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Chen Z, Wang G, Wang W, Wang X, Huang Y, Jia J, Gao Q, Xu H, Xu Y, Ma Z, He L, Cheng J, Li C. PDE9A polymorphism and association analysis with growth performance and gastrointestinal weight of Hu sheep. Gene 2024; 900:148137. [PMID: 38184018 DOI: 10.1016/j.gene.2024.148137] [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: 07/20/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Phosphodiesterase 9A (PDE9A) plays a crucial role in activating the cGMP-dependent signaling pathway and may have important effects on the growth and development of the gastrointestinal tract in Hu sheep. In this study, we analyzed the single nucleotide polymorphisms of PDE9A in 988 Hu sheep and their correlation with growth performance, feed efficiency, and gastrointestinal development. Additionally, we examined the expression level of different PDE9A genotypes in the gastrointestinal tract of Hu sheep by using fluorescence quantitative PCR. The results revealed a moderate level of polymorphism (0.25 < PIC < 0.50) at the g.286248617 T > C mutation site located in the first intron of PDE9A in Hu sheep, with three genotypes: CC, CT, and TT. The weights of the omasum, colon, and cecum were significantly greater in the CC genotype than in the TT genotype (P < 0.05), and the expression level of PDE9A in the tissues of the rumen, ileum, cecum, and colon was notably lower in the CC genotype individuals (P < 0.05). These findings suggest that the polymorphism of PDE9A affects the weight of the stomach, colon, and cecum in Hu sheep through expression regulation. Overall, the results of this study suggest that the g.286248617 T > C mutation site in the first intron of PDE9A can serve as a potential molecular marker for breeding practices related to the gastrointestinal weight of Hu sheep.
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Affiliation(s)
- Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Guoxiu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiale Jia
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qihao Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Haoyu Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yunfei Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Zhang X, Di C, Chen Y, Wang J, Su R, Huang G, Xu C, Chen X, Long F, Yang H, Zhang H. Multilevel regulation and molecular mechanism of poly (rC)-binding protein 1 in cancer. FASEB J 2020; 34:15647-15658. [PMID: 33058239 DOI: 10.1096/fj.202000911r] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/02/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023]
Abstract
Poly (rC)-binding protein 1 (PCBP1), an RNA- or DNA-binding protein with a relative molecular weight of 38 kDa, which is characterized by downregulation in many cancer types. Numerous cases have indicated that PCBP1 could be considered as a tumor suppressor to inhibit tumorigenesis, development, and metastasis. In the current review, we described the multilevel regulatory roles of PCBP1, including gene transcription, alternative splicing, and translation of many cancer-related genes. Additionally, we also provided a brief overview about the inhibitory effect of PCBP1 on most common tumors. More importantly, we summarized the current research status about PCBP1 in hypoxic microenvironment, autophagy, apoptosis, and chemotherapy of cancer cells, aiming to clarify the molecular mechanisms of PCBP1 in cancer. Taken together, in-depth study of PCBP1 in cancer may provide new ideas for cancer therapy.
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Affiliation(s)
- Xuetian Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhong Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Ruowei Su
- The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Guomin Huang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Caipeng Xu
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Long
- Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Hongying Yang
- School of Radiation Medicine and Protection, Medical College of Soochow, Soochow, China
| | - Hong Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
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Chatterjee S, Cottrell E, Rose SJ, Mushtaq T, Maharaj AV, Williams J, Savage MO, Metherell LA, Storr HL. GHR gene transcript heterogeneity may explain phenotypic variability in GHR pseudoexon (6Ψ) patients. Endocr Connect 2020; 9:EC-20-0026. [PMID: 32061156 PMCID: PMC7077524 DOI: 10.1530/ec-20-0026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES The homozygous GH receptor (GHR) pseudoexon (6Ψ) mutation leads to growth hormone insensitivity (GHI) with clinical and biochemical heterogeneity. We investigated whether transcript heterogeneity (6Ψ-GHR to WT-GHR transcript ratio) and/or concurrent defects in other short stature (SS) genes contribute to this. METHODS 6Ψ-GHR and WT-GHR mRNA transcripts of 4 6Ψ patient (height SDS -4.2 to -3.1) and 1 control fibroblasts were investigated by RT-PCR. Transcripts were quantified by qRT-PCR and delta delta CT analysis and compared using ANOVA with Bonferroni correction. In eleven 6Ψ patients, 40 genes known to cause GHI/SS were analysed by targeted next generation sequencing. RESULTS RT-PCR confirmed 6Ψ-GHR transcript in the 6Ψ patients but not control. 6Ψ-GHR transcript levels were comparable in patients 1 and 3 but significantly different among all other patients. The mean 6Ψ:WT transcript ratios ranged from 29-71:1 for patients 1-4 and correlated negatively with height SDS (R=-0.85; p<0.001). Eight deleterious variants in 6 genes were detected but the number of gene hits did not correlate with the degree of SS in individual 6Ψ patients. CONCLUSION Variable amounts of 6Ψ- and WT-GHR transcripts were identified in 6Ψ patients but no 6Ψ transcript was present in the control. Higher 6Ψ:WT GHR transcript ratio correlated with SS severity and may explain the phenotypic variability. Analysis of known SS genes suggested that phenotypic variation is independent of the genetic background. This is the first report of transcript heterogeneity producing a spectrum of clinical phenotypes in different individuals harbouring an identical homozygous genetic mutation.
