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Li Z, Liao Y, Tang C, Xu L, Peng B, Xu X. RBM14 promotes DNA end resection during homologous recombination repair. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1864-1873. [PMID: 37559455 PMCID: PMC10753362 DOI: 10.3724/abbs.2023104] [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: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 08/11/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) is crucial for the maintenance of genome stability and integrity. In this study, we aim to identify novel RNA binding proteins (RBPs) involved in HR repair because little is known about RBP function in HR. For this purpose, we carry out pulldown assays using a synthetic ssDNA/dsDNA structure coated with replication protein A (RPA) to mimic resected DNA, a crucial intermediate in HR-mediated DSB repair. Using this approach, we identify RNA-binding motif protein 14 (RBM14) as a potential binding partner. We further show that RBM14 interacts with an essential HR repair factor, CtIP. RBM14 is crucial for CtIP recruitment to DSB sites and for subsequent RPA coating and RAD51 replacement, facilitating efficient HR repair. Moreover, inhibition of RBM14 expression sensitizes cancer cells to X-ray irradiation. Together, our results demonstrate that RBM14 promotes DNA end resection to ensure HR repair and may serve as a potential target for cancer therapy.
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Affiliation(s)
- Zheng Li
- College of Life SciencesCapital Normal UniversityBeijing100048China
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Yanting Liao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Chen Tang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijing100091China
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM)Dehua HospitalDehua362500China
| | - Linli Xu
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
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2
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Wang X, Ma T, Wei C, Liu J, Yu T, Zou Y, Liu S, Yang Z, Xi J. Toxic effects of exogenous retinoic acid on the neurodevelopment of zebrafish (Danio rerio) embryos. Neurotoxicol Teratol 2023; 100:107291. [PMID: 37689270 DOI: 10.1016/j.ntt.2023.107291] [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: 05/07/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Endogenous retinoic acid (RA) is essential for embryonic development and maintaining adult physiological processes. Human-caused RA residues in the environment threaten the survival of organisms in the environment. We employed zebrafish as a model to explore the developmental impacts of excess RA. We used exogenous RA to raise the amount of RA signal in the embryos and looked at the effects of excess RA on embryonic morphological development. Upregulation of the RA signal significantly reduced embryo hatching and increased embryo malformation. To further understand the neurotoxic impact of RA signaling on early neurodevelopment, we measured the expression of neurodevelopmental marker genes and cell death and proliferation markers in zebrafish embryos. Exogenous RA disrupted stem cell (SC) and neuron marker gene expression and exacerbated apoptosis in the embryos. Furthermore, we looked into the links between the transcriptional coactivator RBM14 and RA signaling to better understand the mechanism of RA neurotoxicity. There was a negative interaction between RA signaling and the transcription coactivator RBM14, and the morpholino-induced RBM14 down-regulation can partially block the effects of RAR antagonist BMS493-induced RA signaling inhibition on embryonic malformation and cell apoptosis. In conclusion, exogenous RA causes neurodevelopmental toxicity, and RBM14 may be involved in this neurotoxic process.
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Affiliation(s)
- Xiaoxuan Wang
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Ting Ma
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Cizhao Wei
- Demonstration Center for Experimental Basic Medicine Education, Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, Hubei, China
| | - Juan Liu
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Ting Yu
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Yu Zou
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Song Liu
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Zheqiong Yang
- Demonstration Center for Experimental Basic Medicine Education, Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, Hubei, China.
| | - Jinlei Xi
- Institute of Pharmaceutical Innovation, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China.
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3
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Ebrahimie E, Rahimirad S, Tahsili M, Mohammadi-Dehcheshmeh M. Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis. World J Stem Cells 2021; 13:1394-1416. [PMID: 34786151 PMCID: PMC8567453 DOI: 10.4252/wjsc.v13.i10.1394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/21/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
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Affiliation(s)
- Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne 3086, Australia
- School of Biosciences, The University of Melbourne, Melbourne 3010, Australia,
| | - Samira Rahimirad
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal H4A 3J1, Quebec, Canada
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4
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Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev 2021; 131:988-1004. [PMID: 34592258 DOI: 10.1016/j.neubiorev.2021.09.049] [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: 04/05/2021] [Revised: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.
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Affiliation(s)
- Manci Li
- University of Minnesota, St. Paul, MN, 55108, United States
| | - Peter A Larsen
- University of Minnesota, St. Paul, MN, 55108, United States.
