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Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G. When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications. Genes (Basel) 2024; 15:245. [PMID: 38397234 PMCID: PMC10888458 DOI: 10.3390/genes15020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain.
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Affiliation(s)
- Xinyue Liu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Junyuan Zheng
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jialan Ding
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jiaxin Wu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
| | - Gongwei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
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Haddad-Mashadrizeh A, Mirahmadi M, Taghavizadeh Yazdi ME, Gholampour-Faroji N, Bahrami A, Zomorodipour A, Moghadam Matin M, Qayoomian M, Saebnia N. Introns and Their Therapeutic Applications in Biomedical Researches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3316. [PMID: 38269198 PMCID: PMC10804063 DOI: 10.30498/ijb.2023.334488.3316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/23/2023] [Indexed: 01/26/2024]
Abstract
Context Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms. Evidence Acquisition In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included. Results & Conclusions The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Mirahmadi
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Nazanin Gholampour-Faroji
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmadreza Bahrami
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Maryam Moghadam Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Qayoomian
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Saebnia
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Chen X, Liu X, Li QH, Lu BF, Xie BM, Ji YM, Zhao Y. A patient-derived organoid-based study identified an ASO targeting SNORD14E for endometrial cancer through reducing aberrant FOXM1 Expression and β-catenin nuclear accumulation. J Exp Clin Cancer Res 2023; 42:230. [PMID: 37667311 PMCID: PMC10478245 DOI: 10.1186/s13046-023-02801-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Most of the endometrial cancer (EC) patients are diagnosis in early stage with a good prognosis while the patients with locally advanced recurrent or metastatic result in a poor prognosis. Adjuvant therapy could benefit the prognosis of patients with high-risk factors. Unfortunately, the molecular classification of great prognostic value has not yet reached an agreement and need to be further refined. The present study aims to identify new targets that have prognostic value in EC based on the method of EC patient-derived organ-like organs (PDOs), and further investigate their efficacy and mechanism. METHODS The Cancer Genome Atlas (TCGA) database was used to determine SNORD14E expression. The effects of SNORD14E were investigated using CCK8, Transwell, wound-healing assays, and a xenograft model experiment; apoptosis was measured by flow cytometry. Antisense oligonucleotide (ASO) targeting SNORD14E was designed and patient-derived organoids (PDO) models in EC patients was established. A xenograft mouse and PDO model were employed to evaluate the effects of ASO targeting SNORD14E. RNA-seq, Nm-seq, and RNA immunoprecipitation (RIP) experiments were employed to confirm the alternative splicing (AS) and modification induced by SNORD14E. A minigene reporter gene assay was conducted to confirm AS and splicing factors on a variable exon. Actinomycin-d (Act-D) and Reverse Transcription at Low deoxy-ribonucleoside triphosphate concentrations followed by PCR (RTL-P) were utilized to confirm the effects of 2'-O methylation modification on FOXM1. RESULTS We found that SNORD14E was overexpressed in EC tissues and patients with high expressed SNORD14E were distributed in the TCGA biomolecular classification subgroups without difference. Further, SNORD14E could reduce disease-free survival (DFS) and recurrence free survival (RFS) of EC patients. SNORD14E promoted proliferation, migration, and invasion and inhibited the apoptosis of EC cells in vitro. ASOs targeting SNORD14E inhibited cell proliferation, migration, invasion while promoted cell apoptosis. ASOs targeting SNORD14E inhibited tumor growth in the xenograft mouse model. TCGA-UCEC database showed that the proportion of patients with high expression of SNORD14E in middle-high risk and high-risk patients recommended by EMSO-ESGO-ESTRO guidelines for adjuvant therapy is more than 50%. Next, we enrolled 8 cases of high-risk and high-risk EC patients according to EMSO-ESGO-ESTRO guidelines and successfully constructed EC-PDOs. ASOs targeting SNORD14E inhibited the EC-PDO growth. Mechanistically, SNORD14E could recognize the mRNA of FOXM1 and recruit SRSF1 to promote the shearing of the variable exon VIIa of FOXM1, resulting in the overexpression of the FOXM1 malignant subtypes FOXM1b and FOXM1c. In addition, SNORD14E modified FOXM1 mRNA with 2`-O-methylation, which prolonged the half-life of FOXM1 mRNA. The nucleus accumulation of β-catenin caused by aberrant FOXM1 expression led to EC progression. CONCLUSIONS ASO targeting SNORD14E can be an effective treatment for EC.
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Affiliation(s)
- Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bing-Feng Lu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bu-Min Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yu-Meng Ji
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China.
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Brand CM, Colbran LL, Capra JA. Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nat Ecol Evol 2023; 7:939-953. [PMID: 37142741 DOI: 10.1038/s41559-023-02053-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.
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Affiliation(s)
- Colin M Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John A Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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Zhang L, Liu Y, Wei G, Lei T, Wu J, Zheng L, Ma H, He G, Wang N. POLLEN WALL ABORTION 1 is essential for pollen wall development in rice. PLANT PHYSIOLOGY 2022; 190:2229-2245. [PMID: 36111856 PMCID: PMC9706457 DOI: 10.1093/plphys/kiac435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The integrity of pollen wall structures is essential for pollen development and maturity in rice (Oryza sativa L.). In this study, we isolated and characterized the rice male-sterile mutant pollen wall abortion 1 (pwa1), which exhibits a defective pollen wall (DPW) structure and has sterile pollen. Map-based cloning, genetic complementation, and gene knockout experiments revealed that PWA1 corresponds to the gene LOC_Os01g55094 encoding a coiled-coil domain-containing protein. PWA1 localized to the nucleus, and PWA1 was expressed in the tapetum and microspores. PWA1 interacted with the transcription factor TAPETUM DEGENERATION RETARDATION (TDR)-INTERACTING PROTEIN2 (TIP2, also named bHLH142) in vivo and in vitro. The tip2-1 mutant, which we obtained by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated gene editing, showed delayed tapetum degradation, sterile pollen, and DPWs. We determined that TIP2/bHLH142 regulates PWA1 expression by binding to its promoter. Analysis of the phenotype of the tip2-1 pwa1 double mutant indicated that TIP2/bHLH142 functions upstream of PWA1. Further studies suggested that PWA1 has transcriptional activation activity and participates in pollen intine development through the β-glucosidase Os12BGlu38. Therefore, we identified a sterility factor, PWA1, and uncovered a regulatory network underlying the formation of the pollen wall and mature pollen in rice.
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Affiliation(s)
- Lisha Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yang Liu
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Gang Wei
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ting Lei
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jingwen Wu
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lintao Zheng
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Honglei Ma
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Nan Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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Chen S, Mo Y, Zhang Y, Zhu H, Ling Y. Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing. PLANTA 2022; 256:72. [PMID: 36083517 DOI: 10.1007/s00425-022-03965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.