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Affiliation(s)
- Sumana Chatterjee
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Emily Cottrell
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Stephen J Rose
- Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Avinaash V Maharaj
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Jack Williams
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Martin O Savage
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Louise A Metherell
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK
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Lemaire S, Fontrodona N, Aubé F, Claude JB, Polvèche H, Modolo L, Bourgeois CF, Mortreux F, Auboeuf D. Characterizing the interplay between gene nucleotide composition bias and splicing. Genome Biol 2019; 20:259. [PMID: 31783898 PMCID: PMC6883713 DOI: 10.1186/s13059-019-1869-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing. RESULTS By analyzing dozens of RNA-seq datasets, we identify two groups of splicing factors that activate either about 3200 GC-rich exons or about 4000 AT-rich exons. We show that splicing factor-dependent GC-rich exons have predicted RNA secondary structures at 5' ss and are dependent on U1 snRNP-associated proteins. In contrast, splicing factor-dependent AT-rich exons have a large number of decoy branch points, SF1- or U2AF2-binding sites and are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization, with consequences for exon recognition during splicing. Interestingly, the GC content of exons correlates with that of their hosting genes, isochores, and topologically associated domains. CONCLUSIONS We propose that regional nucleotide composition bias over several dozens of kilobase pairs leaves a local footprint at the exon level and induces constraints during splicing that can be alleviated by local chromatin organization at the DNA level and recruitment of specific splicing factors at the RNA level. Therefore, nucleotide composition bias establishes a direct link between genome organization and local regulatory processes, like alternative splicing.
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Affiliation(s)
- Sébastien Lemaire
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Nicolas Fontrodona
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Fabien Aubé
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Jean-Baptiste Claude
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | | | - Laurent Modolo
- LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Franck Mortreux
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
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5
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Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels. Int J Mol Sci 2019; 20:ijms20225573. [PMID: 31717266 PMCID: PMC6888083 DOI: 10.3390/ijms20225573] [Citation(s) in RCA: 453] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/29/2022] Open
Abstract
Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels in a variety of ways. They play important roles in biological processes such as chromatin remodeling, transcriptional activation, transcriptional interference, RNA processing, and mRNA translation. lncRNAs have important functions in plant growth and development; biotic and abiotic stress responses; and in regulation of cell differentiation, the cell cycle, and the occurrence of many diseases in humans and animals. In this review, we summarize the functions and mechanisms of lncRNAs in plants, humans, and animals at different regulatory levels.
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6
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Del Corpo O, Goguen RP, Malard CMG, Daher A, Colby-Germinario S, Scarborough RJ, Gatignol A. A U1i RNA that Enhances HIV-1 RNA Splicing with an Elongated Recognition Domain Is an Optimal Candidate for Combination HIV-1 Gene Therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:815-830. [PMID: 31734561 PMCID: PMC6861678 DOI: 10.1016/j.omtn.2019.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 11/30/2022]
Abstract
U1 interference (U1i) RNAs can be designed to correct splicing defects and target pathogenic RNA, such as HIV-1 RNA. In this study, we show that U1i RNAs that enhance HIV-1 RNA splicing are more effective at inhibiting HIV-1 production compared to top U1i RNAs that inhibit polyadenylation of HIV-1 RNA. A U1i RNA was also identified targeting a site upstream of the first splice acceptor site in the Gag coding region that was effective at inhibiting HIV-1 production. U1-T6, which enhanced HIV-1 RNA splicing, was superior to an antiviral short hairpin RNA (shRNA) currently in clinical trials. To increase specificity, the recognition domain of U1-T6 was elongated by 3–6 nt. The elongated molecules inhibited HIV-1 production from different HIV-1 strains, including one with a mismatch in the target site. These results suggest that lengthening the recognition domain can enhance the specificity of U1i RNAs for their intended target sites while at the same time allowing them to tolerate single mismatch mutations. Overall, our results demonstrate that U1-T6 with an elongated recognition domain inhibits HIV-1 production and has both the efficacy and specificity to be a promising candidate for HIV-1 gene therapy.
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Affiliation(s)
- Olivier Del Corpo
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada
| | - Ryan P Goguen
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Camille M G Malard
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Aïcha Daher
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada
| | | | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
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Nazarov IB, Bakhmet EI, Tomilin AN. KH-Domain Poly(C)-Binding Proteins as Versatile Regulators of Multiple Biological Processes. BIOCHEMISTRY (MOSCOW) 2019; 84:205-219. [PMID: 31221059 DOI: 10.1134/s0006297919030039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Five known members of the family of KH-domain poly(C)-binding proteins (Pcbp1-4, hnRNP-K) have an unusually broad spectrum of cellular functions that include regulation of gene transcription, regulation of pre-mRNA processing, splicing, mRNA stability, translational silencing and enhancement, the control of iron turnover, and many others. Mechanistically, these proteins act via nucleic acid binding and protein-protein interactions. Through performing these multiple tasks, the KH-domain poly(C)-binding family members are involved in a wide variety of biological processes such as embryonic development, cell differentiation, and cancer. Deregulation of KH-domain protein expression is frequently associated with severe developmental defects and neoplasia. This review summarizes progress in studies of the KH-domain proteins made over past two decades. The review also reports our recent finding implying an involvement of the KH-factor Pcbp1 into control of transition from naïve to primed pluripotency cell state.