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5
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Ou MY, Xiao Q, Ju XC, Zeng PM, Huang J, Sheng AL, Luo ZG. The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development. Cell Rep 2021; 35:109290. [PMID: 34192541 DOI: 10.1016/j.celrep.2021.109290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/17/2021] [Accepted: 06/02/2021] [Indexed: 12/21/2022] Open
Abstract
Fusion transcripts or RNAs have been found in both disordered and healthy human tissues and cells; however, their physiological functions in the brain development remain unknown. In the analysis of deposited RNA-sequence libraries covering early to middle embryonic stages, we identify 1,055 fusion transcripts present in the developing neocortex. Interestingly, 98 fusion transcripts exhibit distinct expression patterns in various neural progenitors (NPs) or neurons. We focus on CTNNBIP1-CLSTN1 (CTCL), which is enriched in outer radial glial cells that contribute to cortex expansion during human evolution. Intriguingly, downregulation of CTCL in cultured human cerebral organoids causes marked reduction in NPs and precocious neuronal differentiation, leading to impairment of organoid growth. Furthermore, the expression of CTCL fine-tunes Wnt/β-catenin signaling that controls cortex patterning. Together, this work provides evidence indicating important roles of fusion transcript in human brain development and evolution.
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Affiliation(s)
- Min-Yi Ou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Xiao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang-Chun Ju
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Peng-Ming Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ai-Li Sheng
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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6
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Wang Y, Yu Y, Pang Y, Yu H, Zhang W, Zhao X, Yu J. The distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism. RNA Biol 2021; 18:2107-2126. [PMID: 33787465 DOI: 10.1080/15476286.2021.1909320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The zinc finger CCHC-type (ZCCHC) superfamily proteins, characterized with the consensus sequence C-X2-C-X4-H-X4-C, are accepted to have high-affinity binding to single-stranded nucleic acids, especially single-stranded RNAs. In human beings 25 ZCCHC proteins have been annotated in the HGNC database. Of interest is that among the family, most members are involved in the multiple steps of RNA metabolism. In this review, we focus on the diverged roles of human ZCCHC proteins on RNA transcription, biogenesis, splicing, as well as translation and degradation.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Yu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yidan Pang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haojun Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqi Zhang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020; 117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.
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8
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Wang WY, Quan W, Yang F, Wei YX, Chen JJ, Yu H, Xie J, Zhang Y, Li ZF. RBM4 modulates the proliferation and expression of inflammatory factors via the alternative splicing of regulatory factors in HeLa cells. Mol Genet Genomics 2019; 295:95-106. [DOI: 10.1007/s00438-019-01606-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022]
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9
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Yu CY, Chuang CY, Kuo HC. Trans-spliced long non-coding RNA: an emerging regulator of pluripotency. Cell Mol Life Sci 2018; 75:3339-3351. [PMID: 29961157 PMCID: PMC11105688 DOI: 10.1007/s00018-018-2862-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/21/2018] [Accepted: 06/25/2018] [Indexed: 01/08/2023]
Abstract
With dual capacities for unlimited self-renewal and pluripotent differentiation, pluripotent stem cells (PSCs) give rise to many cell types in our body and PSC culture systems provide an unparalleled opportunity to study early human development and disease. Accumulating evidence indicates that the molecular mechanisms underlying pluripotency maintenance in PSCs involve many factors. Among these regulators, recent studies have shown that long non-coding RNAs (lncRNAs) can affect the pluripotency circuitry by cooperating with master pluripotency-associated factors. Additionally, trans-spliced RNAs, which are generated by combining two or more pre-mRNA transcripts to produce a chimeric RNA, have been identified as regulators of various biological processes, including human pluripotency. In this review, we summarize and discuss current knowledge about the roles of lncRNAs, including trans-spliced lncRNAs, in controlling pluripotency.
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Affiliation(s)
- Chun-Ying Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan
| | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan.
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
- College of Medicine, Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan.
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10
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RBM4 Modulates Radial Migration via Alternative Splicing of Dab1 during Cortex Development. Mol Cell Biol 2018; 38:MCB.00007-18. [PMID: 29581187 DOI: 10.1128/mcb.00007-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022] Open
Abstract
The RNA-binding motif 4 (RBM4) protein participates in cell differentiation via its role in regulating the expression of tissue-specific or developmentally regulated mRNA splice isoforms. RBM4 is expressed in embryonic brain during development; it is initially enriched in the ventricular zone/subventricular zone and subsequently distributed throughout the cerebral cortex. Rbm4a knockout brain exhibited delayed migration of late-born neurons. Using in utero electroporation, we confirmed that knockdown of RBM4 impaired cortical neuronal migration. RNA immunoprecipitation with high-throughput sequencing identified Disabled-1 (Dab1), which encodes a critical reelin signaling adaptor, as a potential target of RBM4. Rbm4a knockout embryonic brain showed altered Dab1 isoform ratios. Overexpression of RBM4 promoted the inclusion of Dab1 exons 7 and 8 (7/8), whereas its antagonist polypyrimidine tract-binding protein 1 (PTBP1) acted in an opposite manner. RBM4 directly counteracted the effect of PTBP1 on exon 7/8 selection. Finally, we showed that the full-length Dab1, but not exon 7/8-truncated Dab1, rescued neuronal migration defects in RBM4-depleted neurons, indicating that RBM4 plays a role in neuronal migration via modulating the expression of Dab1 splice isoforms. Our findings imply that RBM4 is necessary during brain development and that its deficiency may lead to developmental brain abnormality.