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Affiliation(s)
- Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Hongbao Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
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Liu L, Wu D, Gu Y, Liu F, Liu B, Mao F, Yi X, Tang T, Zhao X. Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:44. [PMID: 37313517 PMCID: PMC10248609 DOI: 10.1007/s11032-022-01314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level, which increases the transcriptomic diversity. Oilseed rape (Brassica napus L.), one of the main oil crops worldwide, is prone to secondary dormancy. However, how alternative splicing landscape of oilseed rape seed changes in response to secondary dormancy is unknown. Here, we analyzed twelve RNA-seq libraries from varieties "Huaiyou-SSD-V1" and "Huaiyou-WSD-H2" which exhibited high (> 95%) and low (< 5%) secondary dormancy potential, respectively, and demonstrated that alternative splicing changes led to a significant increase with the diversity of the transcripts in response to secondary dormancy induction via polyethylene glycol 6000 (PEG6000) treatment. Among the four basic alternative splicing types, intron retention dominates, and exon skipping shows the rarest frequency. A total of 8% of expressed genes had two or more transcripts after PEG treatment. Further analysis revealed that global isoform expression percentage variations in alternative splicing in differently expressed genes (DEGs) is more than three times as much as those in non-DEGs, suggesting alternative splicing change is associated with the transcriptional activity change in response to secondary dormancy induction. Eventually, 342 differently spliced genes (DSGs) associated with secondary dormancy were identified, five of which were validated by RT-PCR. The number of the overlapped genes between DSGs and DEGs associated with secondary dormancy was much less than that of either DSGs or DEGs, suggesting that DSGs and DEGs may independently regulates secondary dormancy. Functional annotation analysis of DSGs revealed that spliceosome components are overrepresented among the DSGs, including small nuclear ribonucleoprotein particles (snRNPs), serine/arginine-rich (SR) proteins, and other splicing factors. Thus, it is proposed that the spliceosome components could be exploited to reduce secondary dormancy potential in oilseed rape. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01314-8.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei 066600 China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
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Micheli G, Camilloni G. Can Introns Stabilize Gene Duplication? BIOLOGY 2022; 11:941. [PMID: 35741463 PMCID: PMC9220161 DOI: 10.3390/biology11060941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Gene duplication is considered one of the most important events that determine the evolution of genomes. However, the neo-duplication condition of a given gene is particularly unstable due to recombination events. Several mechanisms have been proposed to justify this step. In this "opinion article" we propose a role for intron sequences in stabilizing gene duplication by limiting and reducing the identity of the gene sequence between the two duplicated copies. A review of the topic and a detailed hypothesis are presented.
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Affiliation(s)
- Gioacchino Micheli
- Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro 5, 00185 Roma, Italy;
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Università Sapienza, P.le A. Moro 5, 00185 Roma, Italy
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Ruiz-Gabarre D, Carnero-Espejo A, Ávila J, García-Escudero V. What's in a Gene? The Outstanding Diversity of MAPT. Cells 2022; 11:840. [PMID: 35269461 PMCID: PMC8909800 DOI: 10.3390/cells11050840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
Tau protein is a microtubule-associated protein encoded by the MAPT gene that carries out a myriad of physiological functions and has been linked to certain pathologies collectively termed tauopathies, including Alzheimer's disease, frontotemporal dementia, Huntington's disease, progressive supranuclear palsy, etc. Alternative splicing is a physiological process by which cells generate several transcripts from one single gene and may in turn give rise to different proteins from the same gene. MAPT transcripts have been proven to be subjected to alternative splicing, generating six main isoforms in the central nervous system. Research throughout the years has demonstrated that the splicing landscape of the MAPT gene is far more complex than that, including at least exon skipping events, the use of 3' and 5' alternative splice sites and, as has been recently discovered, also intron retention. In addition, MAPT alternative splicing has been showed to be regulated spatially and developmentally, further evidencing the complexity of the gene's splicing regulation. It is unclear what would drive the need for the existence of so many isoforms encoded by the same gene, but a wide range of functions have been ascribed to these Tau isoforms, both in physiology and pathology. In this review we offer a comprehensive up-to-date exploration of the mechanisms leading to the outstanding diversity of isoforms expressed from the MAPT gene and the functions in which such isoforms are involved, including their potential role in the onset and development of tauopathies such as Alzheimer's disease.
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Affiliation(s)
- Daniel Ruiz-Gabarre
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Almudena Carnero-Espejo
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Jesús Ávila
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Vega García-Escudero
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
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11
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Liang J, Hong Z, Sun B, Guo Z, Wang C, Zhu J. The Alternatively Spliced Isoforms of Key Molecules in the cGAS-STING Signaling Pathway. Front Immunol 2021; 12:771744. [PMID: 34868032 PMCID: PMC8636596 DOI: 10.3389/fimmu.2021.771744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Alternative splicing of pre-mRNA increases transcriptome and proteome diversity by generating distinct isoforms that encode functionally diverse proteins, thus affecting many biological processes, including innate immunity. cGAS-STING signaling pathway, whose key molecules also undergo alternative splicing, plays a crucial role in regulating innate immunity. Protein isoforms of key components in the cGAS-STING-TBK1-IRF3 axis have been detected in a variety of species. A chain of evidence showed that these protein isoforms exhibit distinct functions compared to their normal counterparts. The mentioned isoforms act as positive or negative modulators in interferon response via distinct mechanisms. Particularly, we highlight that alternative splicing serves a vital function for the host to avoid the overactivation of the cGAS-STING signaling pathway and that viruses can utilize alternative splicing to resist antiviral response by the host. These findings could provide insights for potential alternative splicing-targeting therapeutic applications.
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Affiliation(s)
- Jiaqian Liang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Ze Hong
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Boyue Sun
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Zhaoxi Guo
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Chen Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Juanjuan Zhu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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12
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Allison T, Langerman J, Sabri S, Otero-Garcia M, Lund A, Huang J, Wei X, Samarasinghe RA, Polioudakis D, Mody I, Cobos I, Novitch BG, Geschwind DH, Plath K, Lowry WE. Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysis. Stem Cell Reports 2021; 16:2548-2564. [PMID: 34506726 PMCID: PMC8514853 DOI: 10.1016/j.stemcr.2021.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/19/2023] Open
Abstract
The specification of inhibitory neurons has been described for the mouse and human brain, and many studies have shown that pluripotent stem cells (PSCs) can be used to create interneurons in vitro. It is unclear whether in vitro methods to produce human interneurons generate all the subtypes found in brain, and how similar in vitro and in vivo interneurons are. We applied single-nuclei and single-cell transcriptomics to model interneuron development from human cortex and interneurons derived from PSCs. We provide a direct comparison of various in vitro interneuron derivation methods to determine the homogeneity achieved. We find that PSC-derived interneurons capture stages of development prior to mid-gestation, and represent a minority of potential subtypes found in brain. Comparison with those found in fetal or adult brain highlighted decreased expression of synapse-related genes. These analyses highlight the potential to tailor the method of generation to drive formation of particular subtypes.
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Affiliation(s)
- Thomas Allison
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Bioinformatics PhD Program, UCLA, Los Angeles, CA, USA
| | - Marcos Otero-Garcia
- Center for Autism Research and Treatment, Semel Institute, UCLA, Los Angeles, CA, USA
| | - Andrew Lund
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - John Huang
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xiaofei Wei
- Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA
| | - Ranmal A. Samarasinghe
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Department of Neurobiology, UCLA, Los Angeles, CA, USA,Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Istvan Mody
- Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA
| | - Inma Cobos
- Department of Pathology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Bennett G. Novitch
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Department of Neurobiology, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Daniel H. Geschwind
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Center for Autism Research and Treatment, Semel Institute, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Kathrin Plath
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Molecular Biology Institute, UCLA, Los Angeles, CA, USA,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Bioinformatics PhD Program, UCLA, Los Angeles, CA, USA,Corresponding author
| | - William E. Lowry
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, CA, USA,Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Molecular Biology Institute, UCLA, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA,Corresponding author
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13
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Liu S, Striebel J, Pasquini G, Ng AHM, Khoshakhlagh P, Church GM, Busskamp V. Neuronal Cell-type Engineering by Transcriptional Activation. Front Genome Ed 2021; 3:715697. [PMID: 34713262 PMCID: PMC8525383 DOI: 10.3389/fgeed.2021.715697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022] Open
Abstract
Gene activation with the CRISPR-Cas system has great implications in studying gene function, controlling cellular behavior, and modulating disease progression. In this review, we survey recent studies on targeted gene activation and multiplexed screening for inducing neuronal differentiation using CRISPR-Cas transcriptional activation (CRISPRa) and open reading frame (ORF) expression. Critical technical parameters of CRISPRa and ORF-based strategies for neuronal programming are presented and discussed. In addition, recent progress on in vivo applications of CRISPRa to the nervous system are highlighted. Overall, CRISPRa represents a valuable addition to the experimental toolbox for neuronal cell-type programming.