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Affiliation(s)
- I B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - E I Bakhmet
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - A N Tomilin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
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8
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Storr HL, Chatterjee S, Metherell LA, Foley C, Rosenfeld RG, Backeljauw PF, Dauber A, Savage MO, Hwa V. Nonclassical GH Insensitivity: Characterization of Mild Abnormalities of GH Action. Endocr Rev 2019; 40:476-505. [PMID: 30265312 PMCID: PMC6607971 DOI: 10.1210/er.2018-00146] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/31/2018] [Indexed: 12/12/2022]
Abstract
GH insensitivity (GHI) presents in childhood with growth failure and in its severe form is associated with extreme short stature and dysmorphic and metabolic abnormalities. In recent years, the clinical, biochemical, and genetic characteristics of GHI and other overlapping short stature syndromes have rapidly expanded. This can be attributed to advancing genetic techniques and a greater awareness of this group of disorders. We review this important spectrum of defects, which present with phenotypes at the milder end of the GHI continuum. We discuss their clinical, biochemical, and genetic characteristics. The objective of this review is to clarify the definition, identification, and investigation of this clinically relevant group of growth defects. We also review the therapeutic challenges of mild GHI.
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Affiliation(s)
- Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Sumana Chatterjee
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Louise A Metherell
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Corinne Foley
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Ron G Rosenfeld
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon
| | - Philippe F Backeljauw
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Andrew Dauber
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Martin O Savage
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Vivian Hwa
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
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Grelet S, Howe PH. hnRNP E1 at the crossroads of translational regulation of epithelial-mesenchymal transition. ACTA ACUST UNITED AC 2019; 5. [PMID: 31681852 PMCID: PMC6824538 DOI: 10.20517/2394-4722.2018.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The epithelial-mesenchymal transition (EMT), in which cells undergo a switch from a polarized, epithelial phenotype to a highly motile fibroblastic or mesenchymal phenotype is fundamental during embryonic development and can be reactivated in a variety of diseases including cancer. Spatio-temporally-regulated mechanisms are constantly orchestrated to allow cells to adapt to their constantly changing environments when disseminating to distant organs. Although numerous transcriptional regulatory factors are currently well-characterized, the post-transcriptional control of EMT requires continued investigation. The hnRNP E1 protein displays a major role in the control of tumor cell plasticity by regulating the translatome through multiple non-redundant mechanisms, and this role is exemplified when E1 is absent. hnRNP E1 binding to RNA molecules leads to direct or indirect translational regulation of specific sets of proteins: (1) hnRNP E1 binding to specific targets has a direct role in translation by preventing elongation of translation; (2) hnRNP E1-dependent alternative splicing can prevent the generation of a competing long non-coding RNA that acts as a decoy for microRNAs (miRNAs) involved in translational inhibition of EMT master regulators; (3) hnRNP E1 binding to the 3’ untranslated region of transcripts can also positively regulate the stability of certain mRNAs to improve their translation. Globally, hnRNP E1 appears to control proteome reprogramming during cell plasticity, either by direct or indirect regulation of protein translation.
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Affiliation(s)
- Simon Grelet
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA.,Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Philip H Howe
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA.,Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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10
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Guo J, Jia R. Splicing factor poly(rC)-binding protein 1 is a novel and distinctive tumor suppressor. J Cell Physiol 2018; 234:33-41. [PMID: 30132844 DOI: 10.1002/jcp.26873] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 12/20/2022]
Abstract
A lot of evidence has been found on the link between tumorigenesis and the aberrant expression of splicing factors. A number of splicing factors have been reported to be either oncogenic or overexpressed in cancer cells. However, splicing factors can also play negative roles in tumorigenesis. In the current review, we focus on splicing factor poly(rC)-binding protein 1 (PCBP1), a novel tumor suppressor that is characterized by downregulation in many cancer types and shows inhibition of tumor formation and metastasis. Notably, the messenger RNA levels of PCBP1 are not significantly decreased in most cancer types. In fact, PCBP1 protein is often degraded or shows a loss-of-function through phosphorylation in cancer cells. PCBP1 is highly homologous to its family member, PCBP2. Interestingly, PCBP2 appears to be an oncogenic splicing factor. A growing body of evidence has shown that PCBP1 regulates alternative splicing, translation, and RNA stability of many cancer-related genes. Taking together, PCBP1 has distinctive tumor suppressive functions, and increasing PCBP1 expression may represent a new approach for cancer treatment.
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Affiliation(s)
- Jihua Guo
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rong Jia
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
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11
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Shi H, Li H, Yuan R, Guan W, Zhang X, Zhang S, Zhang W, Tong F, Li L, Song Z, Wang C, Yang S, Wang H. PCBP1 depletion promotes tumorigenesis through attenuation of p27 Kip1 mRNA stability and translation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:187. [PMID: 30086790 PMCID: PMC6081911 DOI: 10.1186/s13046-018-0840-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022]
Abstract
Background Poly C Binding Protein 1 (PCBP1) is an RNA-binding protein that binds and regulates translational activity of subsets of cellular mRNAs. Depletion of PCBP1 is implicated in various carcinomas, but the underlying mechanism in tumorigenesis remains elusive. Methods We performed a transcriptome-wide screen to identify novel bounding mRNA of PCBP1. The bind regions between PCBP1 with target mRNA were investigated by using point mutation and luciferase assay. Cell proliferation, cell cycle, tumorigenesis and cell apoptosis were also evaluated in ovary and colon cancer cell lines. The mechanism that PCBP1 affects p27 was analyzed by mRNA stability and ribosome profiling assays. We analyzed PCBP1 and p27 expression in ovary, colon and renal tumor samples and adjacent non-tumor tissues using RT-PCR, Western Blotting and immunohistochemistry. The prognostic significance of PCBP1 and p27 also analyzed using online databases. Results We identified cell cycle inhibitor p27Kip1 (p27) as a novel PCBP1-bound transcript. We then demonstrated that binding of PCBP1 to p27 3’UTR via its KH1 domain mainly stabilizes p27 mRNA, while enhances its translation to fuel p27 expression, prior to p27 protein degradation. The upregulated p27 consequently inhibits cell proliferation, cell cycle progression and tumorigenesis, whereas promotes cell apoptosis under paclitaxel treatment. Conversely, knockdown of PCBP1 in turn compromises p27 mRNA stability, leading to lower p27 level and tumorigenesis in vivo. Moreover, forced depletion of p27 counteracts the tumor suppressive ability of PCBP1 in the same PCBP1 over-expressing cells. Physiologically, we showed that decreases of both p27 mRNA and its protein expressions are well correlated to PCBP1 depletion in ovary, colon and renal tumor samples, independent of the p27 ubiquitin ligase Skp2 level. Correlation of PCBP1 with p27 is also found in the tamoxifen, doxorubincin and lapatinib resistant breast cancer cells of GEO database. Conclusion Our results thereby indicate that loss of PCBP1 expression firstly attenuates p27 expression at post-transcriptional level, and subsequently promotes carcinogenesis. PCBP1 could be used as a diagnostic marker to cancer patients. Electronic supplementary material The online version of this article (10.1186/s13046-018-0840-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongshun Shi
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Hui Li
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Ronghua Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, China
| | - Wen Guan
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Xiaomei Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Shaoyang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Wenliang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Fang Tong
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Li Li
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Zhihong Song
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Changwei Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shulan Yang
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China. .,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.
