48-71-375-4024 (M.D.-M.)
| |
Collapse
|
18
|
Pei W, Xu L, Chen Z, Slevin CC, Pettie KP, Wincovitch S, Burgess SM. A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation. NPJ Regen Med 2020; 5:6. [PMID: 32218991 PMCID: PMC7096462 DOI: 10.1038/s41536-020-0089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common genetic disease in children. SMA is generally caused by mutations in the gene SMN1. The survival of motor neurons (SMN) complex consists of SMN1, Gemins (2-8), and Strap/Unrip. We previously demonstrated smn1 and gemin5 inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identified gemin3 as another regeneration-essential gene. These three genes are likely pan-regenerative, since they affect the regeneration of hair cells, liver, and caudal fin. RNA-Seq analysis reveals that smn1, gemin3, and gemin5 are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.
Collapse
Affiliation(s)
- Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Claire C. Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Kade P. Pettie
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Stephen Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| |
Collapse
|
19
|
Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:491-503. [PMID: 30563832 PMCID: PMC6385987 DOI: 10.1534/g3.118.200874] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Spinal Muscular Atrophy (SMA) is caused by homozygous mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. SMN is part of an oligomeric complex with core binding partners, collectively called Gemins. Biochemical and cell biological studies demonstrate that certain Gemins are required for proper snRNP assembly and transport. However, the precise functions of most Gemins are unknown. To gain a deeper understanding of the SMN complex in the context of metazoan evolution, we investigated its composition in Drosophila melanogaster Using transgenic flies that exclusively express Flag-tagged SMN from its native promoter, we previously found that Gemin2, Gemin3, Gemin5, and all nine classical Sm proteins, including Lsm10 and Lsm11, co-purify with SMN. Here, we show that CG2941 is also highly enriched in the pulldown. Reciprocal co-immunoprecipitation reveals that epitope-tagged CG2941 interacts with endogenous SMN in Schneider2 cells. Bioinformatic comparisons show that CG2941 shares sequence and structural similarity with metazoan Gemin4. Additional analysis shows that three other genes (CG14164, CG31950 and CG2371) are not orthologous to Gemins 6-7-8, respectively, as previously suggested. In D.melanogaster, CG2941 is located within an evolutionarily recent genomic triplication with two other nearly identical paralogous genes (CG32783 and CG32786). RNAi-mediated knockdown of CG2941 and its two close paralogs reveals that Gemin4 is essential for organismal viability.
Collapse
|
20
|
Jha NN, Kim JK, Monani UR. Motor neuron biology and disease: A current perspective on infantile-onset spinal muscular atrophy. FUTURE NEUROLOGY 2018; 13:161-172. [PMID: 31396020 DOI: 10.2217/fnl-2018-0008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infantile-onset spinal muscular atrophy (SMA) is a prototypical disease in which to investigate selective neurodegenerative phenotypes. Caused by low levels of the ubiquitously expressed Survival Motor Neuron (SMN) protein, the disease mainly targets the spinal motor neurons. This selective phenotype remains largely unexplained, but has not hindered the development of SMN repletion as a means to a treatment. Here we chronicle recent advances in the area of SMA biology. We provide a brief background to the disease, highlight major advances that have shaped our current understanding of SMA, trace efforts to treat the condition, discuss the outcome of two promising new therapies and conclude by considering contemporary as well as new challenges stemming from recent successes within the field.
Collapse
Affiliation(s)
- Narendra N Jha
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
| | - Jeong-Ki Kim
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
| | - Umrao R Monani
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Department of Neurology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
| |
Collapse
|
21
|
Abstract
Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro, it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function. This review article focuses on the known roles of Gemin3, first as a core member of the survival motor neuron (SMN) complex, in small nuclear ribonucleoprotein biogenesis. Although mechanistic details are lacking, a critical function for Gemin3 in this pathway is supported by numerous in vitro and in vivo studies. Gene expression activities of Gemin3 are next underscored, mainly messenger ribonucleoprotein trafficking, gene silencing via microRNA processing, and transcriptional regulation. The involvement of Gemin3 in abnormal cell signal transduction pathways involving p53 and NF-κB is also highlighted. Finally, the clinical implications of Gemin3 deregulation are discussed including links to spinal muscular atrophy, poliomyelitis, amyotrophic lateral sclerosis, and cancer. Impressive progress made over the past two decades since the discovery of Gemin3 bodes well for further work that refines the mechanism(s) underpinning its multiple activities.
Collapse
|
22
|
Meier ID, Walker MP, Matera AG. Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm. Biol Open 2018; 7:bio.032409. [PMID: 29371219 PMCID: PMC5861365 DOI: 10.1242/bio.032409] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gemin4 is a member of the Survival Motor Neuron (SMN) protein complex, which is responsible for the assembly and maturation of Sm-class small nuclear ribonucleoproteins (snRNPs). In metazoa, Sm snRNPs are assembled in the cytoplasm and subsequently imported into the nucleus. We previously showed that the SMN complex is required for snRNP import in vitro, although it remains unclear which specific components direct this process. Here, we report that Gemin4 overexpression drives SMN and the other Gemin proteins from the cytoplasm into the nucleus. Moreover, it disrupts the subnuclear localization of the Cajal body marker protein, coilin, in a dose-dependent manner. We identified three putative nuclear localization signal (NLS) motifs within Gemin4, one of which is necessary and sufficient to direct nuclear import. Overexpression of Gemin4 constructs lacking this NLS sequestered Gemin3 and, to a lesser extent Gemin2, in the cytoplasm but had little effect on the nuclear accumulation of SMN. We also investigated the effects of Gemin4 depletion in the laboratory mouse, Mus musculus. Gemin4 null mice die early in embryonic development, demonstrating that Gemin4 is an essential mammalian protein. When crossed onto a severe SMA mutant background, heterozygous loss of Gemin4 failed to modify the early postnatal mortality phenotype of SMA type I (Smn−/−;SMN2+/+) mice. We conclude that Gemin4 plays an essential role in mammalian snRNP biogenesis, and may facilitate import of the SMN complex (or subunits thereof) into the nucleus. Summary:Gemin4 loss-of-function is recessive lethal in mice, whereas in cell culture its overexpression results in a dominant, gain-of-function relocalization of SMN and other Gemin proteins to the nucleus.