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Affiliation(s)
- Songlei Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Johannes Striebel
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Giovanni Pasquini
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - George M. Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
- GC Therapeutics, Inc, Cambridge, MA, United States
| | - Volker Busskamp
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
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14
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Huang R, Zheng Z, Liu S, Yan P, Song D, Yin H, Hu P, Zhu X, Chang Z, Liu Y, Zhuang J, Meng T, Huang Z, Zhang J. Identification of prognostic and bone metastasis-related alternative splicing signatures in mesothelioma. Cancer Med 2021; 10:4478-4492. [PMID: 34041868 PMCID: PMC8267146 DOI: 10.1002/cam4.3977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/18/2023] Open
Abstract
Mesothelioma (MESO) is an infrequent tumor derived from mesothelial cells of pleura, peritoneum, pericardium, and tunica vaginalis testis. Despite advancement in technologies and better understanding of tumor progression mechanism, the prognosis of MESO remains poor. The role of alternative splicing events (ASEs) in the oncogenesis, tumor metastasis and drug resistance has been widely discussed in multiple cancers. But the prognosis and potential therapeutic value of ASEs in MESO were not clearly studied by now. We constructed a prognostic model using RNA sequencing data and matched ASE data of MESO patients obtained from the TCGA and TCGASpliceSeq database. A total of 3,993 ASEs were identified associated with overall survival using Cox regression analysis. Eight of them were finally figured out to institute the model by lasso regression analysis. The risk score of the model can predict the prognosis independently. Among the identified 390 splicing factors (SF), HSPA1A and DDX3Y was significantly associated with 43 OS-SEs. Among these OS-SEs, SNX5-58744-AT (p = 0.048) and SNX5-58745-AT (p = 0.048) were significantly associated with bone metastasis. Co-expression analysis of signal pathways and SNX5-58744-AT, SNX5-58745-AT was also depicted using GSVA. Finally, we proposed that splicing factor (SF) HSPA1A could regulate SNX5-58744-AT (R = -0.414) and SNX5-58745-AT (R = 0.414) through the pathway "Class I MHC mediated antigen processing and presentation" (R = 0.400). In this way, tumorigenesis and bone metastasis of MESO were controlled.
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Affiliation(s)
- Runzhi Huang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Zixuan Zheng
- Tongji University School of Medicine, Shanghai, China
| | - Sijia Liu
- Tongji University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dianwen Song
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Huabin Yin
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yihan Liu
- Tongji University School of Medicine, Shanghai, China
| | - Juanwei Zhuang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Meng
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
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15
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Yu H, Du Q, Campbell M, Yu B, Walia H, Zhang C. Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice. THE NEW PHYTOLOGIST 2021; 230:1273-1287. [PMID: 33453070 PMCID: PMC8048671 DOI: 10.1111/nph.17189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VaSP). VaSP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions. In total, 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na+ accumulation, which identified six GSS events in five genes significantly associated with the shoot Na+ content. Two of these genes, OsNUC1 and OsRAD23 emerged as top candidate genes with splice variants that exhibited significant divergence between the variants for shoot growth under salt stress conditions. VaSP is a versatile tool for alternative splicing analysis in plants and a powerful tool for prioritising candidate causal pre-mRNA splicing and corresponding genomic variations in GWAS.
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Affiliation(s)
- Huihui Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Qian Du
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Malachy Campbell
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Department of Plant BiologyCornell UniversityIthacaNY14850USA
| | - Bin Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Chi Zhang
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
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16
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Dong S, Lu LJ. An alternative splicing signature model for predicting hepatocellular carcinoma-specific survival. J Gastrointest Oncol 2020; 11:1054-1064. [PMID: 33209497 PMCID: PMC7657838 DOI: 10.21037/jgo-20-377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a transcriptional regulation mechanism, which can expand the coding ability of genome and contribute to the occurrence and development of cancer. A systematic analysis of AS in hepatocellular carcinoma (HCC) is lacking and urgently needed. METHODS Univariate and multivariate Cox regression analyses were used to distinguish survival-related AS events and to calculate the risk score. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves were used to evaluate the AS events' clinical significance to build a risk model in HCC. RESULTS Data of AS events was obtained from the Splice-Seq database. The corresponding clinical information of HCC was downloaded from The Cancer Genome Atlas (TCGA) data portal. We analyzed 78,878 AS events from 13,045 genes in HCC patients. A total of 2,440 and 2,888 AS events were significantly related to HCC patients' disease-free survival (DFS) and overall survival (OS). The two prognostic models (DFS and OS) were constructed based on a total of seven AS types from survival-related AS events above. The area under the curve (AUC) of the ROC curves was 0.769 in the DFS cohort and 0.886 in the OS cohort. CONCLUSIONS The prognostic model constructed by AS events can be used to predict the prognosis of HCC patients and provide potential therapeutic targets for further validation.
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Affiliation(s)
- Sheng Dong
- Department of Surgery, Wuxi No.9 People's Hospital affiliated to Soochow University, Wuxi, China
| | - Li-Jun Lu
- Department of Surgery, Wuxi No.9 People's Hospital affiliated to Soochow University, Wuxi, China
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17
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Li X, Chen W, Zhangsun D, Luo S. Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus. Mar Drugs 2020; 18:md18090464. [PMID: 32937857 PMCID: PMC7551347 DOI: 10.3390/md18090464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/02/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
The venom of various Conus species is composed of a rich variety of unique bioactive peptides, commonly referred to as conotoxins (conopeptides). Most conopeptides have specific receptors or ion channels as physiologically relevant targets. In this paper, high-throughput transcriptome sequencing was performed to analyze putative conotoxin transcripts from the venom duct of a vermivorous cone snail species, Conus litteratus native to the South China Sea. A total of 128 putative conotoxins were identified, most of them belonging to 22 known superfamilies, with 43 conotoxins being regarded as belonging to new superfamilies. Notably, the M superfamily was the most abundant in conotoxins among the known superfamilies. A total of 15 known cysteine frameworks were also described. The largest proportion of cysteine frameworks were VI/VII (C-C-CC-C-C), IX (C-C-C-C-C-C) and XIV (C-C-C-C). In addition, five novel cysteine patterns were also discovered. Simple sequence repeat detection results showed that di-nucleotide was the major type of repetition, and the codon usage bias results indicated that the codon usage bias of the conotoxin genes was weak, but the M, O1, O2 superfamilies differed in codon preference. Gene cloning indicated that there was no intron in conotoxins of the B1- or J superfamily, one intron with 1273-1339 bp existed in a mature region of the F superfamily, which is different from the previously reported gene structure of conotoxins from other superfamilies. This study will enhance our understanding of conotoxin diversity, and the new conotoxins discovered in this paper will provide more potential candidates for the development of pharmacological probes and marine peptide drugs.
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18
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Sun Y, Zhang Q, Liu B, Lin K, Zhang Z, Pang E. CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. BMC PLANT BIOLOGY 2020; 20:119. [PMID: 32183712 PMCID: PMC7079458 DOI: 10.1186/s12870-020-2312-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation. DESCRIPTION To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene. CONCLUSION We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.
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Affiliation(s)
- Ying Sun
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Bing Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
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19
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A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing. Int J Mol Sci 2020; 21:ijms21062018. [PMID: 32188023 PMCID: PMC7139555 DOI: 10.3390/ijms21062018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 12/11/2022] Open
Abstract
Pollen development plays crucial roles in the life cycle of higher plants. Here we characterized a rice mutant with complete male-sterile phenotype, pollen-less 1 (pl1). pl1 exhibited smaller anthers with arrested pollen development, absent Ubisch bodies, necrosis-like tapetal hypertrophy, and smooth anther cuticular surface. Molecular mapping revealed a synonymous mutation in the fourth exon of PL1 co-segregated with the mutant phenotype. This mutation disrupts the exon-intron splice junction in PL1, generating aberrant mRNA species and truncated proteins. PL1 is highly expressed in the tapetal cells of developing anther, and its protein is co-localized with plasma membrane (PM) and endoplasmic reticulum (ER) signal. PL1 encodes an integrin-α FG-GAP repeat-containing protein, which has seven β-sheets and putative Ca2+-binding motifs and is broadly conserved in terrestrial plants. Our findings therefore provide insights into both the role of integrin-α FG-GAP repeat-containing protein in rice male fertility and the influence of exonic mutation on intronic splice donor site selection.