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12
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Kiweler N, Krämer OH. PNUTS at the crossroads of tumorigenesis and metastasis formation. J Thorac Dis 2018; 10:560-563. [PMID: 29607112 DOI: 10.21037/jtd.2017.12.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nicole Kiweler
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
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13
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Howley BV, Howe PH. TGF-beta signaling in cancer: post-transcriptional regulation of EMT via hnRNP E1. Cytokine 2018; 118:19-26. [PMID: 29396052 DOI: 10.1016/j.cyto.2017.12.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
Abstract
The TGFβ signaling pathway is a critical regulator of cancer progression in part through induction of the epithelial to mesenchymal transition (EMT). This process is aberrantly activated in cancer cells, facilitating invasion of the basement membrane, survival in the circulatory system, and dissemination to distant organs. The mechanisms through which epithelial cells transition to a mesenchymal state involve coordinated transcriptional and post-transcriptional control of gene expression. One such mechanism of control is through the RNA binding protein hnRNP E1, which regulates splicing and translation of a cohort of EMT and stemness-associated transcripts. A growing body of evidence indicates a major role for hnRNP E1 in the control of epithelial cell plasticity, especially in the context of carcinoma progression. Here, we review the multiple mechanisms through which hnRNP E1 functions to control EMT and metastatic progression.
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Affiliation(s)
- Breege V Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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14
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Grelet S, Link LA, Howley B, Obellianne C, Palanisamy V, Gangaraju VK, Diehl JA, Howe PH. A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression. Nat Cell Biol 2017; 19:1105-1115. [PMID: 28825698 PMCID: PMC5578890 DOI: 10.1038/ncb3595] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/19/2017] [Indexed: 12/12/2022]
Abstract
The contribution of lncRNAs to tumour progression and the regulatory mechanisms driving their expression are areas of intense investigation. Here, we characterize the binding of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) to a nucleic acid structural element located in exon 12 of PNUTS (also known as PPP1R10) pre-RNA that regulates its alternative splicing. HnRNP E1 release from this structural element, following its silencing, nucleocytoplasmic translocation or in response to TGFβ, allows alternative splicing and generates a non-coding isoform of PNUTS. Functionally the lncRNA-PNUTS serves as a competitive sponge for miR-205 during epithelial-mesenchymal transition (EMT). In mesenchymal breast tumour cells and in breast tumour samples, the expression of lncRNA-PNUTS is elevated and correlates with levels of ZEB mRNAs. Thus, PNUTS is a bifunctional RNA encoding both PNUTS mRNA and lncRNA-PNUTS, each eliciting distinct biological functions. While PNUTS mRNA is ubiquitously expressed, lncRNA-PNUTS appears to be tightly regulated dependent on the status of hnRNP E1 and tumour context.
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Affiliation(s)
- Simon Grelet
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Laura A Link
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Breege Howley
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Clémence Obellianne
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Viswanathan Palanisamy
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Vamsi K Gangaraju
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - J Alan Diehl
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Philip H Howe
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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15
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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16
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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17
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Matos L, Gonçalves V, Pinto E, Laranjeira F, Prata MJ, Jordan P, Desviat LR, Pérez B, Alves S. Functional analysis of splicing mutations in the IDS gene and the use of antisense oligonucleotides to exploit an alternative therapy for MPS II. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2712-21. [PMID: 26407519 DOI: 10.1016/j.bbadis.2015.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/16/2015] [Accepted: 09/21/2015] [Indexed: 12/12/2022]
Abstract
Mucopolysaccharidosis II is a lysosomal storage disorder caused by mutations in the IDS gene, including exonic alterations associated with aberrant splicing. In the present work, cell-based splicing assays were performed to study the effects of two splicing mutations in exon 3 of IDS, i.e., c.241C>T and c.257C>T, whose presence activates a cryptic splice site in exon 3 and one in exon 8, i.e., c.1122C>T that despite being a synonymous mutation is responsible for the creation of a new splice site in exon 8 leading to a transcript shorter than usual. Mutant minigene analysis and overexpression assays revealed that SRSF2 and hnRNP E1 might be involved in the use and repression of the constitutive 3' splice site of exon 3 respectively. For the c.1122C>T the use of antisense therapy to correct the splicing defect was explored, but transfection of patient fibroblasts with antisense morpholino oligonucleotides (n=3) and a locked nucleic acid failed to abolish the abnormal transcript; indeed, it resulted in the appearance of yet another aberrant splicing product. Interestingly, the oligonucleotides transfection in control fibroblasts led to the appearance of the aberrant transcript observed in patients' cells after treatment, which shows that the oligonucleotides are masking an important cis-acting element for 5' splice site regulation of exon 8. These results highlight the importance of functional studies for understanding the pathogenic consequences of mis-splicing and highlight the difficulty in developing antisense therapies involving gene regions under complex splicing regulation.