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Zhou LT, Ye SH, Yang HX, Zhou YT, Zhao QH, Sun WW, Gao MM, Yi YH, Long YS. A novel role of fragile X mental retardation protein in pre-mRNA alternative splicing through RNA-binding protein 14. Neuroscience 2017; 349:64-75. [PMID: 28257890 DOI: 10.1016/j.neuroscience.2017.02.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 02/08/2023]
Abstract
Fragile X mental retardation protein (FMRP), an important RNA-binding protein responsible for fragile X syndrome, is involved in posttranscriptional control of gene expression that links with brain development and synaptic functions. Here, we reveal a novel role of FMRP in pre-mRNA alternative splicing, a general event of posttranscriptional regulation. Using co-immunoprecipitation and immunofluorescence assays, we identified that FMRP interacts with an alternative-splicing-associated protein RNA-binding protein 14 (RBM14) in a RNA-dependent fashion, and the two proteins partially colocalize in the nuclei of hippocampal neurons. We show that the relative skipping/inclusion ratio of the micro-exon L in the Protrudin gene and exon 10 in the Tau gene decreased in the hippocampus of Fmr1 knockout (KO) mice. Knockdown of either FMRP or RBM14 alters the relative skipping/inclusion ratio of Protrudin and Tau in cultured Neuro-2a cells, similar to that in the Fmr1 KO mice. Furthermore, overexpression of FMRP leads to an opposite pattern of the splicing, which can be offset by RBM14 knockdown. RNA immunoprecipitation assays indicate that FMRP promotes RBM14's binding to the mRNA targets. In addition, overexpression of the long form of Protrudin or the short form of Tau promotes protrusion growth of the retinoic acid-treated, neuronal-differentiated Neuro-2a cells. Together, these data suggest a novel function of FMRP in the regulation of pre-mRNA alternative splicing through RBM14 that may be associated with normal brain function and FMRP-related neurological disorders.
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Affiliation(s)
- Lin-Tao Zhou
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Shun-Hua Ye
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Hai-Xuan Yang
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Yong-Ting Zhou
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Qi-Hua Zhao
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Wei-Wen Sun
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Mei-Mei Gao
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Yong-Hong Yi
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China; Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Yue-Sheng Long
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China.
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12
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Li Y, Ito M, Sun S, Chida T, Nakashima K, Suzuki T. LUC7L3/CROP inhibits replication of hepatitis B virus via suppressing enhancer II/basal core promoter activity. Sci Rep 2016; 6:36741. [PMID: 27857158 PMCID: PMC5114668 DOI: 10.1038/srep36741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/20/2016] [Indexed: 02/08/2023] Open
Abstract
The core promoter of hepatitis B virus (HBV) genome is a critical region for transcriptional initiation of 3.5 kb, pregenome and precore RNAs and for the viral replication. Although a number of host-cell factors that potentially regulate the viral promoter activities have been identified, the molecular mechanisms of the viral gene expression, in particular, regulatory mechanisms of the transcriptional repression remain elusive. In this study, we identified LUC7 like 3 pre-mRNA splicing factor (LUC7L3, also known as hLuc7A or CROP) as a novel interacting partner of HBV enhancer II and basal core promoter (ENII/BCP), key elements within the core promoter, through the proteomic screening and found that LUC7L3 functions as a negative regulator of ENII/BCP. Gene silencing of LUC7L3 significantly increased expression of the viral genes and antigens as well as the activities of ENII/BCP and core promoter. In contrast, overexpression of LUC7L3 inhibited their activities and HBV replication. In addition, LUC7L3 possibly contributes to promotion of the splicing of 3.5 kb RNA, which may also be involved in negative regulation of the pregenome RNA level. This is the first to demonstrate the involvement of LUC7L3 in regulation of gene transcription and in viral replication.
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Affiliation(s)
- Yuan Li
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Masahiko Ito
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Suofeng Sun
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Takeshi Chida
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Kenji Nakashima
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Tetsuro Suzuki
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
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13
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Tarn WY, Kuo HC, Yu HI, Liu SW, Tseng CT, Dhananjaya D, Hung KY, Tu CC, Chang SH, Huang GJ, Chiu IM. RBM4 promotes neuronal differentiation and neurite outgrowth by modulating Numb isoform expression. Mol Biol Cell 2016; 27:1676-83. [PMID: 27009199 PMCID: PMC4865323 DOI: 10.1091/mbc.e15-11-0798] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/18/2016] [Indexed: 01/22/2023] Open
Abstract
RBM4 modulates alternative exon selection of Numb and up-regulates proneural Mash1 gene expression, possibly via specific Numb isoforms. RBM4 overexpression promotes neuronal cell differentiation. Moreover, RBM4 is essential for neurite outgrowth in primary cortical neurons by modulating specific Numb isoform expression. RBM4 participates in cell differentiation by regulating tissue-specific alternative pre-mRNA splicing. RBM4 also has been implicated in neurogenesis in the mouse embryonic brain. Using mouse embryonal carcinoma P19 cells as a neural differentiation model, we observed a temporal correlation between RBM4 expression and a change in splicing isoforms of Numb, a cell-fate determination gene. Knockdown of RBM4 affected the inclusion/exclusion of exons 3 and 9 of Numb in P19 cells. RBM4-deficient embryonic mouse brain also exhibited aberrant splicing of Numb pre-mRNA. Using a splicing reporter minigene assay, we demonstrated that RBM4 promoted exon 3 inclusion and exon 9 exclusion. Moreover, we found that RBM4 depletion reduced the expression of the proneural gene Mash1, and such reduction was reversed by an RBM4-induced Numb isoform containing exon 3 but lacking exon 9. Accordingly, induction of ectopic RBM4 expression in neuronal progenitor cells increased Mash1 expression and promoted cell differentiation. Finally, we found that RBM4 was also essential for neurite outgrowth from cortical neurons in vitro. Neurite outgrowth defects of RBM4-depleted neurons were rescued by RBM4-induced exon 9–lacking Numb isoforms. Therefore our findings indicate that RBM4 modulates exon selection of Numb to generate isoforms that promote neuronal cell differentiation and neurite outgrowth.