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20
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Wang L, Zhu R, Wang J, Yu S, Wang J, Zhang Y. Nrf2 Activation Enhances Muscular MCT1 Expression and Hypoxic Exercise Capacity. Med Sci Sports Exerc 2020; 52:1719-1728. [PMID: 32079911 DOI: 10.1249/mss.0000000000002312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Skeletal muscle is the major producing and metabolizing site of lactic acid. A family of monocarboxylate transporter (MCT) proteins, especially MCT1 and MCT4, are involved in the lactate-pyruvate exchange and metabolism. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a pivotal coordinator of antioxidant response and energy metabolism, and has been reported to associate with the physiological functions of the skeletal muscle. METHODS In this study, C57BL/6 J mice were administrated with an Nrf2 activator, sulforaphane (SFN) before taking incremental treadmill exercise to exhaustion under hypoxia; then the effects of SFN on exercise endurance and molecular/biochemical makers of the skeletal muscle were evaluated. RESULTS The results indicated that SFN pretreatment enhanced the exercise endurance under hypoxia. SFN not only increased the expressions of antioxidant genes and activity of antioxidant enzymes, but also significantly increased the mRNA and protein levels of MCT1 and CD147, but not MCT4. Moreover, the expressions of LDH-B and LDH activity of converting lactate into pyruvate, as well as citrate synthase activity were significantly higher, whereas the LDH activity of converting pyruvate into lactate and blood lactate level were remarkably lower in the SFN-exercise mice than those of the phosphate-buffered saline-exercise group. Furthermore, Atf3Δzip2 (the alternatively spliced isoform of activating transcription factor-3) mRNA was increased by the exercise and further potentiated by SFN. CONCLUSION These results show, for the first time, that SFN increases MCT1 expression in the skeletal muscle under acute hypoxic exercise and suggest that Nrf2 activation is a promising strategy to enhance exercise performance under hypoxia.
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Affiliation(s)
- Linjia Wang
- School of Sport Science, Beijing Sport University, Beijing, CHINA
| | - Rongxin Zhu
- Shanghai Research Institute of Sports Science, Shanghai, CHINA
| | - Jiahui Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, CHINA
| | - Siwang Yu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, CHINA
| | - Jianxiong Wang
- Faculty of Health, Engineering, and Sciences, University of Southern Queensland, Toowoomba, Queensland, AUSTRALIA
| | - Ying Zhang
- School of Sport Science, Beijing Sport University, Beijing, CHINA
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21
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Huang B, Li WX, Wang ZX, Liang Y, Huang WS, Nie P. Identification of a novel splice variant isoform of interferon regulatory factor 10, IRF10, in orange spotted grouper Epinephelus coioides. FISH & SHELLFISH IMMUNOLOGY 2020; 97:637-647. [PMID: 31866452 DOI: 10.1016/j.fsi.2019.12.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Interferon regulatory factors (IRFs) are a family of transcription factors essential to the control of antiviral immune response, cell growth, differentiation and apoptosis. IRF10 was originally found in chicken, which was induced by the v-Rel oncoprotein in lymphoid cell lines and involved in the upregulation of major histocompatibility complex (MHC) class I and guanylate-binding protein. In fish, IRF10 plays negative roles in regulation of the interferon (IFN) response. Here, we identified a splice variant of IRF10, named as EcIRF10-SF in orange spotted grouper, which shares the first three exons with the long form (EcIRF10-LF) and retains part of intron 3, creating a premature termination codon. Furthermore, we observed that the EcIRF10-SF exhibits similar expression pattern compared to its native counterparts. Functional studies demonstrate that the two EcIRF10 isoforms repress DrIFNϕ1 and DrIFNϕ3 promoter activity and negatively regulate fish antiviral gene expression. Subcellular localization analysis shows that the amino acids from 57 to 86 within DBD are required for IRF10 nuclear import. Overall, our description of transcript diversification of IRF10 in the grouper provides a coherent framework to further dissect its roles in immune response.
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Affiliation(s)
- B Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China
| | - W X Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Z X Wang
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Y Liang
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - W S Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China.
| | - P Nie
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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22
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An Intricate Connection between Alternative Splicing and Phenotypic Plasticity in Development and Cancer. Cells 2019; 9:cells9010034. [PMID: 31877720 PMCID: PMC7016785 DOI: 10.3390/cells9010034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
During tumor progression, hypoxia, nutrient deprivation or changes in the extracellular environment (i.e., induced by anti-cancer drugs) elicit adaptive responses in cancer cells. Cellular plasticity increases the chance that tumor cells may survive in a challenging microenvironment, acquire new mechanisms of resistance to conventional drugs, and spread to distant sites. Re-activation of stem pathways appears as a significant cause of cellular plasticity because it promotes the acquisition of stem-like properties through a profound phenotypic reprogramming of cancer cells. In addition, it is a major contributor to tumor heterogeneity, depending on the coexistence of phenotypically distinct subpopulations in the same tumor bulk. Several cellular mechanisms may drive this fundamental change, in particular, high-throughput sequencing technologies revealed a key role for alternative splicing (AS). Effectively, AS is one of the most important pre-mRNA processes that increases the diversity of transcriptome and proteome in a tissue- and development-dependent manner. Moreover, defective AS has been associated with several human diseases. However, its role in cancer cell plasticity and tumor heterogeneity remains unclear. Therefore, unravelling the intricate relationship between AS and the maintenance of a stem-like phenotype may explain molecular mechanisms underlying cancer cell plasticity and improve cancer diagnosis and treatment.
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23
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Parenteau J, Abou Elela S. Introns: Good Day Junk Is Bad Day Treasure. Trends Genet 2019; 35:923-934. [PMID: 31668856 DOI: 10.1016/j.tig.2019.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023]
Abstract
Introns are ubiquitous in eukaryotic transcripts. They are often viewed as junk RNA but the huge energetic burden of transcribing, removing, and degrading them suggests a significant evolutionary advantage. Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. However, recent studies have revealed an entirely new class of trans-acting functions where the presence of intronic RNA in the cell impacts the expression of other genes in trans. Here, we review possible new mechanisms of intron functions, with a focus on the role of yeast introns in regulating the cell growth response to starvation.
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Affiliation(s)
- Julie Parenteau
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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24
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Gust KA, Kennedy AJ, Laird JG, Wilbanks MS, Barker ND, Guan X, Melby NL, Burgoon LD, Kjelland ME, Swannack TM. Different as night and day: Behavioural and life history responses to varied photoperiods in Daphnia magna. Mol Ecol 2019; 28:4422-4438. [PMID: 31486145 PMCID: PMC6856852 DOI: 10.1111/mec.15230] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/08/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023]
Abstract
Nearly all animal species have utilized photoperiod to cue seasonal behaviours and life history traits. We investigated photoperiod responses in keystone species, Daphnia magna, to identify molecular processes underlying ecologically important behaviours and traits using functional transcriptomic analyses. Daphnia magna were photoperiod‐entrained immediately posthatch to a standard control photoperiod of 16 light/ 8 dark hours (16L:8D) relative to shorter (4L:20D, 8L:16D, 12L:12L) and longer (20L:4D) day length photoperiods. Short‐day photoperiods induced significantly increased light‐avoidance behaviours relative to controls. Correspondingly, significant differential transcript expression for genes involved in glutamate signalling was observed, a critical signalling pathway in arthropod light‐avoidance behaviour. Additionally, period circadian protein and proteins coding F‐box/LRR‐repeat domains were differentially expressed which are recognized to establish circadian rhythms in arthropods. Indicators of metabolic rate increased in short‐day photoperiods which corresponded with broadscale changes in transcriptional expression across system‐level energy metabolism pathways. The most striking observations included significantly decreased neonate production at the shortest day length photoperiod (4L:20D) and significantly increased male production across short‐day and equinox photoperiods (4L:20D, 8L:16D and 12L:12D). Transcriptional expression consistent with putative mechanisms of male production was observed including photoperiod‐dependent expression of transformer‐2 sex‐determining protein and small nuclear ribonucleoprotein particles (snRNPs) which control splice variant expression for genes like transformer. Finally, increased transcriptional expression of glutamate has also been shown to induce male production in Daphnia pulex via photoperiod‐sensitive mechanisms. Overall, photoperiod entrainment affected molecular pathways that underpin critical behavioural and life history traits in D. magna providing fundamental insights into biological responses to this primary environmental cue.