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Affiliation(s)
- Liliana Matos
- Research and Development Unit, Department of Human Genetics, INSA, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
| | - Vânia Gonçalves
- Research and Development Unit, Department of Human Genetics, INSA, Lisbon, Portugal.
| | - Eugénia Pinto
- Biochemical Genetics Unit, Center for Medical Genetics Jacinto Magalhães, Porto Hospital Center, Porto, Portugal.
| | - Francisco Laranjeira
- Biochemical Genetics Unit, Center for Medical Genetics Jacinto Magalhães, Porto Hospital Center, Porto, Portugal.
| | - Maria João Prata
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde/IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
| | - Peter Jordan
- Research and Development Unit, Department of Human Genetics, INSA, Lisbon, Portugal.
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; IDIPaz, Madrid, Spain.
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; IDIPaz, Madrid, Spain.
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, INSA, Porto, Portugal.
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18
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Ren Z, Wang Y, Peng J, Zhang L, Xu W, Liang X, Zhao Q, Lu S. Protein expression of sensory and motor nerves: Two-dimensional gel electrophoresis and mass spectrometry. Neural Regen Res 2015; 7:369-75. [PMID: 25774177 PMCID: PMC4350121 DOI: 10.3969/j.issn.1673-5374.2012.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/05/2012] [Indexed: 01/12/2023] Open
Abstract
The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.
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Affiliation(s)
- Zhiwu Ren
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China ; Medical College of Nankai University, Tianjin 300071, China
| | - Yu Wang
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jiang Peng
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Zhang
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Wenjing Xu
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiangdang Liang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Qing Zhao
- Department of Orthopedics, First Affiliated Hospital of Chinese PLA General Hospital, Beijing 100037, China
| | - Shibi Lu
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
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19
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Role of pseudoexons and pseudointrons in human cancer. Int J Cell Biol 2013; 2013:810572. [PMID: 24204383 PMCID: PMC3800588 DOI: 10.1155/2013/810572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/09/2013] [Indexed: 11/18/2022] Open
Abstract
In all eukaryotic organisms, pre-mRNA splicing and alternative splicing processes play an essential role in regulating the flow of information required to drive complex developmental and metabolic pathways. As a result, eukaryotic cells have developed a very efficient macromolecular machinery, called the spliceosome, to correctly recognize the pre-mRNA sequences that need to be inserted in a mature mRNA (exons) from those that should be removed (introns). In healthy individuals, alternative and constitutive splicing processes function with a high degree of precision and fidelity in order to ensure the correct working of this machinery. In recent years, however, medical research has shown that alterations at the splicing level play an increasingly important role in many human hereditary diseases, neurodegenerative processes, and especially in cancer origin and progression. In this minireview, we will focus on several genes whose association with cancer has been well established in previous studies, such as ATM, BRCA1/A2, and NF1. In particular, our objective will be to provide an overview of the known mechanisms underlying activation/repression of pseudoexons and pseudointrons; the possible utilization of these events as biomarkers of tumor staging/grading; and finally, the treatment options for reversing pathologic splicing events.
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20
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Hörnberg H, Holt C. RNA-binding proteins and translational regulation in axons and growth cones. Front Neurosci 2013; 7:81. [PMID: 23734093 PMCID: PMC3661996 DOI: 10.3389/fnins.2013.00081] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/06/2013] [Indexed: 01/11/2023] Open
Abstract
RNA localization and regulation play an important role in the developing and adult nervous system. In navigating axons, extrinsic cues can elicit rapid local protein synthesis that mediates directional or morphological responses. The mRNA repertoire in axons is large and dynamically changing, yet studies suggest that only a subset of these mRNAs are translated after cue stimulation, suggesting the need for a high level of translational regulation. Here, we review the role of RNA-binding proteins (RBPs) as local regulators of translation in developing axons. We focus on their role in growth, guidance, and synapse formation, and discuss the mechanisms by which they regulate translation in axons.
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Affiliation(s)
- Hanna Hörnberg
- Department of Physiology Development and Neuroscience, University of Cambridge Cambridge, UK
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21
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Lian WX, Yin RH, Kong XZ, Zhang T, Huang XH, Zheng WW, Yang Y, Zhan YQ, Xu WX, Yu M, Ge CH, Guo JT, Li CY, Yang XM. THAP11, a novel binding protein of PCBP1, negatively regulates CD44 alternative splicing and cell invasion in a human hepatoma cell line. FEBS Lett 2012; 586:1431-8. [PMID: 22673507 DOI: 10.1016/j.febslet.2012.04.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/22/2012] [Accepted: 04/07/2012] [Indexed: 10/28/2022]
Abstract
THAP11 is an essential factor involved in ES cell pluripotency and cell growth. Here, we identified THAP11 as a novel physiological binding partner of PCBP1. In HepG2 cells, THAP11 overexpression inhibited CD44 v6 expression and cell invasion. However, when deleting the binding domain with PCBP1 or endogenous PCBP1 was knocked down, THAP11 failed to inhibit CD44 v6 expression, indicating that THAP11 regulates CD44 v6 expression through interacting with PCBP1. In HCC patients, the expression of THAP11 mRNA significantly correlated with PCBP1 mRNA expression. Our results suggest a novel role of THAP11 in CD44 alternative splicing and hepatoma invasion.