Collapse
Affiliation(s)
- Ingo D Meier
- Integrative Program for Biological and Genome Sciences, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Michael P Walker
- Integrative Program for Biological and Genome Sciences, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-3280, USA.,Department of Genetics, Case Western Reserve University, Cleveland, OH 44106-4955, USA
| | | |
Collapse
|
23
|
Bhuvanalakshmi G, Arfuso F, Kumar AP, Dharmarajan A, Warrier S. Epigenetic reprogramming converts human Wharton's jelly mesenchymal stem cells into functional cardiomyocytes by differential regulation of Wnt mediators. Stem Cell Res Ther 2017; 8:185. [PMID: 28807014 PMCID: PMC5557557 DOI: 10.1186/s13287-017-0638-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
Background Lineage commitment of mesenchymal stem cells (MSCs) to cardiac differentiation is controlled by transcription factors that are regulated by epigenetic events, mainly histone deacetylation and promoter DNA methylation. Here, we studied the differentiation of human Wharton’s jelly MSCs (WJMSCs) into the cardiomyocyte lineage via epigenetic manipulations. Methods We introduced these changes using inhibitors of DNA methyl transferase and histone deacetylase, DC301, DC302, and DC303, in various combinations. We characterized for cardiogenic differentiation by assessing the expression of cardiac-specific markers by immunolocalization, quantitative RT-PCR, and flow cytometry. Cardiac functional studies were performed by FURA2AM staining and Greiss assay. The role of Wnt signaling during cardiac differentiation was analyzed by quantitative RT-PCR. In-vivo studies were performed in a doxorubicin-induced cardiotoxic mouse model by injecting cardiac progenitor cells. Promoter methylation status of the cardiac transcription factor Nkx2.5 and the Wnt antagonist, secreted frizzled-related protein 4 (sFRP4), after cardiac differentiation was studied by bisulfite sequencing. Results By induction with DC301 and DC302, WJMSCs differentiated into cardiomyocyte-like structures with an upregulation of Wnt antagonists, sFRP3 and sFRP4, and Dickkopf (Dkk)1 and Dkk3. The cardiac function enhancer, vinculin, and DDX20, a DEAD-box RNA helicase, were also upregulated in differentiated cardiomyocytes. Additionally, bisulfite sequencing revealed, for the first time in cardiogenesis, that sFRP4 is activated by promoter CpG island demethylation. In vivo, these MSC-derived cardiac progenitors could not only successfully engraft to the site of cardiac injury in mice with doxorubicin-induced cardiac injury, but also form functional cardiomyocytes and restore cardiac function. Conclusion The present study unveils a link between Wnt inhibition and epigenetic modification to initiate cardiac differentiation, which could enhance the efficacy of stem cell therapy for ischemic heart disorders. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0638-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- G Bhuvanalakshmi
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, 560 065, India
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6845, Australia.,School of Anatomy, Physiology and Human Biology, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Alan Prem Kumar
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, 560 065, India.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6102, Australia.,National University Cancer Institute, Singapore, 119074, Singapore.,Department of Biological Sciences, University of North Texas, Denton, TX, 76203-5017, USA
| | - Arun Dharmarajan
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6845, Australia
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore, 560 065, India. .,School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6102, Australia. .,Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, 6875, Australia.
| |
Collapse
|
24
|
Tian C, Tan S, Bao L, Zeng Q, Liu S, Yang Y, Zhong X, Liu Z. DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:109-119. [DOI: 10.1016/j.cbd.2017.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/21/2017] [Accepted: 02/24/2017] [Indexed: 01/19/2023]
|
25
|
Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes). Sci Rep 2017; 7:40241. [PMID: 28071684 PMCID: PMC5223123 DOI: 10.1038/srep40241] [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: 08/15/2016] [Accepted: 12/05/2016] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.
Collapse
|
26
|
Chen CY, Chan CH, Chen CM, Tsai YS, Tsai TY, Wu Lee YH, You LR. Targeted inactivation of murine Ddx3x: essential roles of Ddx3x in placentation and embryogenesis. Hum Mol Genet 2016; 25:2905-2922. [PMID: 27179789 DOI: 10.1093/hmg/ddw143] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 04/30/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022] Open
Abstract
The X-linked DEAD-box RNA helicase DDX3 (DDX3X) is a multifunctional protein that has been implicated in gene regulation, cell cycle control, apoptosis, and tumorigenesis. However, the precise physiological function of Ddx3x during development remains unknown. Here, we show that loss of Ddx3x results in an early post-implantation lethality in male mice. The size of the epiblast marked by Oct3/4 is dramatically reduced in embryonic day 6.5 (E6.5) Ddx3x-/Y embryos. Preferential paternal X chromosome inactivation (XCI) in extraembryonic tissues of Ddx3x heterozygous (Ddx3x-/+) female mice with a maternally inherited null allele leads to placental abnormalities and embryonic lethality during development. In the embryonic tissues, Ddx3x exhibits developmental- and tissue-specific differences in escape from XCI. Targeted Ddx3x ablation in the epiblast leads to widespread apoptosis and abnormal growth, which causes embryonic lethality in the Sox2-cre/+;Ddx3xflox/Y mutant around E11.5. The observation of significant increases in γH2AX and p-p53Ser15 indicates DNA damage, which suggests that loss of Ddx3x leads to higher levels of genome damage. Significant upregulation of p21WAF1/Cip1 and p15Ink4b results in cell cycle arrest and apoptosis in Ddx3x-deficient cells. These results have uncovered that mouse Ddx3x is essential for both embryo and extraembryonic development.