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Affiliation(s)
- Kurt A Gust
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Alan J Kennedy
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Jennifer G Laird
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Mitchell S Wilbanks
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | | | - Xin Guan
- Bennett Aerospace, Cary, NC, USA
| | - Nicolas L Melby
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Lyle D Burgoon
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Michael E Kjelland
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
| | - Todd M Swannack
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, MS, USA
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25
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Ye X, Tang X, Wang X, Che J, Wu M, Liang J, Ye L, Qian Q, Li J, You Z, Zhang Y, Wang S, Zhong B. Improving Silkworm Genome Annotation Using a Proteogenomics Approach. J Proteome Res 2019; 18:3009-3019. [PMID: 31250652 DOI: 10.1021/acs.jproteome.8b00965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.
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Affiliation(s)
- Xiaogang Ye
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Xiaoli Tang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Xiaoxiao Wang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jiaqian Che
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Meiyu Wu
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jianshe Liang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Lupeng Ye
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Qiujie Qian
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jianying Li
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Zhengying You
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Yuyu Zhang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Shaohua Wang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Boxiong Zhong
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
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26
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Nakamura SI, Wongkaew A, Nakai Y, Rai H, Ohkama-Ohtsu N. Foliar-applied glutathione activates zinc transport from roots to shoots in oilseed rape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:424-434. [PMID: 31128714 DOI: 10.1016/j.plantsci.2018.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/24/2018] [Accepted: 10/21/2018] [Indexed: 05/28/2023]
Abstract
Glutathione is a tripeptide involved in diverse aspects of plant metabolism. We investigated how the reduced form of glutathione, GSH, applied site-specifically to plants, affects zinc (Zn) distribution and behavior in oilseed rape plants (Brassica napus) cultured hydroponically. Foliar-applied GSH significantly increased the Zn content in shoots and the root-to-shoot Zn translocation ratio; furthermore, this treatment raised the Zn concentration in the cytosol of root cells and substantially enhanced Zn xylem loading. Notably, microarray analysis revealed that the gene encoding pectin methylesterase was upregulated in roots following foliar GSH treatment. We conclude that certain physiological signals triggered in response to foliar-applied GSH were transported via sieve tubes and functioned in root cells, which, in turn, increased Zn availability in roots by releasing Zn from their cell wall. Consequently, root-to-shoot translocation of Zn was activated and Zn accumulation in the shoot was markedly increased.
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Affiliation(s)
- Shin-Ichi Nakamura
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-ku, Tokyo, 156-8502, Japan; Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan.
| | - Arunee Wongkaew
- United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, 2-1-1 Yanagawa, Aomori-shi, Aomori, 038-0012, Japan
| | - Hiroki Rai
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita-shi, Akita, 010-0195, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
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27
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Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
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28
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Zhang L, Vielle A, Espinosa S, Zhao R. RNAs in the spliceosome: Insight from cryoEM structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1523. [PMID: 30729694 DOI: 10.1002/wrna.1523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 12/28/2022]
Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Anne Vielle
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
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29
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Spatzle4 gene of silkworm, Bombyx mori: identification, immune response, and the effect of RNA interference on the antimicrobial peptides' expression in the integument. Saudi J Biol Sci 2018; 25:1817-1825. [PMID: 30591806 PMCID: PMC6303178 DOI: 10.1016/j.sjbs.2018.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/07/2018] [Accepted: 07/08/2018] [Indexed: 11/22/2022] Open
Abstract
Insects, including silkworms, can protect themselves from exotic invasions by innate immune responses. In the immune response of Drosophila, the activation of Toll receptors is strictly dependent on the product of Spatzle. In this study, we cloned the 1567 bp BmSpz4 cDNA which contained a complete 1386 bp open reading frame, encoding 461 amino acids, out of which the forgoing 19 residues were signal peptide. The result of the cDNA sequencing showed that we found a longer transcript than the one included in large scale full-Length cDNA sequencing data by Yoshitaka Suetsugu et al. in 2013. Several spliced variants of BmSpz4 have been found, based on our preliminary results. It was shown by the RT-PCR that BmSpz4 was expressed highest in the head, lower in the integument and testis. The expression of BmSpz4 in the integument of silkworm was upregulated by formalin-inactivated Gram-positive bacteria and fungi but not by Gram-negative bacteria, when compared to the control group of PBS injection. This phenomenon was the same as the one found in the Toll signaling pathway of Drosophila. In addition, the result of double-stranded RNA interference of BmSpz4 also demonstrated that it had a corresponding interference effect on the expression of the integument antimicrobial peptides induced by bacillus and yeast. Thus, it may be concluded that BmSpz4 plays an important role in the innate immunity against microbe infection in the integument of silkworm, Bombyx mori.
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30
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Yu S, Wang G, Liao J, Tang M. Five alternative splicing variants of the TYR gene and their different roles in melanogenesis in the Muchuan black-boned chicken. Br Poult Sci 2018; 60:8-14. [PMID: 30293452 DOI: 10.1080/00071668.2018.1533633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
1. The TYR gene encodes tyrosinase, a multifunctional enzyme that is essential for melanin biosynthesis in melanocytes. This experiment involved the cloning and characterisation of the TYR gene in chicken. Five alternative splice variants were identified in the black feather bulb and designated as TYR-AS1, TYR-AS2, TYR-AS3, TYR-AS4 and TYR-AS5. 2. Among the 11 chicken tissues examined, the feather bulb, comb and skin showed higher levels of all TYR variants. All TYR variants were expressed at significantly different levels in black and white feather bulbs (P < 0.05) and may be involved in melanin formation in plumage. Only TYR-AS1, which plays an important role in muscle melanogenesis, was significantly differentially expressed between black and white muscle (P < 0.01). All TYR variants were expressed at significantly different levels in black and white skin (P < 0.01). 3. The mRNA expression levels of the 5 variants were closely associated with skin melanogenesis in the chicken. These findings provide new clues to the molecular mechanism of melanin formation in the Muchuan black-boned chicken.
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Affiliation(s)
- S Yu
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - G Wang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - J Liao
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
| | - M Tang
- a Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialisation in Southern Sichuan, College of Life Science , Leshan Normal University , Leshan , China
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31
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Monedero Cobeta I, Stadler CB, Li J, Yu P, Thor S, Benito-Sipos J. Specification of Drosophila neuropeptidergic neurons by the splicing component brr2. PLoS Genet 2018; 14:e1007496. [PMID: 30133436 PMCID: PMC6122834 DOI: 10.1371/journal.pgen.1007496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/04/2018] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
During embryonic development, a number of genetic cues act to generate neuronal diversity. While intrinsic transcriptional cascades are well-known to control neuronal sub-type cell fate, the target cells can also provide critical input to specific neuronal cell fates. Such signals, denoted retrograde signals, are known to provide critical survival cues for neurons, but have also been found to trigger terminal differentiation of neurons. One salient example of such target-derived instructive signals pertains to the specification of the Drosophila FMRFamide neuropeptide neurons, the Tv4 neurons of the ventral nerve cord. Tv4 neurons receive a BMP signal from their target cells, which acts as the final trigger to activate the FMRFa gene. A recent FMRFa-eGFP genetic screen identified several genes involved in Tv4 specification, two of which encode components of the U5 subunit of the spliceosome: brr2 (l(3)72Ab) and Prp8. In this study, we focus on the role of RNA processing during target-derived signaling. We found that brr2 and Prp8 play crucial roles in controlling the expression of the FMRFa neuropeptide specifically in six neurons of the VNC (Tv4 neurons). Detailed analysis of brr2 revealed that this control is executed by two independent mechanisms, both of which are required for the activation of the BMP retrograde signaling pathway in Tv4 neurons: (1) Proper axonal pathfinding to the target tissue in order to receive the BMP ligand. (2) Proper RNA splicing of two genes in the BMP pathway: the thickveins (tkv) gene, encoding a BMP receptor subunit, and the Medea gene, encoding a co-Smad. These results reveal involvement of specific RNA processing in diversifying neuronal identity within the central nervous system. The nervous system displays daunting cellular diversity, largely generated through complex regulatory input operating on stem cells and their neural lineages during development. Most of the reported mechanisms acting to generate neural diversity pertain to transcriptional regulation. In contrast, little is known regarding the post-transcriptional mechanisms involved. Here, we use a specific group of neurons, Apterous neurons, in the ventral nerve cord of Drosophila melanogaster as our model, to analyze the function of two essential components of the spliceosome; Brr2 and Prp8. Apterous neurons require a BMP retrograde signal for terminal differentiation, and we find that brr2 and Prp8 play crucial roles during this process. brr2 is critical for two independent events; axon pathfinding and BMP signaling, both of which are required for the activation of the retrograde signaling pathway necessary for Apterous neurons. These results identify a post-transcriptional mechanism as key for specifying neuronal identity, by ensuring the execution of a retrograde signal.