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Affiliation(s)
- Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Che Kuo
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-I Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Shin-Wu Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Tzu Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Dodda Dhananjaya
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kuan-Yang Hung
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Chiang Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Shuo-Hsiu Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Guo-Jen Huang
- Graduate Institute of Biomedical Sciences, Chung-Gung University, Tao-Yuan City 33302, Taiwan
| | - Ing-Ming Chiu
- National Health Research Institutes, Chu-Nan 35053, Taiwan
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14
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Lei Q, Li C, Zuo Z, Huang C, Cheng H, Zhou R. Evolutionary Insights into RNA trans-Splicing in Vertebrates. Genome Biol Evol 2016; 8:562-77. [PMID: 26966239 PMCID: PMC4824033 DOI: 10.1093/gbe/evw025] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pre-RNA splicing is an essential step in generating mature mRNA. RNA trans-splicing combines two separate pre-mRNA molecules to form a chimeric non-co-linear RNA, which may exert a function distinct from its original molecules. Trans-spliced RNAs may encode novel proteins or serve as noncoding or regulatory RNAs. These novel RNAs not only increase the complexity of the proteome but also provide new regulatory mechanisms for gene expression. An increasing amount of evidence indicates that trans-splicing occurs frequently in both physiological and pathological processes. In addition, mRNA reprogramming based on trans-splicing has been successfully applied in RNA-based therapies for human genetic diseases. Nevertheless, clarifying the extent and evolution of trans-splicing in vertebrates and developing detection methods for trans-splicing remain challenging. In this review, we summarize previous research, highlight recent advances in trans-splicing, and discuss possible splicing mechanisms and functions from an evolutionary viewpoint.
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Affiliation(s)
- Quan Lei
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Cong Li
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Zhixiang Zuo
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Chunhua Huang
- Department of Cell Biology, College of Life Sciences, Wuhan University, P.R. China
| | - Hanhua Cheng
- Department of Cell Biology, College of Life Sciences, Wuhan University, P.R. China
| | - Rongjia Zhou
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
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15
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Kai M. Roles of RNA-Binding Proteins in DNA Damage Response. Int J Mol Sci 2016; 17:310. [PMID: 26927092 PMCID: PMC4813173 DOI: 10.3390/ijms17030310] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/31/2022] Open
Abstract
Living cells experience DNA damage as a result of replication errors and oxidative metabolism, exposure to environmental agents (e.g., ultraviolet light, ionizing radiation (IR)), and radiation therapies and chemotherapies for cancer treatments. Accumulation of DNA damage can lead to multiple diseases such as neurodegenerative disorders, cancers, immune deficiencies, infertility, and also aging. Cells have evolved elaborate mechanisms to deal with DNA damage. Networks of DNA damage response (DDR) pathways are coordinated to detect and repair DNA damage, regulate cell cycle and transcription, and determine the cell fate. Upstream factors of DNA damage checkpoints and repair, “sensor” proteins, detect DNA damage and send the signals to downstream factors in order to maintain genomic integrity. Unexpectedly, we have discovered that an RNA-processing factor is involved in DNA repair processes. We have identified a gene that contributes to glioblastoma multiforme (GBM)’s treatment resistance and recurrence. This gene, RBM14, is known to function in transcription and RNA splicing. RBM14 is also required for maintaining the stem-like state of GBM spheres, and it controls the DNA-PK-dependent non-homologous end-joining (NHEJ) pathway by interacting with KU80. RBM14 is a RNA-binding protein (RBP) with low complexity domains, called intrinsically disordered proteins (IDPs), and it also physically interacts with PARP1. Furthermore, RBM14 is recruited to DNA double-strand breaks (DSBs) in a poly(ADP-ribose) (PAR)-dependent manner (unpublished data). DNA-dependent PARP1 (poly-(ADP) ribose polymerase 1) makes key contributions in the DNA damage response (DDR) network. RBM14 therefore plays an important role in a PARP-dependent DSB repair process. Most recently, it was shown that the other RBPs with intrinsically disordered domains are recruited to DNA damage sites in a PAR-dependent manner, and that these RBPs form liquid compartments (also known as “liquid-demixing”). Among the PAR-associated IDPs are FUS/TLS (fused in sarcoma/translocated in sarcoma), EWS (Ewing sarcoma), TARF15 (TATA box-binding protein-associated factor 68 kDa) (also called FET proteins), a number of heterogeneous nuclear ribonucleoproteins (hnRNPs), and RBM14. Importantly, various point mutations within the FET genes have been implicated in pathological protein aggregation in neurodegenerative diseases, specifically with amyotrophic lateral sclerosis (ALS), and frontotemporal lobe degeneration (FTLD). The FET proteins also frequently exhibit gene translocation in human cancers, and emerging evidence shows their physical interactions with DDR proteins and thus implies their involvement in the maintenance of genome stability.