Collapse
Affiliation(s)
| | | | - Chun-Ming Chen
- Department of Life Sciences and Institute of Genome Sciences.,VYM Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | | | | | - Yan-Hwa Wu Lee
- Institute of Biochemistry and Molecular Biology .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Li-Ru You
- Institute of Biochemistry and Molecular Biology .,VYM Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan
| |
Collapse
|
27
|
Hildebrandt MR, Germain DR, Monckton EA, Brun M, Godbout R. Ddx1 knockout results in transgenerational wild-type lethality in mice. Sci Rep 2015; 5:9829. [PMID: 25909345 PMCID: PMC4408975 DOI: 10.1038/srep09829] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022] Open
Abstract
DEAD box 1 (DDX1) is a member of the DEAD box family of RNA helicases which are
involved in all aspects of RNA metabolism. DDX1 has been implicated in a variety of
biological processes, including 3’-end processing of mRNA, DNA repair,
microRNA processing, tRNA maturation and mRNA transport. To study the role of DDX1
during development, we have generated mice carrying a constitutive Ddx1
knock-out allele. Ddx1+/− mice have no obvious
phenotype and express similar levels of DDX1 as wild-type mice indicating
compensation from the intact Ddx1 allele. Heterozygote matings produce no
viable Ddx1−/− progeny, with
Ddx1−/− embryos dying prior to
embryonic day (E) 3.5. Intriguingly, the number of wild-type progeny is
significantly decreased in heterozygote crosses, with two different heterozygote
populations identified based on parental genotype: (i) normal
Ddx1+/− mice which generate the expected number
of wild-type progeny and (ii) Ddx1*/− mice (with *
signifying a non-genetically altered allele) which generate a significantly reduced
number of wild-type mice. The transgenerational inheritance of wild-type lethality
observed upon crossing Ddx1*/− mice is independent
of parental sex and occurs in cis through a mechanism that is different from
other types of previously reported transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Matthew R Hildebrandt
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Devon R Germain
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Elizabeth A Monckton
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Miranda Brun
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| |
Collapse
|
28
|
Borg R, Cauchi RJ. GEMINs: potential therapeutic targets for spinal muscular atrophy? Front Neurosci 2014; 8:325. [PMID: 25360080 PMCID: PMC4197776 DOI: 10.3389/fnins.2014.00325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/26/2014] [Indexed: 01/28/2023] Open
Abstract
The motor neuron degenerative disease spinal muscular atrophy (SMA) remains one of the most frequently inherited causes of infant mortality. Afflicted patients loose the survival motor neuron 1 (SMN1) gene but retain one or more copies of SMN2, a homolog that is incorrectly spliced. Primary treatment strategies for SMA aim at boosting SMN protein levels, which are insufficient in patients. SMN is known to partner with a set of diverse proteins collectively known as GEMINs to form a macromolecular complex. The SMN-GEMINs complex is indispensible for chaperoning the assembly of small nuclear ribonucleoproteins (snRNPs), which are key for pre-mRNA splicing. Pharmaceutics that alleviate the neuromuscular phenotype by restoring the fundamental function of SMN without augmenting its levels are also crucial in the development of an effective treatment. Their use as an adjunct therapy is predicted to enhance benefit to patients. Inspired by the surprising discovery revealing a premier role for GEMINs in snRNP biogenesis together with in vivo studies documenting their requirement for the correct function of the motor system, this review speculates on whether GEMINs constitute valid targets for SMA therapeutic development.
Collapse
Affiliation(s)
- Rebecca Borg
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta Msida, Malta
| | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta Msida, Malta
| |
Collapse
|
29
|
Shin EM, Hay HS, Lee MH, Goh JN, Tan TZ, Sen YP, Lim SW, Yousef EM, Ong HT, Thike AA, Kong X, Wu Z, Mendoz E, Sun W, Salto-Tellez M, Lim CT, Lobie PE, Lim YP, Yap CT, Zeng Q, Sethi G, Lee MB, Tan P, Goh BC, Miller LD, Thiery JP, Zhu T, Gaboury L, Tan PH, Hui KM, Yip GWC, Miyamoto S, Kumar AP, Tergaonkar V. DEAD-box helicase DP103 defines metastatic potential of human breast cancers. J Clin Invest 2014; 124:3807-24. [PMID: 25083991 DOI: 10.1172/jci73451] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 05/23/2014] [Indexed: 12/12/2022] Open
Abstract
Despite advancement in breast cancer treatment, 30% of patients with early breast cancers experience relapse with distant metastasis. It is a challenge to identify patients at risk for relapse; therefore, the identification of markers and therapeutic targets for metastatic breast cancers is imperative. Here, we identified DP103 as a biomarker and metastasis-driving oncogene in human breast cancers and determined that DP103 elevates matrix metallopeptidase 9 (MMP9) levels, which are associated with metastasis and invasion through activation of NF-κB. In turn, NF-κB signaling positively activated DP103 expression. Furthermore, DP103 enhanced TGF-β-activated kinase-1 (TAK1) phosphorylation of NF-κB-activating IκB kinase 2 (IKK2), leading to increased NF-κB activity. Reduction of DP103 expression in invasive breast cancer cells reduced phosphorylation of IKK2, abrogated NF-κB-mediated MMP9 expression, and impeded metastasis in a murine xenograft model. In breast cancer patient tissues, elevated levels of DP103 correlated with enhanced MMP9, reduced overall survival, and reduced survival after relapse. Together, these data indicate that a positive DP103/NF-κB feedback loop promotes constitutive NF-κB activation in invasive breast cancers and activation of this pathway is linked to cancer progression and the acquisition of chemotherapy resistance. Furthermore, our results suggest that DP103 has potential as a therapeutic target for breast cancer treatment.