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Abstract
The predominate form of DNA diagnostics remains nucleic acid sequencing in the research and clinical setting. While DNA sequencing allows a mutation to be correctly identified, only RNA sequencing can confirm the effect of that mutation on the resulting mRNA transcript. In the absence of RNA sequencing, predictions are reliant on either experimental studies or bioinformatic modelling. While each of these approaches provides insights into cellular splicing choices, of which exon skipping is but one, both possess inherent weaknesses. A method which is able to integrate and appropriately weigh the various factors influencing cellular splicing choices into an accurate, comprehensive modelling tool still remains elusive.In this overview chapter, the current methods utilised for DNA diagnostics and the impact of the emerging next-generation sequencing techniques are considered. We explore why RNA remains a problematic medium with which to work. To understand how exon skipping can be predicted from a DNA sequence, the key cis-acting elements influencing splicing are reviewed. Finally, the current methods used to predict exon skipping including RNA-based studies, experimental studies, and bioinformatic modelling approaches are outlined.
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23
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Savage MO, Hwa V, David A, Rosenfeld RG, Metherell LA. Genetic Defects in the Growth Hormone-IGF-I Axis Causing Growth Hormone Insensitivity and Impaired Linear Growth. Front Endocrinol (Lausanne) 2011; 2:95. [PMID: 22654835 PMCID: PMC3356141 DOI: 10.3389/fendo.2011.00095] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 11/21/2011] [Indexed: 11/13/2022] Open
Abstract
Human genetic defects in the growth hormone (GH)-IGF-I axis affecting the IGF system present with growth failure as their principal clinical feature. This is usually associated with GH insensitivity (GHI) presenting in childhood as severe or mild short stature. Dysmorphic features and metabolic abnormalities may also be present. The field of GHI due to mutations affecting GH action has evolved rapidly since the first description of the extreme phenotype related to homozygous GH receptor (GHR) mutations in 1966. A continuum of genetic, phenotypic, and biochemical abnormalities can be defined associated with clinically relevant defects in linear growth. The mechanisms of the GH-IGF-I axis in the regulation of normal human growth is discussed followed by descriptions of mutations in GHR, STAT5B, IGF-I, IGFALS, IGF1R, and GH1 defects causing bio-inactive GH or anti-GH antibodies. These GH-IGF-I axis defects are associated with a range of clinical, and hormonal characteristics. An up-dated approach to the clinical assessment of the patient with GHI focusing on investigation of the GH-IGF-I axis and relevant molecular studies contributing to the identification of causative genetic defects is also discussed.
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Affiliation(s)
- Martin O. Savage
- Department of Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryLondon, UK
| | - Vivian Hwa
- Department of Pediatrics, Oregon Health and Science UniversityPortland, OR, USA
| | - Alessia David
- Department of Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryLondon, UK
| | - Ron G. Rosenfeld
- Department of Pediatrics, Oregon Health and Science UniversityPortland, OR, USA
| | - Louise A. Metherell
- Department of Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryLondon, UK
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24
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David A, Hwa V, Metherell LA, Netchine I, Camacho-Hübner C, Clark AJL, Rosenfeld RG, Savage MO. Evidence for a continuum of genetic, phenotypic, and biochemical abnormalities in children with growth hormone insensitivity. Endocr Rev 2011; 32:472-97. [PMID: 21525302 DOI: 10.1210/er.2010-0023] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
GH insensitivity (GHI) presents in childhood as growth failure and in its severe form is associated with dysmorphic and metabolic abnormalities. GHI may be caused by genetic defects in the GH-IGF-I axis or by acquired states such as chronic illness. This article discusses the former category. The field of GHI due to mutations affecting GH action has evolved considerably since the original description of the extreme phenotype related to homozygous GH receptor (GHR) mutations over 40 yr ago. A continuum of genetic, phenotypic, and biochemical abnormalities can be defined associated with clinically relevant defects in linear growth. The role and mechanisms of the GH-IGF-I axis in normal human growth is discussed, followed by descriptions of mutations in GHR, STAT5B, PTPN11, IGF1, IGFALS, IGF1R, and GH1 defects causing bioinactive GH or anti-GH antibodies. These defects are associated with a range of genetic, clinical, and hormonal characteristics. Genetic abnormalities causing growth failure that is less severe than the extreme phenotype are emphasized, together with an analysis of height and serum IGF-I across the spectrum of different types of GHR defects. An overall view of genotype and phenotype relationships is presented, together with an updated approach to the assessment of the patient with GHI, focusing on investigation of the GH-IGF-I axis and relevant molecular studies contributing to this diagnosis.
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Affiliation(s)
- Alessia David
- Department of Endocrinology, Barts and the London School of Medicine and Dentistry, London, United Kingdom
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25
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Chaudhury A, Chander P, Howe PH. Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles. RNA (NEW YORK, N.Y.) 2010; 16:1449-62. [PMID: 20584894 PMCID: PMC2905745 DOI: 10.1261/rna.2254110] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins. The complexity and diversity associated with the hnRNPs render them multifunctional, involved not only in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs, but also acting as trans-factors in regulating gene expression. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1), a subgroup of hnRNPs, is a KH-triple repeat containing RNA-binding protein. It is encoded by an intronless gene arising from hnRNP E2 through a retrotransposition event. hnRNP E1 is ubiquitously expressed and functions in regulating major steps of gene expression, including pre-mRNA processing, mRNA stability, and translation. Given its wide-ranging functions in the nucleus and cytoplasm and interaction with multiple proteins, we propose a post-transcriptional regulon model that explains hnRNP E1's widespread functional diversity.