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Affiliation(s)
- Ignacio Monedero Cobeta
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | | | - Jin Li
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Peng Yu
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Jonathan Benito-Sipos
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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32
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Ma L, Shan Y, Ma H, Elshoura I, Nafees M, Yang K, Yin W. Identification of a novel splice variant of the human musashi-1 gene. Oncol Lett 2018; 16:5441-5448. [PMID: 30250616 DOI: 10.3892/ol.2018.9300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/28/2018] [Indexed: 11/06/2022] Open
Abstract
Musashi-1 (Msi1) is an evolutionarily conserved RNA-binding protein that has been reported to be the key regulator in malignancies and with involvement in cancer stemness. In the present study, a novel Msi1 transcript variant generated by alternative splicing was identified and termed Msi1 variant 2. This variant was observed to be ubiquitously expressed in cancerous and non-cancerous cells compared with its wild-type variant, which is preferentially expressed in cancer cells. Notably, the expression levels of Msi1 variant 2 were inversely associated with the protein expression levels of Msi1 in various cancer cells. This naturally truncated variant contains 899 nucleotides and a skipping event of exons 3 and 4, which leads to the emergence of a premature TGA stop codon in exon 5. The present results also demonstrated that hypoxia increased the resistance of H460 cells to cisplatin by suppressing the exon 3 and 4 skipping event of Msi1. In summary, the present study identified a novel splice variant of Msi1 lacking two complete RNA recognition motifs, and revealed the role of exon 3 and 4 skipping of Msi1 pre-mRNA in regulating cisplatin resistance under hypoxia. These observations indicate that targeting Msi1 alternative splicing could represent a valuable strategy to repress Msi1 signaling in tumors overexpressing this RNA-binding protein.
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Affiliation(s)
- Lin Ma
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Yating Shan
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Heliang Ma
- Department of Radiology, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Ihab Elshoura
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Muhammad Nafees
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Kaiyong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Wu Yin
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
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Li Z, Xu Y, Lin Y. Transcriptome analyses reveal genes of alternative splicing associated with muscle development in chickens. Gene 2018; 676:146-155. [PMID: 30010040 DOI: 10.1016/j.gene.2018.07.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/26/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023]
Abstract
Alternative splicing (AS) of pre-mRNA is a central mode of genetic regulation in higher eukaryotes. High-throughput experimental verification of alternative splice forms, functional characterization, and regulation of alternative splicing are key directions for research. However, little information is available on the transcriptome-wide changes during different ages in different chicken breeds. In this study, the sequencing reads of chicken muscle tissues collected from White feather broiler (day 42) and Luning Chicken (day 70, 120, 150) were mapped to the chicken genome. Results showed that a total of 16,958 genes were annotated, with 2230 differentially expressed genes (DEGs) when comparing White feather broiler and Luning Chicken, and an average of 700 DEGs when comparing different ages in Luning Chicken. Functional classification by Gene Ontology (GO) and pathways analysis for selecting the genes showed most DEGs were related to muscle development and immune response. Of the 16,958 genes, a total of 6249 genes (36.85%) underwent AS events, and over 40% were specifically expressed in each library. Additionally, 6 DEGs (SRPK3, ENSGALG00000022884, CCL4, GATM, SESN1, PTTG1IP) involved in muscle development and immunity response were found to be alternatively spliced among all the four muscle tissues. In conclusion, we present a complete dataset involving the spatial and temporal transcriptome of chicken muscle tissue using RNA -seq. These data will facilitate the understanding of the effects of breed and age on the development of muscle and uncover that AS events of candidate genes may have important functional roles in regulation of muscle development in chicken.
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Affiliation(s)
- Zhixiong Li
- College of Life Science and Technology, Southwest Minzu University, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, Sichuan 610041, PR China.
| | - Yaou Xu
- College of Life Science and Technology, Southwest Minzu University, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, Sichuan 610041, PR China
| | - Yaqiu Lin
- College of Life Science and Technology, Southwest Minzu University, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, Sichuan 610041, PR China
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Kannan S, Halter G, Renner T, Waters ER. Patterns of alternative splicing vary between species during heat stress. AOB PLANTS 2018; 10:ply013. [PMID: 29564081 PMCID: PMC5846289 DOI: 10.1093/aobpla/ply013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 02/20/2018] [Indexed: 05/09/2023]
Abstract
Plants have evolved a variety of mechanisms to respond and adapt to abiotic stress. High temperature stress induces the heat shock response. During the heat shock response a large number of genes are up-regulated, many of which code for chaperone proteins that prevent irreversible protein aggregation and cell death. However, it is clear that heat shock is not the only mechanism involved in the plant heat stress response. Alternative splicing (AS) is also important during heat stress since this post-transcriptional regulatory mechanism can produce significant transcriptome and proteome variation. In this study, we examine AS during heat stress in the model species Arabidopsis thaliana and in the highly thermotolerant native California mustard Boechera depauperata. Analyses of AS during heat stress revealed that while a significant number of genes undergo AS and are differentially expressed (DE) during heat stress, some undergo both AS and DE. Analysis of the functional categories of genes undergoing AS indicated that enrichment patterns are different in the two species. Categories enriched in B. depauperata included light response genes and numerous abiotic stress response genes. Categories enriched in A. thaliana, but not in B. depauperata, included RNA processing and nucleotide binding. We conclude that AS and DE are largely independent responses to heat stress. Furthermore, this study reveals significant differences in the AS response to heat stress in the two related mustard species. This indicates AS responses to heat stress are species-specific. Future studies will explore the role of AS of specific genes in organismal thermotolerance.
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Affiliation(s)
- Sumetha Kannan
- Department of Biology, San Diego State University, Campanile Drive, San Diego, CA, USA
| | - Gillian Halter
- Department of Biology, San Diego State University, Campanile Drive, San Diego, CA, USA
| | - Tanya Renner
- Department of Biology, San Diego State University, Campanile Drive, San Diego, CA, USA
- Department of Entomology, Pennsylvania State University, University Park, PA, USA
| | - Elizabeth R Waters
- Department of Biology, San Diego State University, Campanile Drive, San Diego, CA, USA
- Corresponding author’s e-mail address:
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Sun Y, Hou H, Song H, Lin K, Zhang Z, Hu J, Pang E. The comparison of alternative splicing among the multiple tissues in cucumber. BMC PLANT BIOLOGY 2018; 18:5. [PMID: 29301488 PMCID: PMC5755334 DOI: 10.1186/s12870-017-1217-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored. RESULTS To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts. CONCLUSIONS Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.