Collapse
|
30
|
Cauchi RJ. Gem depletion: amyotrophic lateral sclerosis and spinal muscular atrophy crossover. CNS Neurosci Ther 2014; 20:574-81. [PMID: 24645792 DOI: 10.1111/cns.12242] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/25/2014] [Accepted: 01/27/2014] [Indexed: 12/22/2022] Open
Abstract
The determining factor of spinal muscular atrophy (SMA), the most common motor neuron degenerative disease of childhood, is the survival motor neuron (SMN) protein. SMN and its Gemin associates form a complex that is indispensible for the biogenesis of small nuclear ribonucleoproteins (snRNPs), which constitute the building blocks of spliceosomes. It is as yet unclear whether a decreased capacity of SMN in snRNP assembly, and, hence, transcriptome abnormalities, account for the specific neuromuscular phenotype in SMA. Across metazoa, the SMN-Gemins complex concentrates in multiple nuclear gems that frequently neighbour or overlap Cajal bodies. The number of gems has long been known to be a faithful indicator of SMN levels, which are linked to SMA severity. Intriguingly, a flurry of recent studies have revealed that depletion of this nuclear structure is also a signature feature of amyotrophic lateral sclerosis (ALS), the most common adult-onset motor neuron disease. This review discusses such a surprising crossover in addition to highlighting the most recent work on the intricate world of spliceosome building, which seems to be at the heart of motor neuron physiology and survival.
Collapse
Affiliation(s)
- Ruben J Cauchi
- Department of Physiology and Biochemistry, University of Malta, Msida 2080, Malta
| |
Collapse
|
31
|
Robert F, Pelletier J. Perturbations of RNA helicases in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:333-49. [PMID: 23658027 DOI: 10.1002/wrna.1163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process--either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology.
Collapse
Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | |
Collapse
|
32
|
Takata A, Otsuka M, Yoshikawa T, Kishikawa T, Hikiba Y, Obi S, Goto T, Kang YJ, Maeda S, Yoshida H, Omata M, Asahara H, Koike K. MicroRNA-140 acts as a liver tumor suppressor by controlling NF-κB activity by directly targeting DNA methyltransferase 1 (Dnmt1) expression. Hepatology 2013; 57:162-70. [PMID: 22898998 PMCID: PMC3521841 DOI: 10.1002/hep.26011] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/18/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED MicroRNAs (miRNAs) are small RNAs that regulate the expression of specific target genes. While deregulated miRNA expression levels have been detected in many tumors, whether miRNA functional impairment is also involved in carcinogenesis remains unknown. We investigated whether deregulation of miRNA machinery components and subsequent functional impairment of miRNAs are involved in hepatocarcinogenesis. Among miRNA-containing ribonucleoprotein complex components, reduced expression of DDX20 was frequently observed in human hepatocellular carcinomas, in which enhanced nuclear factor-κB (NF-κB) activity is believed to be closely linked to carcinogenesis. Because DDX20 normally suppresses NF-κB activity by preferentially regulating the function of the NF-κB-suppressing miRNA-140, we hypothesized that impairment of miRNA-140 function may be involved in hepatocarcinogenesis. DNA methyltransferase 1 (Dnmt1) was identified as a direct target of miRNA-140, and increased Dnmt1 expression in DDX20-deficient cells hypermethylated the promoters of metallothionein genes, resulting in decreased metallothionein expression leading to enhanced NF-κB activity. MiRNA-140-knockout mice were prone to hepatocarcinogenesis and had a phenotype similar to that of DDX20 deficiency, suggesting that miRNA-140 plays a central role in DDX20 deficiency-related pathogenesis. CONCLUSION These results indicate that miRNA-140 acts as a liver tumor suppressor, and that impairment of miRNA-140 function due to a deficiency of DDX20, a miRNA machinery component, could lead to hepatocarcinogenesis.