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Affiliation(s)
- Mihoko Kai
- Department of Radiation Oncology, Johns Hopkins University, School of Medicine, Baltimore, MD 21231, USA.
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16
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Yamada E, Demachi-Okamura A, Kondo S, Akatsuka Y, Suzuki S, Shibata K, Kikkawa F, Kuzushima K. Identification of a naturally processed HLA-Cw7-binding peptide that cross-reacts with HLA-A24-restricted ovarian cancer-specific CTLs. ACTA ACUST UNITED AC 2015. [PMID: 26216489 DOI: 10.1111/tan.12607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Here, we describe an human leukocyte antigen (HLA)-A*24:02-restricted cytotoxic T-lymphocyte (CTL) clone, 1G3, established from naïve CD8(+) T-lymphocytes obtained from a healthy donor stimulated with HLA-modified TOV21G, an ovarian cancer cell line. The 1G3 clone responds not only to ovarian cancer cells in the context of HLA-A*24:02 but also to allogeneic HLA-Cw*07:02 molecules through cross-reactive T-cell receptor recognition. Expression screening using a complementary DNA library constructed from TOV21G messenger RNA revealed that this alloreactivity was mediated through the nine-mer peptide VRTPYTMSY, derived from RNA-binding motif protein 4. To our knowledge, this study presents the first example of the allorecognition of an HLA-Cw molecule by HLA-A-restricted T-cells, thereby revealing a naturally processed epitope peptide. These findings provide the structural bases for the allorecognition of human T-cells. In addition, this study suggests that unexpected alloresponses occur in certain HLA combinations, and further study is needed to understand the mechanisms of alloreactivity for better prediction of alloresponses in clinical settings.
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Affiliation(s)
- E Yamada
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - A Demachi-Okamura
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - S Kondo
- Department of Gynecologic Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Y Akatsuka
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Hematology & Oncology, Fujita Health University, Toyoake, Japan
| | - S Suzuki
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - K Shibata
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - F Kikkawa
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - K Kuzushima
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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17
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Mohamed AM, Thénoz M, Solly F, Balsat M, Mortreux F, Wattel E. How mRNA is misspliced in acute myelogenous leukemia (AML)? Oncotarget 2015; 5:9534-45. [PMID: 25375204 PMCID: PMC4259418 DOI: 10.18632/oncotarget.2304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/09/2023] Open
Abstract
Approximately one-third of expressed genes are misspliced in AML, opening the possibility that additional factors than splicing factor mutations might cause RNA missplicing in these diseases. AML cells harbor a constellation of epigenetic modifications and regularly express large amounts of WT1 transcripts. Histone acetylation/methylation and DNA CpG methylation favor either exon skipping or inclusion, mainly through interfering with RNA Pol II-mediated elongation. This can result either from the binding of various factors on Pol II or alternatively from the recruitment of DNA binding factors that create roadblocks to Pol II-induced elongation. WT1 exhibits pleiotropic effects on mRNA splicing, which mainly result from the binding properties of WT1 via its zinc fingers domains to DNA, RNA, and proteins. Through the repression of the kinase SRPK1, WT1 modifies the splicing of VEGF, which plays important roles in hematopoiesis and angiogenesis. At the protein level, WT1 interacts with the splicing factors U2AF2, WTAP, and RPM4. Therefore, AML cells appear to have acquired numerous properties known to interfere with mRNA splicing. The challenge is now to elucidate these links in order to trigger mRNA splicing at the therapeutic level.