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Affiliation(s)
- Arindam Chaudhury
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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26
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Homolova K, Zavadakova P, Doktor TK, Schroeder LD, Kozich V, Andresen BS. The deep intronic c.903+469T>C mutation in the MTRR gene creates an SF2/ASF binding exonic splicing enhancer, which leads to pseudoexon activation and causes the cblE type of homocystinuria. Hum Mutat 2010; 31:437-44. [PMID: 20120036 PMCID: PMC3429857 DOI: 10.1002/humu.21206] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Deep intronic mutations are often ignored as possible causes of human diseases. A deep intronic mutation in the MTRR gene, c.903+469T>C, is the most frequent mutation causing the cblE type of homocystinuria. It is well known to be associated with pre-mRNA mis-splicing, resulting in pseudoexon inclusion; however, the pathological mechanism remains unknown. We used minigenes to demonstrate that this mutation is the direct cause of MTRR pseudoexon inclusion, and that the pseudoexon is normally not recognized due to a suboptimal 5' splice site. Within the pseudoexon we identified an exonic splicing enhancer (ESE), which is activated by the mutation. Cotransfection and siRNA experiments showed that pseudoexon inclusion depends on the cellular amounts of SF2/ASF and in vitro RNA-binding assays showed dramatically increased SF2/ASF binding to the mutant MTRR ESE. The mutant MTRR ESE sequence is identical to an ESE of the alternatively spliced MST1R proto-oncogene, which suggests that this ESE could be frequently involved in splicing regulation. Our study conclusively demonstrates that an intronic single nucleotide change is sufficient to cause pseudoexon activation via creation of a functional ESE, which binds a specific splicing factor. We suggest that this mechanism may cause genetic disease much more frequently than previously reported.
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Affiliation(s)
- Katerina Homolova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague 2, Czech Republic
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Huo LR, Ju W, Yan M, Zou JH, Yan W, He B, Zhao XL, Jenkins EC, Brown WT, Zhong N. Identification of differentially expressed transcripts and translatants targeted by knock-down of endogenous PCBP1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1954-64. [PMID: 20624489 DOI: 10.1016/j.bbapap.2010.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 06/29/2010] [Accepted: 07/01/2010] [Indexed: 11/30/2022]
Abstract
PCBP1 is a member of the hnRNP family and participates in the regulation of transcription and translation. Previously, we identified transcripts targeted by overexpression of exogenous PCBP1. To further determine if these altered transcripts may also be targeted by a lack of PCBP1, we depleted endogenous PCBP1 in human SH-SY5Y cells. We identified 941 transcripts with the Affymetrix and 1362 with the Agilent expression platforms. There were 375 transcripts identified by both platforms, including 328 down-regulated and 47 up-regulated. The identified transcripts could be grouped into neuronal, cell signaling, metabolic, developmental, and differentiation categories, with pathway involvement in Wnt signaling, TGF beta signaling, translation factors and nuclear receptors. A proteomic profiling study with a two-dimensional chromatographic platform showed global translational changes over a range of isoelectric points (pI)=4.84-8.42. This study identifies the transcripts affected by knock-down of endogenous PCBP1 and compares them to the transcripts affected by overexpression of PCBP1.
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Affiliation(s)
- Li-Rong Huo
- Peking University Center of Medical Genetics, Beijing 100083, China
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David A, Srirangalingam U, Metherell LA, Khoo B, Clark AJL. Repair of aberrant splicing in growth hormone receptor by antisense oligonucleotides targeting the splice sites of a pseudoexon. J Clin Endocrinol Metab 2010; 95:3542-6. [PMID: 20427506 DOI: 10.1210/jc.2009-1968] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT The GH receptor (GHR) pseudoexon 6Psi defect is a frequent cause of GH insensitivity (GHI) resulting from a non-functioning GH receptor (GHR). It results in a broad range of phenotypes and may also be present in patients diagnosed as idiopathic short stature. OBJECTIVE Our objective was to correct aberrant GHR splicing and inclusion of 6Psi using exon-skipping antisense oligonucleotides (ASOs). DESIGN AND SETTING Three ASOs binding the 5' (ASO-5), 3' (ASO-3), and branch site (ASO-Br) of 6Psi were tested in an in vitro splicing assay and a cell transfection system. The wild-type (wt) and mutant (mt) DNA minigenes (wt- and mtL1-GHR6Psi-L2, respectively) were created by inserting the GHR 6Psi in a well-characterized splice reporter (Adml-par). For the in vitro splicing assay, the wt- and mtL1-GHR6Psi-L2 were transcribed into pre-mRNA in the presence of [alpha(32)P]GTP and incubated with ASOs in HeLa nuclear extracts. For the cell transfection studies, wt- and mtL1-GHR6Psi-L2 cloned into pcDNA 3.1 were transfected with ASOs into HEK293 cells. After 48 h, RNA was extracted and radiolabeled RT-PCR products quantified. RESULTS ASO-3 induced an almost complete pseudoexon skipping in vitro and in HEK293 cells. This effect was dose dependent and maximal at 125-250 nm. ASO-5 produced modest pseudoexon skipping, whereas ASO-Br had no effect. Targeting of two splice elements simultaneously was less effective than targeting one. ASO-Br was tested on the wtL1-GHR6Psi-L2 and did not act as an enhancer of 6Psi inclusion. CONCLUSIONS The exon-skipping ASO approach was effective in correcting aberrant GHR splicing and may be a promising therapeutic tool.