Collapse
Affiliation(s)
- Akemi Takata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takeshi Yoshikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yohko Hikiba
- Division of Gastroenterology, Institute for Adult Diseases, Asahi Life Foundation, Tokyo 100-0005, Japan
| | - Shuntaro Obi
- Department of Hepatology, Kyoundo Hospital, Tokyo 101-0062, Japan
| | - Tadashi Goto
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Young Jun Kang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shin Maeda
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Haruhiko Yoshida
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Masao Omata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiroshi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA,Department of Systems BioMedicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan,CREST, Japan Science and Technology Agency (JST), Tokyo 113-0033, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| |
Collapse
|
33
|
Caburet S, Georges A, L'Hôte D, Todeschini AL, Benayoun BA, Veitia RA. The transcription factor FOXL2: at the crossroads of ovarian physiology and pathology. Mol Cell Endocrinol 2012; 356:55-64. [PMID: 21763750 DOI: 10.1016/j.mce.2011.06.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/21/2011] [Indexed: 12/20/2022]
Abstract
FOXL2 is a gene encoding a forkhead transcription factor. Its mutations or misregulation have been shown to cause the blepharophimosis-ptosis-epicanthus inversus (BPES) syndrome and more recently have been associated with the development of Ovarian Granulosa Cell Tumors (OGCT). BPES is a genetic disorder involving mild craniofacial abnormalities often associated with premature ovarian failure. OGCTs are endocrine malignancies, accounting for 2-5% of ovarian cancers, the treatment of which is still challenging. In this review we summarize recent data concerning FOXL2 transcriptional targets and molecular partners, its post-translational modifications, its mutations and its involvement in newly discovered pathophysiological processes. In the ovary, FOXL2 is involved in the regulation of cholesterol and steroid metabolism, apoptosis, reactive oxygen species detoxification and cell proliferation. Interestingly, one of the main roles of FOXL2 is also to preserve the identity of ovarian granulosa cells even at the adult stage and to prevent their transdifferentiation into Sertoli-like cells. All these recent advances indicate that FOXL2 is central to ovarian development and maintenance. The elucidation of the impact of FOXL2 germinal and somatic mutations will allow a better understanding of the pathogenesis of BPES and of OGCTs.
Collapse
Affiliation(s)
- Sandrine Caburet
- CNRS UMR 7592, Institut Jacques Monod, Equipe Génétique et Génomique du Développement Gonadique, 75205 Paris Cedex 13, France
| | | | | | | | | | | |
Collapse
|
34
|
Abstract
RNA helicases unwind their RNA substrates in an ATP-dependent reaction, and are central to all cellular processes involving RNA. They have important roles in viral life cycles, where RNA helicases are either virus-encoded or recruited from the host. Vertebrate RNA helicases sense viral infections, and trigger the innate antiviral immune response. RNA helicases have been implicated in protozoic, bacterial and fungal infections. They are also linked to neurological disorders, cancer, and aging processes. Genome-wide studies continue to identify helicase genes that change their expression patterns after infection or disease outbreak, but the mechanism of RNA helicase action has been defined for only a few diseases. RNA helicases are prognostic and diagnostic markers and suitable drug targets, predominantly for antiviral and anti-cancer therapies. This review summarizes the current knowledge on RNA helicases in infection and disease, and their growing potential as drug targets.
Collapse
Affiliation(s)
- Lenz Steimer
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany
| | | |
Collapse
|
35
|
Takata A, Otsuka M, Yoshikawa T, Kishikawa T, Kudo Y, Goto T, Yoshida H, Koike K. A miRNA machinery component DDX20 controls NF-κB via microRNA-140 function. Biochem Biophys Res Commun 2012; 420:564-9. [PMID: 22445758 DOI: 10.1016/j.bbrc.2012.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 03/07/2012] [Indexed: 01/20/2023]
Abstract
Hepatocellular carcinoma is the third leading cause of cancer mortality worldwide, but the molecular mechanisms in tumorigenesis remain largely unknown. Previously, a DEAD-box protein DDX20, a component of microRNA-containing ribonucleoprotein complexes, was identified as a liver tumor suppressor candidate in an oncogenomics-based in vivo RNAi screen. However, the molecular mechanisms were unknown. Here, we show that deficiency of DDX20 results in the enhancement of NF-κB activity, a crucial intracellular signaling pathway closely linked with hepatocarcinogenesis. While DDX20 normally suppresses NF-κB activity by regulating NF-κB-suppressing miRNA-140 function, this suppressive effect was lost in DDX20-deficient cells. The impairment of miRNA function due to DDX20 deficiency appears to be miRNA species-specific at the point of loading miRNAs into the RNA-induced silencing complex. These results indicate that DDX20 deficiency enhances NF-κB activity by impairing the NF-κB-suppressive action of microRNAs, and suggest that dysregulation of the microRNA machinery components may also be involved in pathogenesis in various human diseases.
Collapse
Affiliation(s)
- Akemi Takata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Cauchi RJ. Conserved requirement for DEAD-box RNA helicase Gemin3 in Drosophila oogenesis. BMC Res Notes 2012; 5:120. [PMID: 22361416 PMCID: PMC3392723 DOI: 10.1186/1756-0500-5-120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 02/23/2012] [Indexed: 11/10/2022] Open
Abstract
Background DEAD-box RNA helicase Gemin3 is an essential protein since its deficiency is lethal in both vertebrates and invertebrates. In addition to playing a role in transcriptional regulation and RNA silencing, as a core member of the SMN (survival of motor neurons) complex, Gemin3 is required for the biogenesis of spliceosomal snRNPs (small nuclear ribonucleoproteins), and axonal mRNA metabolism. Studies in the mouse and C. elegans revealed that loss of Gemin3 function has a negative impact on ovarian physiology and development. Findings This work reports on the generation and characterisation of gemin3 mutant germline clones in Drosophila adult females. Gemin3 was found to be required for the completion of oogenesis and its loss led to egg polarity defects, oocyte mislocalisation, and abnormal chromosome morphology. Canonical Cajal bodies were absent in the majority of gemin3 mutant egg chambers and histone locus bodies displayed an atypical morphology. snRNP distribution was perturbed so that on gemin3 loss, snRNP cytoplasmic aggregates (U bodies) were only visible in wild type. Conclusions These findings establish a conserved requirement for Gemin3 in Drosophila oogenesis. Furthermore, in view of the similarity to the phenotypes described previously in smn mutant germ cells, the present results confirm the close functional relationship between SMN and Gemin3 on a cellular level.