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18
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Tomita T, Ieguchi K, Sawamura T, Maru Y. Human serum amyloid A3 (SAA3) protein, expressed as a fusion protein with SAA2, binds the oxidized low density lipoprotein receptor. PLoS One 2015; 10:e0118835. [PMID: 25738827 PMCID: PMC4349446 DOI: 10.1371/journal.pone.0118835] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Abstract
Serum amyloid A3 (SAA3) possesses characteristics distinct from the other serum amyloid A isoforms, SAA1, SAA2, and SAA4. High density lipoprotein contains the latter three isoforms, but not SAA3. The expression of mouse SAA3 (mSAA3) is known to be up-regulated extrahepatically in inflammatory responses, and acts as an endogenous ligand for the toll-like receptor 4/MD-2 complex. We previously reported that mSAA3 plays an important role in facilitating tumor metastasis by attracting circulating tumor cells and enhancing hyperpermeability in the lungs. On the other hand, human SAA3 (hSAA3) has long been regarded as a pseudogene, which is in contrast to the abundant expression levels of the other isoforms. Although the nucleotide sequence of hSAA3 is very similar to that of the other SAAs, a single oligonucleotide insertion in exon 2 causes a frame-shift to generate a unique amino acid sequence. In the present study, we identified that hSAA3 was transcribed in the hSAA2-SAA3 fusion transcripts of several human cell lines. In the fusion transcript, hSAA2 exon 3 was connected to hSAA3 exon 1 or hSAA3 exon 2, located approximately 130kb downstream from hSAA2 exon 3 in the genome, which suggested that it is produced by alternative splicing. Furthermore, we succeeded in detecting and isolating hSAA3 protein for the first time by an immunoprecipitation-enzyme linked immune assay system using monoclonal and polyclonal antibodies that recognize the hSAA3 unique amino acid sequence. We also demonstrated that hSAA3 bound oxidized low density lipoprotein receptor (oxLDL receptor, LOX-1) and elevated the phosphorylation of ERK, the intracellular MAP-kinase signaling protein.
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Affiliation(s)
- Takeshi Tomita
- Department of Pharmacology, Tokyo Women’s Medical University, Tokyo, Japan
- * E-mail: (TT); (YM)
| | - Katsuaki Ieguchi
- Department of Pharmacology, Tokyo Women’s Medical University, Tokyo, Japan
| | - Tatsuya Sawamura
- Department of Vascular Physiology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Yoshiro Maru
- Department of Pharmacology, Tokyo Women’s Medical University, Tokyo, Japan
- * E-mail: (TT); (YM)
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19
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Chang SH, Chang WL, Lu CC, Tarn WY. Alanine repeats influence protein localization in splicing speckles and paraspeckles. Nucleic Acids Res 2014; 42:13788-98. [PMID: 25414336 PMCID: PMC4267627 DOI: 10.1093/nar/gku1159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ.
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Affiliation(s)
- Shuo-Hsiu Chang
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Lun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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20
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Greger L, Su J, Rung J, Ferreira PG, Lappalainen T, Dermitzakis ET, Brazma A. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PLoS One 2014; 9:e104567. [PMID: 25133550 PMCID: PMC4136775 DOI: 10.1371/journal.pone.0104567] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/14/2014] [Indexed: 01/18/2023] Open
Abstract
Chimeric RNAs originating from two or more different genes are known to exist not only in cancer, but also in normal tissues, where they can play a role in human evolution. However, the exact mechanism of their formation is unknown. Here, we use RNA sequencing data from 462 healthy individuals representing 5 human populations to systematically identify and in depth characterize 81 RNA tandem chimeric transcripts, 13 of which are novel. We observe that 6 out of these 81 chimeras have been regarded as cancer-specific. Moreover, we show that a prevalence of long introns at the fusion breakpoint is associated with the chimeric transcripts formation. We also find that tandem RNA chimeras have lower abundances as compared to their partner genes. Finally, by combining our results with genomic data from the same individuals we uncover intronic genetic variants associated with the chimeric RNA formation. Taken together our findings provide an important insight into the chimeric transcripts formation and open new avenues of research into the role of intronic genetic variants in post-transcriptional processing events.
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Affiliation(s)
- Liliana Greger
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
- * E-mail:
| | - Jing Su
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Johan Rung
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Pedro G. Ferreira
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Alvis Brazma
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
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21
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Eul J, Patzel V. Homologous SV40 RNA trans-splicing: a new mechanism for diversification of viral sequences and phenotypes. RNA Biol 2013; 10:1689-99. [PMID: 24178438 DOI: 10.4161/rna.26707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Simian Virus 40 (SV40) is a polyomavirus found in both monkeys and humans, which causes cancer in some animal models. In humans, SV40 has been reported to be associated with cancers but causality has not been proven yet. The transforming activity of SV40 is mainly due to its 94-kD large T antigen, which binds to the retinoblastoma (pRb) and p53 tumor suppressor proteins, and thereby perturbs their functions. Here we describe a 100 kD super T antigen harboring a duplication of the pRB binding domain that was associated with unusual high cell transformation activity and that was generated by a novel mechanism involving homologous RNA trans-splicing of SV40 early transcripts in transformed rodent cells. Enhanced trans-splice activity was observed in clones carrying a single point mutation in the large T antigen 5' donor splice site (ss). This mutation impaired cis-splicing in favor of an alternative trans-splice reaction via a cryptic 5'ss within a second cis-spliced SV40 pre-mRNA molecule and enabled detectable gene expression. Next to the cryptic 5'ss we identified additional trans-splice helper functions, including putative dimerization domains and a splice enhancer sequence. Our findings suggest RNA trans-splicing as a SV40-intrinsic mechanism that supports the diversification of viral RNA and phenotypes.