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Affiliation(s)
- Alessia David
- Centre for Endocrinology, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK.
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Proteomic analysis of ACTN4-interacting proteins reveals it’s a putative involvement in mRNA metabolism. Biochem Biophys Res Commun 2010; 397:192-6. [DOI: 10.1016/j.bbrc.2010.05.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 05/13/2010] [Indexed: 11/21/2022]
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The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO J 2010; 29:749-60. [PMID: 20094034 DOI: 10.1038/emboj.2009.397] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 12/08/2009] [Indexed: 12/30/2022] Open
Abstract
Abundance of pseudo splice sites in introns can potentially give rise to innumerable pseudoexons, outnumbering the real ones. Nonetheless, these are efficiently ignored by the splicing machinery, a process yet to be understood completely. Although numerous 5' splice site-like sequences functioning as splicing silencers have been found to be enriched in predicted human pseudoexons, the lack of active pseudoexons pose a fundamental challenge to how these U1snRNP-binding sites function in splicing inhibition. Here, we address this issue by focusing on a previously described pathological ATM pseudoexon whose inhibition is mediated by U1snRNP binding at intronic splicing processing element (ISPE), composed of a consensus donor splice site. Spliceosomal complex assembly demonstrates inefficient A complex formation when ISPE is intact, implying U1snRNP-mediated unproductive U2snRNP recruitment. Furthermore, interaction of SF2/ASF with its motif seems to be dependent on RNA structure and U1snRNP interaction. Our results suggest a complex combinatorial interplay of RNA structure and trans-acting factors in determining the splicing outcome and contribute to understanding the intronic splicing code for the ATM pseudoexon.
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Dhir A, Buratti E. Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 2010; 277:841-55. [PMID: 20082636 DOI: 10.1111/j.1742-4658.2009.07520.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What makes a nucleotide sequence an exon (or an intron) is a question that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full of sequences that look like perfect exons, but which are nonetheless ignored by the splicing machinery (hence the name 'pseudoexons'). The existence of these pseudoexons has been known since the earliest days of splicing research, but until recently the tendency has been to view them as an interesting, but rather rare, curiosity. In recent years, however, the importance of pseudoexons in regulating splicing processes has been steadily revalued. Even more importantly, clinically oriented screening studies that search for splicing mutations are beginning to uncover a situation where aberrant pseudoexon inclusion as a cause of human disease is more frequent than previously thought. Here we aim to provide a review of the mechanisms that lead to pseudoexon activation in human genes and how the various cis- and trans-acting cellular factors regulate their inclusion. Moreover, we list the potential therapeutic approaches that are being tested with the aim of inhibiting their inclusion in the final mRNA molecules.
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Affiliation(s)
- Ashish Dhir
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Raponi M, Buratti E, Dassie E, Upadhyaya M, Baralle D. Low U1 snRNP dependence at the NF1 exon 29 donor splice site. FEBS J 2009; 276:2060-73. [PMID: 19292874 DOI: 10.1111/j.1742-4658.2009.06941.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many disease-causing splicing mutations described in the literature produce changes in splice sites (SS) or in exon-regulatory sequences. The delineation of these splice aberrations can provide important insights into novel regulation mechanisms. In this study, we evaluated the effect of patient variations in neurofibromatosis type 1 (NF1) exon 29 and its 5'SS surrounding area on its splicing process. Only two of all nonsense, missense, synonymous and intronic variations analyzed in this study clearly altered exon 29 inclusion/exclusion levels. In particular, the intronic mutation +5g>a had the strongest effect, resulting in total exon exclusion. This finding prompted us to evaluate the exon 29 5'SS in relation to its ability to bind U1 snRNP. This was performed by direct analysis of the ability of U1 to bind to wild-type and mutant donor sites, by engineering an in vitro splicing system to directly evaluate the functional importance of U1 snRNA base pairing with the exon 29 donor site, and by coexpression of mutant U1 snRNP molecules to try to rescue exon 29 inclusion in vivo. The results revealed a low dependency on the presence of U1 snRNP, and suggest that exon 29 donor site definition may depend on alternative mechanisms of 5'SS recognition.
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Raponi M, Buratti E, Llorian M, Stuani C, Smith CWJ, Baralle D. Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. FEBS J 2008; 275:6101-8. [PMID: 19016857 DOI: 10.1111/j.1742-4658.2008.06734.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In disease-associated genes, understanding the functional significance of deep intronic nucleotide variants represents a difficult challenge. We previously reported that an NF1 intron 30 exonization event is triggered from a single correct nomenclature is 'c.293-279 A>G' mutation [Raponi M, Upadhyaya M & Baralle D (2006) Hum Mutat 27, 294-295]. In this paper, we investigate which characteristics play a role in regulating inclusion of the aberrant pseudoexon. Our investigation shows that pseudoexon inclusion levels are strongly downregulated by polypyrimidine tract binding protein and its homologue neuronal polypyrimidine tract binding protein. In particular, we provide evidence that the functional effect of polypyrimidine tract binding protein is proportional to its concentration, and map the cis-acting elements that are principally responsible for this negative regulation. These results highlight the importance of evaluating local sequence context for diagnostic purposes, and the utility of developing therapies to turn off activated pseudoexons.
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