Collapse
Affiliation(s)
- Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine & Surgery, University of Malta, Msida MSD 2080, Malta G.C.
| |
Collapse
|
37
|
Cai Q, Guo Y, Xiao B, Banerjee S, Saha A, Lu J, Glisovic T, Robertson ES. Epstein-Barr virus nuclear antigen 3C stabilizes Gemin3 to block p53-mediated apoptosis. PLoS Pathog 2011; 7:e1002418. [PMID: 22174681 PMCID: PMC3234233 DOI: 10.1371/journal.ppat.1002418] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/20/2011] [Indexed: 01/10/2023] Open
Abstract
The Epstein-Barr nuclear antigen 3C (EBNA3C), one of the essential latent antigens for Epstein-Barr virus (EBV)-induced immortalization of primary human B lymphocytes in vitro, has been implicated in regulating cell proliferation and anti-apoptosis via interaction with several cellular and viral factors. Gemin3 (also named DDX20 or DP103) is a member of DEAD RNA helicase family which exhibits diverse cellular functions including DNA transcription, recombination and repair, and RNA metabolism. Gemin3 was initially identified as a binding partner to EBNA2 and EBNA3C. However, the mechanism by which EBNA3C regulates Gemin3 function remains unclear. Here, we report that EBNA3C directly interacts with Gemin3 through its C-terminal domains. This interaction results in increased stability of Gemin3 and its accumulation in both B lymphoma cells and EBV transformed lymphoblastoid cell lines (LCLs). Moreover, EBNA3C promotes formation of a complex with p53 and Gemin3 which blocks the DNA-binding affinity of p53. Small hairpin RNA based knockdown of Gemin3 in B lymphoma or LCL cells remarkably attenuates the ability of EBNA3C to inhibit the transcription activity of p53 on its downstream genes p21 and Bax, as well as apoptosis. These findings provide the first evidence that Gemin3 may be a common target of oncogenic viruses for driving cell proliferation and anti-apoptotic activities. Gemin3 (DDX20 or DP103) is a member of the DEAD-box family of RNA helicases involved in various cellular processes including DNA transcription and RNA processing. The Epstein-Barr virus (EBV) encoded nuclear antigen 3C (EBNA3C) is essential for EBV-induced immortalization of primary human B-lymphocytes in vitro. In this study, we discovered that Gemin3 directly binds to the tumor suppressor p53, and acts as a negative regulator blocking p53 functions. Importantly, EBNA3C induces Gemin3 accumulation and enhances the formation of the complex of Gemin3 and p53 in EBV- transformed primary human B lymphocytes. Remarkably, inhibition of Gemin3 production leads to cell death of B lymphoma cells, particularly EBNA3C positive cells. This is the first evidence which shows that Gemin3 directly impairs p53 function in EBV positive cells, and that Gemin3 could be a potential target for EBV-associated cancer therapy.
Collapse
Affiliation(s)
- Qiliang Cai
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yi Guo
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Key Laboratory of AIDS Immunology, Ministry of Health, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Bingyi Xiao
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shuvomoy Banerjee
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Abhik Saha
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jie Lu
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tina Glisovic
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erle S. Robertson
- Department of Microbiology and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
38
|
Ginter-Matuszewska B, Kusz K, Spik A, Grzeszkowiak D, Rembiszewska A, Kupryjanczyk J, Jaruzelska J. NANOS1 and PUMILIO2 bind microRNA biogenesis factor GEMIN3, within chromatoid body in human germ cells. Histochem Cell Biol 2011; 136:279-87. [PMID: 21800163 DOI: 10.1007/s00418-011-0842-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2011] [Indexed: 11/28/2022]
Abstract
Nanos and pumilio bind each other to regulate translation of specific mRNAs in germ cells of model organisms, such as D. melanogaster or C. elegans. Recently described human homologues NANOS1 and PUMILIO2 form a complex similar to their ancestors. This study was aimed to identify the proteins interacting with NANOS1-PUMILIO2 complex in the human spermatogenic cells. Here, using the yeast two-hybrid system we found that NANOS1 and PUMILIO2 proteins interact with RNA DEAD-box helicase GEMIN3, a microRNA biogenesis factor. Moreover, GEMIN3 coimmunoprecipitates with NANOS1 and PUMILIO2 in transfected mammalian cells. By double immunofluorescence staining, we observed that complexes built of NANOS1, PUMILIO2 and GEMIN3 are located within cytoplasmic region of germ cells. These proteins condense to form a compact aggregate in the round spermatids of the human and mouse germ cells. This aggregate was reminiscent of the chromatoid body (CB), a perinuclear structure present in the mammalian male germ line. This structure is considered evolutionary remnant of germ plasm, a hallmark structure of germ cells in lower metazoan. Using a CB marker VASA protein, we demonstrated that CBs are present in the human round spermatids, as they are in the mouse. Moreover, NANOS1, PUMILIO2 and GEMIN3 colocalize with VASA protein. We demonstrated for the first time that a mammalian Nanos-Pumilio complex functions within CB, a center of RNA storing and processing, involving microRNAs. NANOS1-PUMILIO2 complex, together with GEMIN3 and small noncoding RNAs, possibly regulate mRNA translation within CB of the human germ cells.