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Affiliation(s)
- Joachim Eul
- Institut fuer Molekularbiologie und Biochemie; Freie Universität Berlin; Berlin, German
| | - Volker Patzel
- Department of Microbiology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
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22
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Peng M, Yang Z, Zhang H, Jaafar L, Wang G, Liu M, Flores-Rozas H, Xu J, Mivechi NF, Ko L. GT198 Splice Variants Display Dominant-Negative Activities and Are Induced by Inactivating Mutations. Genes Cancer 2013; 4:26-38. [PMID: 23946869 DOI: 10.1177/1947601913486345] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/16/2013] [Indexed: 11/16/2022] Open
Abstract
Alternative pre-mRNA splicing yields functionally distinct splice variants in regulating normal cell differentiation as well as cancer development. The putative tumor suppressor gene GT198 (PSMC3IP), encoding a protein also known as TBPIP and Hop2, has been shown to regulate steroid hormone receptor-mediated transcription and to stimulate homologous recombination in DNA repair. Here, we have identified 6 distinct GT198 splice variant transcripts generated by alternative promoter usage or alternative splicing. Various splice variant transcripts preserve a common open reading frame, which encodes the DNA binding domain of GT198. The splice variants act as dominant negatives to counteract wild-type GT198 activity in transcription and to abolish Rad51 foci formation during radiation-induced DNA damage. In fallopian tube cancer, we have identified 44 point mutations in GT198 clustered in 2 mutation hotspot sequences. The mutation hotspots coincide with the regulatory sequences responsible for alternative splicing, strongly supporting that imbalanced alternative splicing is a selected consequence in cancer. In addition, splice variant-associated cytoplasmic expression is found in tumors carrying germline or somatic GT198 mutations. An altered alternative splicing pattern with increased variants is also present in lymphoblastoid cells derived from familial breast cancer patients carrying GT198 germline mutations. Furthermore, GT198 and its variant are reciprocally expressed during mouse stem cell differentiation. The constitutive expression of the GT198 variant but not the wild type induces tumor growth in nude mice. Our results collectively suggest that mutations in the GT198 gene deregulate alternative splicing. Defective alternative splicing promotes antagonizing variants and in turn induces a loss of the wild type in tumorigenesis. The study highlights the role of alternative splicing in tumor suppressor gene inactivation.
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Affiliation(s)
- Min Peng
- Cancer Center, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA
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23
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The coactivator activator CoAA regulates PEA3 group member transcriptional activity. Biochem J 2011; 439:469-77. [PMID: 21736557 DOI: 10.1042/bj20110728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The PEA3 (polyoma enhancer activator 3) group members [ERM (ETS-related molecule), ER81 (ETS-related 81) and PEA3] of the Ets transcription factor family are involved in migration and dissemination processes during organogenesis and cancer development. In the present study, we report that the hnRNP (heterogeneous nuclear ribonucleoprotein)-like protein CoAA (Coactivator activator) interacts with the PEA3 group members and modulates their transcriptional activity. We also demonstrate that the CoAA YQ domain, containing tyrosine/glutamine-rich hexapeptide repeats, is necessary for the interaction, whereas the two N-terminal RRMs (RNA recognition motifs) of CoAA are required to enhance transcriptional activity. Finally, we show that CoAA is involved in the migration-enhancing action of PEA3 on MCF7 human cancer cells, suggesting that CoAA might be an important regulator of PEA3 group member activity during metastasis.
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24
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Guillaumond F, Boyer B, Becquet D, Guillen S, Kuhn L, Garin J, Belghazi M, Bosler O, Franc J, François‐Bellan A. Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF. FASEB J 2011; 25:2740-56. [DOI: 10.1096/fj.10-178616] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Fabienne Guillaumond
- Institut des Sciences Moleculaires de Marseille (ISM2)UMR6263 Université Aix‐Marseille IIIMarseilleFrance
| | - Benedicte Boyer
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Denis Becquet
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Severine Guillen
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Lauriane Kuhn
- Plateforme Étude de la Dynamique des Protéomes (EDyP)‐ServiceGrenobleFrance
| | - Jerome Garin
- Centre d'Analyse Protéomique de MarseilleInstitut Fédératif de Recherche (IFR) Jean‐RocheMarseilleFrance
| | - Maya Belghazi
- Plateforme Protéomique de l'Esplanade Institut de Biologie Moléculaire et Cellulaire (IBMC)StrasbourgFrance
| | - Olivier Bosler
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Jean‐Louis Franc
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
| | - Anne‐Marie François‐Bellan
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M)Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6231Université Aix‐Marseille II, IIIMarseilleFrance
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25
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McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. ACTA ACUST UNITED AC 2011; 27:1481-8. [PMID: 21478487 DOI: 10.1093/bioinformatics/btr184] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
MOTIVATION Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and whole genome shotgun sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data. RESULTS We have applied Comrad to the discovery of gene fusions and read-throughs in prostate cancer cell line C4-2, a derivative of the LNCaP cell line with androgen-independent characteristics. As a proof of concept, we have rediscovered in the C4-2 data 4 of the 6 fusions previously identified in LNCaP. We also identified six novel fusion transcripts and associated genomic breakpoints, and verified their existence in LNCaP, suggesting that Comrad may be more sensitive than previous methods that have been applied to fusion discovery in LNCaP. We show that many of the gene fusions discovered using Comrad would be difficult to identify using currently available techniques. AVAILABILITY A C++ and Perl implementation of the method demonstrated in this article is available at http://compbio.cs.sfu.ca/.