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Affiliation(s)
- Ying Sun
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Han Hou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101 China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinglu Hu
- Graduate School of Information, Production and Systems, Waseda University, Kitakyushu-shi, 808-0135 Japan
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
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Zhang W, Niu C, Fu RY, Peng ZY. Mycobacterium tuberculosis H37Rv infection regulates alternative splicing in Macrophages. Bioengineered 2018; 9:203-208. [PMID: 29433383 PMCID: PMC5972922 DOI: 10.1080/21655979.2017.1387692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Objective: The objective of this study was to evaluate the expression of genes encoding SR proteinsand alternative splicing of IL4 and TLR4 in Mycobacterium tuberculosis (M. tb) H37Rv-infected macrophages. Materials and methods: THP-1 cells were induced to differentiate into macrophages with 200 nM PMA, and H37Rv strains were used for macrophage infection. After RNA extraction, qRT-PCR was performed to evaluate the expression of many SR proteins as well as the alternative splicing of IL4 and TLR4. Results: IL4 and TLR4 play significant roles in host immunity to tuberculosis. The level of IL-4 splice variants in THP-1 cells increased after M. tb H37Rv infection. Three splice variants of TLR4 were detected in M. tb-infected THP-1 cells, when compared with uninfected controls; the expression level of these splicing variants in M. tb-infected THP-1 cell was down-regulated. Since SR proteins are RNA-binding proteins that regulate RNA splicing, the expression of SR proteins was examined, and SRSF2 and SRSF3 were significantly down-regulated. In addition, splicing factors SRp75 and SF3a were also significantly down-regulated post M. tb infection. Conclusion: Our findings indicate that alternative splicing may be involved in host gene regulation post M. tb infection of macrophage cells.
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Affiliation(s)
- Wei Zhang
- a School of Medicine, Zhejiang University City College , Hangzhou , China
| | - Chen Niu
- b MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University , Shanghai , China
| | - Rui-Yang Fu
- c Department of Rehabilitation , Traditional Chinese Medical Hospital of HuZhou , HuZhou , China
| | - Zheng-Yu Peng
- d Institute of Biomedical Sciences, Fudan University , Shanghai , China
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Zhang Y, O'Leary MN, Peri S, Wang M, Zha J, Melov S, Kappes DJ, Feng Q, Rhodes J, Amieux PS, Morris DR, Kennedy BK, Wiest DL. Ribosomal Proteins Rpl22 and Rpl22l1 Control Morphogenesis by Regulating Pre-mRNA Splicing. Cell Rep 2017; 18:545-556. [PMID: 28076796 DOI: 10.1016/j.celrep.2016.12.034] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/15/2016] [Accepted: 12/12/2016] [Indexed: 01/13/2023] Open
Abstract
Most ribosomal proteins (RP) are regarded as essential, static components that contribute only to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing "extraribosomal," regulatory functions involving binding to select critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog Rpl22-Like1 (Rpl22l1 or Like1) play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally regulated localization to the nucleus, where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-β signaling. During gastrulation, Rpl22 binds to intronic sequences of smad2 pre-mRNA and induces exon 9 skipping in cooperation with hnRNP-A1. This action is opposed by its paralog, Like1, which promotes exon 9 inclusion in the mature transcript. The nuclear roles of these RP in controlling morphogenesis represent a fundamentally different and paradigm-shifting mode of action for RP.
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Affiliation(s)
- Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Suraj Peri
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jikun Zha
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Dietmar J Kappes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Qing Feng
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Paul S Amieux
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - David R Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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Zhang L, Liu X, Liu J, Ma L, Zhou Z, Song Y, Cao B. The developmental transcriptome landscape of receptive endometrium during embryo implantation in dairy goats. Gene 2017; 633:82-95. [PMID: 28866083 DOI: 10.1016/j.gene.2017.08.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/08/2017] [Accepted: 08/28/2017] [Indexed: 01/24/2023]
Abstract
Under natural conditions, some embryos cannot implant successfully because of the dysfunction of receptive endometrium (RE). Thus, it is imperative for us to study the molecular mechanisms involved in the formation of the RE from pre-receptive endometrium (PE). In this study, the endometrium from gestational day 5 (D5, PE) and gestational day 15 (D15, RE) dairy goats were selected to systematically analyze the transcriptome using strand-specific Ribo-Zero RNA-Seq, >120 million high-quality paired-end reads were generated and 47,616 transcripts were identified in the endometrium of dairy goats. A total of 810 mRNAs were differentially expressed genes (DEGs) between the RE and PE meeting the criteria of P-values<0.05. Bioinformatics analysis of the DEGs revealed that a number of biological processes and pathways were potentially involved in the establishment of the RE, notably energy metabolism and amino acid metabolism. Furthermore, we speculated that CXCL14, IGFBP3, and LGALS15 potentially participated in the development of endometrium. What's more, putative SNPs, InDels and AS events were identified and analyzed in the endometrium. In a word, this resulting view of the transcriptome greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during the formation of receptive endometrium in dairy goats.
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Affiliation(s)
- Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - XiaoRui Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - JunZe Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - ZhanQin Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - YuXuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - BinYun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Nishida S, Kakei Y, Shimada Y, Fujiwara T. Genome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:741-753. [PMID: 28586097 DOI: 10.1111/tpj.13606] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 05/04/2023]
Abstract
The alteration of transcript structure contributes to transcriptome plasticity. In this study, we analyzed the genome-wide response of exon combination patterns to deficiencies in 12 different nutrients in Arabidopsis thaliana roots. RNA sequencing analysis and bioinformatics using a simulation survey revealed more than 600 genes showing varying exon combinations. The overlap between genes showing differential expression (DE) and genes showing differential exon combination (DC) was notably low. Additionally, gene ontology analysis showed that gene functions were not shared between the DE and DC genes, suggesting that the genes showing DC had different roles than those showing DE. Most of the DC genes were nutrient specific. For example, two homologs of the MYB transcription factor genes MYB48 and MYB59 showed differential alternative splicing only in response to low levels of potassium. Alternative splicing of those MYB genes modulated DNA-binding motifs, and MYB59 is reportedly involved in the inhibition of root elongation. Therefore, the increased abundance of MYB isoforms with an intact DNA-binding motif under low potassium may be involved in the active inhibition of root elongation. Overall, we provide global and comprehensive data for DC genes affected by nutritional deficiencies, which contribute to elucidating an unknown mechanism involved in adaptation to nutrient deficiency.
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Affiliation(s)
- Sho Nishida
- Faculty of Science and Engineering, Chuo University, Tokyo, Japan
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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40
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Moschall R, Gaik M, Medenbach J. Promiscuity in post-transcriptional control of gene expression: Drosophila sex-lethal and its regulatory partnerships. FEBS Lett 2017; 591:1471-1488. [PMID: 28391641 PMCID: PMC5488161 DOI: 10.1002/1873-3468.12652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
The Drosophila RNA‐binding protein Sex‐lethal (Sxl) is a potent post‐transcriptional regulator of gene expression that controls female development. It regulates the expression of key factors involved in sex‐specific differences in morphology, behavior, and dosage compensation. Functional Sxl protein is only expressed in female flies, where it binds to U‐rich RNA motifs present in its target mRNAs to regulate their fate. Sxl is a very versatile regulator that, by shuttling between the nucleus and the cytoplasm, can regulate almost all aspects of post‐transcriptional gene expression including RNA processing, nuclear export, and translation. For these functions, Sxl employs multiple interactions to either antagonize RNA‐processing factors or to recruit various coregulators, thus allowing it to establish a female‐specific gene expression pattern. Here, we summarize the current knowledge about Sxl function and review recent mechanistic and structural studies that further our understanding of how such a seemingly ‘simple’ RNA‐binding protein can exert this plethora of different functions.