Collapse
|
39
|
Mouillet JF, Chu T, Sadovsky Y. Expression patterns of placental microRNAs. ACTA ACUST UNITED AC 2011; 91:737-43. [PMID: 21425434 DOI: 10.1002/bdra.20782] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/24/2010] [Accepted: 12/07/2010] [Indexed: 12/22/2022]
Abstract
Among different types of small RNA molecules, distinct types of microRNAs (miRNAs) are expressed in many cell types, where they modulate RNA stability and translation, thus controlling virtually every aspect of tissue development, proliferation, differentiation, and function. Aberrant miRNA expression has been linked to discrete pathologic processes. As the placenta plays a pivotal role in governing fetal development, it is not surprising that the placenta expresses numerous types of miRNAs. Whereas many of these miRNAs are ubiquitously expressed, certain miRNA species are largely unique to the placenta. Research in the field of placental miRNAs is in its early phase, with most studies centering on cataloging placental miRNA species or examining differences in placental miRNA expression between placentas from normal pregnancies and those from pregnancies complicated by pathologies that are associated with placental dysfunction. Recent research endeavors ventured to assess the function of miRNAs in cultured placental trophoblasts, using in vitro conditions that model relevant pathophysiological processes. The impact of miRNA-mediated repression on the trophoblast transcriptome, particularly in response to genetic and environmental perturbations, remains largely unknown. Further in-depth studies are required to unravel the functional significance of miRNAs in molding placental robustness, which must constantly adapt to altered maternal physiologic status to sustain optimal support to the developing embryo. In this review, we summarize the current information about placental miRNAs expression, and the lingering challenges in this field.
Collapse
Affiliation(s)
- Jean-Francois Mouillet
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA 15213, USA
| | | | | |
Collapse
|
40
|
|
41
|
Sun X, Fontaine JM, Hoppe AD, Carra S, DeGuzman C, Martin JL, Simon S, Vicart P, Welsh MJ, Landry J, Benndorf R. Abnormal interaction of motor neuropathy-associated mutant HspB8 (Hsp22) forms with the RNA helicase Ddx20 (gemin3). Cell Stress Chaperones 2010; 15:567-82. [PMID: 20157854 PMCID: PMC3006614 DOI: 10.1007/s12192-010-0169-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 01/07/2010] [Accepted: 01/08/2010] [Indexed: 01/16/2023] Open
Abstract
A number of missense mutations in the two related small heat shock proteins HspB8 (Hsp22) and HspB1 (Hsp27) have been associated with the inherited motor neuron diseases (MND) distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. HspB8 and HspB1 interact with each other, suggesting that these two etiologic factors may act through a common biochemical mechanism. However, their role in neuron biology and in MND is not understood. In a yeast two-hybrid screen, we identified the DEAD box protein Ddx20 (gemin3, DP103) as interacting partner of HspB8. Using co-immunoprecipitation, chemical cross-linking, and in vivo quantitative fluorescence resonance energy transfer, we confirmed this interaction. We also show that the two disease-associated mutant HspB8 forms have abnormally increased binding to Ddx20. Ddx20 itself binds to the survival-of-motor-neurons protein (SMN protein), and mutations in the SMN1 gene cause spinal muscular atrophy, another MND and one of the most prevalent genetic causes of infant mortality. Thus, these protein interaction data have linked the three etiologic factors HspB8, HspB1, and SMN protein, and mutations in any of their genes cause the various forms of MND. Ddx20 and SMN protein are involved in spliceosome assembly and pre-mRNA processing. RNase treatment affected the interaction of the mutant HspB8 with Ddx20 suggesting RNA involvement in this interaction and a potential role of HspB8 in ribonucleoprotein processing.
Collapse
Affiliation(s)
- Xiankui Sun
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jean-Marc Fontaine
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Adam D. Hoppe
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Serena Carra
- Le Centre de recherche en cancérologie, l’Université Laval, L’Hôtel-Dieu de Québec, Laval, Québec Canada G1R 2J6
- Section for Radiation and Stress Cell Biology, Department of Cell Biology, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Cheryl DeGuzman
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jody L. Martin
- Department of Medicine, Cardiovascular Institute, Loyola University Medical Center, Maywood, IL 60153 USA
| | - Stephanie Simon
- Laboratory BFA, University Paris Diderot/CNRS, 75013 Paris, France
| | - Patrick Vicart
- Laboratory BFA, University Paris Diderot/CNRS, 75013 Paris, France
| | - Michael J. Welsh
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jacques Landry
- Le Centre de recherche en cancérologie, l’Université Laval, L’Hôtel-Dieu de Québec, Laval, Québec Canada G1R 2J6
| | - Rainer Benndorf
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Pediatrics, Ohio State University, Columbus, OH 43205 USA
- The Center for Clinical and Translational Research, The Research Institute at Nationwide Children’s Hospital, Research Building II, Room WA2109, 700 Children’s Drive, Columbus, OH 43205 USA
| |
Collapse
|
42
|
Gustafson EA, Wessel GM. DEAD-box helicases: posttranslational regulation and function. Biochem Biophys Res Commun 2010; 395:1-6. [PMID: 20206133 DOI: 10.1016/j.bbrc.2010.02.172] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 02/26/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Eric A Gustafson
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | | |
Collapse
|
43
|
Li JY, Chen X, Fan W, Moghaddam SHH, Chen M, Zhou ZH, Yang HJ, Chen JE, Zhong BX. Proteomic and bioinformatic analysis on endocrine organs of domesticated silkworm, Bombyx mori L. for a comprehensive understanding of their roles and relations. J Proteome Res 2009; 8:2620-32. [PMID: 19382758 DOI: 10.1021/pr8006123] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Three organs of silkworm larva endocrine system, including brain (Br), subesophageal ganglion (SG) and prothoracic glands (PG), were studied employing shotgun LC-MS/MS combined with bioinformatic analysis to comprehensively understand their roles and relations. Totally, 3430, 2683, and 3395 proteins were identified including 1885 common and 652, 253, and 790 organ-specific ones in Br, SG, and PG, respectively. Identified common-expressed proteins indicated the existence of intrinsic complex interactions among these parts of endocrine system. Most of the reputed organs-specific proteins were identified by this approach. KEGG pathway analysis showed 162 same pathways among the 169, 164, and 171 relating Br, SG, and PG. This analysis revealed functional similarities with exceptional resemblance in their metabolism and signaling pathways of the three organs. On the other hand, 70, 57, and 114 organ-specific enzymes related pathways were detected for Br, SG, and PG confirming their functional differences. These results reveal a cooperative mechanism among the three endocrine organs in regulating various physiological and developmental events, and also suggest that the organ-specific proteins might be the fundamental factors responsible for the functional differentiation of these organs.