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Affiliation(s)
- Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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Fang X, Yoon JG, Li L, Tsai YS, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B. Landscape of the SOX2 protein-protein interactome. Proteomics 2011; 11:921-34. [PMID: 21280222 DOI: 10.1002/pmic.201000419] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 11/19/2010] [Accepted: 12/05/2010] [Indexed: 01/21/2023]
Abstract
SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells that appears to re-activate in several human cancers including glioblastoma multiforme. Using immunoprecipitation (IP)/MS/MS, we identified 144 proteins that are putative SOX2 interacting proteins. Of note, SOX2 was found to interact with several heterogeneous nuclear ribonucleoprotein family proteins, including HNRNPA2B1, HNRNPA3, HNRNPC, HNRNPK, HNRNPL, HNRNPM, HNRNPR, HNRNPU, as well as other ribonucleoproteins, DNA repair proteins and helicases. Gene ontology (GO) analysis revealed that the SOX2 interactome was enriched for GO terms GO:0030529 ribonucleoprotein complex and GO:0004386 helicase activity. These findings indicate that SOX2 associates with the heterogeneous nuclear ribonucleoprotein complex, suggesting a possible role for SOX2 in post-transcriptional regulation in addition to its function as a transcription factor.
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Affiliation(s)
- Xuefeng Fang
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA, USA
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Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics 2011; 4:11. [PMID: 21261984 PMCID: PMC3041646 DOI: 10.1186/1755-8794-4-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 01/24/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. METHODS We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. RESULTS Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. CONCLUSIONS Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer.
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Affiliation(s)
- Serban Nacu
- Department of Bioinformatics and Molecular Biology, Genentech, Inc, South San Francisco, California 94080, USA
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Bulynko YA, O'Malley BW. Nuclear receptor coactivators: structural and functional biochemistry. Biochemistry 2010; 50:313-28. [PMID: 21141906 DOI: 10.1021/bi101762x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transcription of eukaryotic cell is a multistep process tightly controlled by concerted action of macromolecules. Nuclear receptors are ligand-activated sequence-specific transcription factors that bind DNA and activate (or repress) transcription of specific sets of nuclear target genes. Successful activation of transcription by nuclear receptors and most other transcription factors requires "coregulators" of transcription. Coregulators make up a diverse family of proteins that physically interact with and modulate the activity of transcription factors and other components of the gene expression machinery via multiple biochemical mechanisms. The coregulators include coactivators that accomplish reactions required for activation of transcription and corepressors that suppress transcription. This review summarizes our current knowledge of nuclear receptor coactivators with an emphasis on their biochemical mechanisms of action and means of regulation.
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Affiliation(s)
- Yaroslava A Bulynko
- Molecular and Cellular Biology, BCM130 Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Abstract
Paraspeckles are a relatively new class of subnuclear bodies found in the interchromatin space of mammalian cells. They are RNA-protein structures formed by the interaction between a long nonprotein-coding RNA species, NEAT1/Men epsilon/beta, and members of the DBHS (Drosophila Behavior Human Splicing) family of proteins: P54NRB/NONO, PSPC1, and PSF/SFPQ. Paraspeckles are critical to the control of gene expression through the nuclear retention of RNA containing double-stranded RNA regions that have been subject to adenosine-to-inosine editing. Through this mechanism paraspeckles and their components may ultimately have a role in controlling gene expression during many cellular processes including differentiation, viral infection, and stress responses.
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Affiliation(s)
- Archa H Fox
- Western Australian Institute for Medical Research and Centre For Medical Research, University of Western Australia, Crawley, 6009 Western Australia, Australia.
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Alternative splicing in stem cell self-renewal and diferentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:92-104. [PMID: 21222201 DOI: 10.1007/978-1-4419-7037-4_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature messenger RNA sequences. This regulated, selective removal of whole or portions of exons by alternative splicing provides avenues for control of RNA abundance and proteome diversity. We discuss several examples of key alternative splicing events in stem cell biology and provide an overview of recently developed microarray and sequencing technologies that enable systematic and genome-wide assessment of the extent of alternative splicing during stem cell differentiation.
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