Collapse
Affiliation(s)
- Jian-Ying Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310029, P. R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Minasaki R, Puoti A, Streit A. The DEAD-box protein MEL-46 is required in the germ line of the nematode Caenorhabditis elegans. BMC DEVELOPMENTAL BIOLOGY 2009; 9:35. [PMID: 19534797 PMCID: PMC2711086 DOI: 10.1186/1471-213x-9-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 06/17/2009] [Indexed: 01/09/2023]
Abstract
Background In the hermaphrodite of the nematode Caenorhabditis elegans, the first germ cells differentiate as sperm. Later the germ line switches to the production of oocytes. This process requires the activity of a genetic regulatory network that includes among others the fem, fog and mog genes. The function of some of these genes is germline specific while others also act in somatic tissues. DEAD box proteins have been shown to be involved in the control of gene expression at different steps such as transcription and pre-mRNA processing. Results We show that the Caenorhabditis elegans gene mel-46 (maternal effect lethal) encodes a DEAD box protein that is related to the mammalian DDX20/Gemin3/DP103 genes. mel-46 is expressed throughout development and mutations in mel-46 display defects at multiple developmental stages. Here we focus on the role of mel-46 in the hermaphrodite germ line. mel-46(yt5) mutant hermaphrodites are partially penetrant sterile and fully penetrant maternal effect lethal. The germ line of mutants shows variable defects in oogenesis. Further, mel-46(yt5) suppresses the complete feminization caused by mutations in fog-2 and fem-3, two genes that are at the top and the center, respectively, of the genetic germline sex determining cascade, but not fog-1 that is at the bottom of this cascade. Conclusion The C. elegans gene mel-46 encodes a DEAD box protein that is required maternally for early embryogenesis and zygotically for postembryonic development. In the germ line, it is required for proper oogenesis. Although it interacts genetically with genes of the germline sex determination machinery its primary function appears to be in oocyte differentiation rather than sex determination.
Collapse
Affiliation(s)
- Ryuji Minasaki
- Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | | | | |
Collapse
|
45
|
Cauchi RJ, Davies KE, Liu JL. A motor function for the DEAD-box RNA helicase, Gemin3, in Drosophila. PLoS Genet 2008; 4:e1000265. [PMID: 19023405 PMCID: PMC2577925 DOI: 10.1371/journal.pgen.1000265] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 10/16/2008] [Indexed: 02/07/2023] Open
Abstract
The survival motor neuron (SMN) protein, the determining factor for spinal muscular atrophy (SMA), is complexed with a group of proteins in human cells. Gemin3 is the only RNA helicase in the SMN complex. Here, we report the identification of Drosophila melanogaster Gemin3 and investigate its function in vivo. Like in vertebrates, Gemin3 physically interacts with SMN in Drosophila. Loss of function of gemin3 results in lethality at larval and/or prepupal stages. Before they die, gemin3 mutant larvae exhibit declined mobility and expanded neuromuscular junctions. Expression of a dominant-negative transgene and knockdown of Gemin3 in mesoderm cause lethality. A less severe Gemin3 disruption in developing muscles leads to flightless adults and flight muscle degeneration. Our findings suggest that Drosophila Gemin3 is required for larval development and motor function.
Collapse
Affiliation(s)
- Ruben J. Cauchi
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay E. Davies
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
46
|
Shpargel KB, Praveen K, Rajendra TK, Matera AG. Gemin3 is an essential gene required for larval motor function and pupation in Drosophila. Mol Biol Cell 2008; 20:90-101. [PMID: 18923150 DOI: 10.1091/mbc.e08-01-0024] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The assembly of metazoan Sm-class small nuclear ribonucleoproteins (snRNPs) is an elaborate, step-wise process that takes place in multiple subcellular compartments. The initial steps, including formation of the core RNP, are mediated by the survival motor neuron (SMN) protein complex. Loss-of-function mutations in human SMN1 result in a neuromuscular disease called spinal muscular atrophy. The SMN complex is comprised of SMN and a number of tightly associated proteins, collectively called Gemins. In this report, we identify and characterize the fruitfly ortholog of the DEAD box protein, Gemin3. Drosophila Gemin3 (dGem3) colocalizes and interacts with dSMN in vitro and in vivo. RNA interference for dGem3 codepletes dSMN and inhibits efficient Sm core assembly in vitro. Transposon insertion mutations in Gemin3 are larval lethals and also codeplete dSMN. Transgenic overexpression of dGem3 rescues lethality, but overexpression of dSMN does not, indicating that loss of dSMN is not the primary cause of death. Gemin3 mutant larvae exhibit motor defects similar to previously characterized Smn alleles. Remarkably, appreciable numbers of Gemin3 mutants (along with one previously undescribed Smn allele) survive as larvae for several weeks without pupating. Our results demonstrate the conservation of Gemin3 protein function in metazoan snRNP assembly and reveal that loss of either Smn or Gemin3 can contribute to neuromuscular dysfunction.
Collapse
Affiliation(s)
- Karl B Shpargel
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA
| | | | | | | |
Collapse
|