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Affiliation(s)
| | - Monika Gaik
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Germany
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41
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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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WITHDRAWN: Identifying differentially expressed genes in the intestine of healthy and diarrheal Rex Rabbits by RNA-Seq. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Li Y, Yuan Y. Alternative RNA splicing and gastric cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 773:263-273. [PMID: 28927534 DOI: 10.1016/j.mrrev.2016.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/06/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) linked to diseases, especially to tumors. Recently, more and more studies focused on the relationship between AS and gastric cancer (GC). This review surveyed the hot topic from four aspects: First, the common types of AS in cancer, including exon skipping, intron retention, mutually exclusive exon, alternative 5 ' or 3' splice site, alternative first or last exon and alternative 3' untranslated regions. Second, basic mechanisms of AS and its relationship with cancer. RNA splicing in eukaryotes follows the GT-AG rule by both cis-elements and trans-acting factors regulatory. Through RNA splicing, different proteins with different forms and functions can be produced and may be associated with carcinogenesis. Third, AS types of GC-related genes and their splicing variants. In this paper, we listed 10 common genes with AS and illustrated its possible molecular mechanisms owing to genetic variation (mutation and /or polymorphism). Fourth, the splicing variants of GC-associated genes and gastric carcinogenesis, invasion and metastasis. Many studies have found that the different splicing variants of the same gene are differentially expressed in GC and its precancerous diseases, suggesting AS has important implications in GC development. Taking together, this review highlighted the role of AS and splicing variants in the process of GC. We hope that this is not only beneficial to advances in the study field of GC, but also can provide valuable information to other similar tumor research.Although we already know some gene splicing and splicing variants play an important role in the development of GC, but many phenomena and mechanisms are still unknown. For example, how the tumor microenvironment and signal transduction pathway effect the forming and function of AS? Unfortunately, this review did not cover the contents because the current study is limited. It is no doubt that clarifying the phenomena and mechanisms of these unknown may help to reveal the relationship of AS with complex tumor genetic variation and the occurrence and development of tumors.
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Affiliation(s)
- Ying Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.
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Involvement of PARP1 in the regulation of alternative splicing. Cell Discov 2016; 2:15046. [PMID: 27462443 PMCID: PMC4860959 DOI: 10.1038/celldisc.2015.46] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 11/11/2015] [Indexed: 12/18/2022] Open
Abstract
Specialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the nucleosomes at exon/intron boundaries of specific genes, suggestive of a role for this enzyme in alternative splicing. Poly (ADP) ribose polymerase has previously been implicated in the PARylation of splicing factors as well as regulation of the histone modification H3K4me3, a mark critical for co-transcriptional splicing. In light of these studies, we hypothesized that interaction of the chromatin-modifying factor, Poly (ADP) ribose polymerase with nucleosomal structures at exon–intron boundaries, might regulate pre-mRNA splicing. Using genome-wide approaches validated by gene-specific assays, we show that depletion of PARP1 or inhibition of its PARylation activity results in changes in alternative splicing of a specific subset of genes. Furthermore, we observed that PARP1 bound to RNA, splicing factors and chromatin, suggesting that Poly (ADP) ribose polymerase serves as a gene regulatory hub to facilitate co-transcriptional splicing. These studies add another function to the multi-functional protein, Poly (ADP) ribose polymerase, and provide a platform for further investigation of this protein’s function in organizing chromatin during gene regulatory processes.
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Hsu MK, Pan CL, Chen FC. Functional divergence and convergence between the transcript network and gene network in lung adenocarcinoma. Onco Targets Ther 2016; 9:335-47. [PMID: 26834492 PMCID: PMC4716766 DOI: 10.2147/ott.s94897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Alternative RNA splicing is a critical regulatory mechanism during tumorigenesis. However, previous oncological studies mainly focused on the splicing of individual genes. Whether and how transcript isoforms are coordinated to affect cellular functions remain underexplored. Also of great interest is how the splicing regulome cooperates with the transcription regulome to facilitate tumorigenesis. The answers to these questions are of fundamental importance to cancer biology. RESULTS Here, we report a comparative study between the transcript-based network (TN) and the gene-based network (GN) derived from the transcriptomes of paired tumor-normal tissues from 77 lung adenocarcinoma patients. We demonstrate that the two networks differ significantly from each other in terms of patient clustering and the number and functions of network modules. Interestingly, the majority (89.5%) of multi-transcript genes have their transcript isoforms distributed in at least two TN modules, suggesting regulatory and functional divergences between transcript isoforms. Furthermore, TN and GN modules share onlŷ50%-60% of their biological functions. TN thus appears to constitute a regulatory layer separate from GN. Nevertheless, our results indicate that functional convergence and divergence both occur between TN and GN, implying complex interactions between the two regulatory layers. Finally, we report that the expression profiles of module members in both TN and GN shift dramatically yet concordantly during tumorigenesis. The mechanisms underlying this coordinated shifting remain unclear yet are worth further explorations. CONCLUSION We show that in lung adenocarcinoma, transcript isoforms per se are coordinately regulated to conduct biological functions not conveyed by the network of genes. However, the two networks may interact closely with each other by sharing the same or related biological functions. Unraveling the effects and mechanisms of such interactions will significantly advance our understanding of this deadly disease.
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Affiliation(s)
- Min-Kung Hsu
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu, Taiwan
| | - Chia-Lin Pan
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Chi Chen
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu, Taiwan; Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan; School of Dentistry, China Medical University, Taichung, Taiwan
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Identification of novel alternative splicing transcript and expression analysis of bovine TMEM95 gene. Gene 2015; 575:531-536. [PMID: 26385321 DOI: 10.1016/j.gene.2015.09.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/30/2015] [Accepted: 09/14/2015] [Indexed: 01/15/2023]
Abstract
Transmembrane protein 95 (TMEM95) is closely related to male reproductive performance in cattle, but does not affect semen quality. Alternative splicing plays an important role in regulating biological function as well as in generating proteomic and functional diversity in metazoan organisms. Thus, the aim of this study was to clone and identify transcripts of the TMEM95 gene in cattle using RT-PCR, characterize them via bioinformatics analysis, and detect their expression patterns using qRT-PCR. Two transcripts of TMEM95 were identified in cattle, including TMEM95-SV1 and TMEM95-SV2. Bioinformatics predicted that TMEM95-SV1 has a leucine-rich repeat C-terminal domain and a Pfam: IZUMO. These regions are closely related to protein interactions and the acrosome reaction, respectively. Interestingly, the two transcripts were exclusively expressed in the testes and brain in male fetus cattle, and TMEM95-SV1 was expressed in the brain at significantly higher levels than in the testis (P<0.05, 4.06-fold) and TMEM95-SV2 in the brain (P<0.05, 4.95-fold). These findings enrich the understanding of the TMEM95 gene function and benefit for enhancing male reproduction in cattle industry.
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Schmieg N, Thomas C, Yabe A, Lynch DS, Iglesias T, Chakravarty P, Schiavo G. Novel Kidins220/ARMS Splice Isoforms: Potential Specific Regulators of Neuronal and Cardiovascular Development. PLoS One 2015; 10:e0129944. [PMID: 26083449 PMCID: PMC4470590 DOI: 10.1371/journal.pone.0129944] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/14/2015] [Indexed: 01/19/2023] Open
Abstract
Kidins220/ARMS is a transmembrane protein playing a crucial role in neuronal and cardiovascular development. Kidins220/ARMS is a downstream target of neurotrophin receptors and interacts with several signalling and trafficking factors. Through computational modelling, we found two potential sites for alternative splicing of Kidins220/ARMS. The first is located between exon 24 and exon 29, while the second site replaces exon 32 by a short alternative terminal exon 33. Here we describe the conserved occurrence of several Kidins220/ARMS splice isoforms at RNA and protein levels. Kidins220/ARMS splice isoforms display spatio-temporal regulation during development with distinct patterns in different neuronal populations. Neurotrophin receptor stimulation in cortical and hippocampal neurons and neuroendocrine cells induces specific Kidins220/ARMS splice isoforms and alters the appearance kinetics of the full-length transcript. Remarkably, alternative terminal exon splicing generates Kidins220/ARMS variants with distinct cellular localisation: Kidins220/ARMS containing exon 32 is targeted to the plasma membrane and neurite tips, whereas Kidins220/ARMS without exon 33 mainly clusters the full-length protein in a perinuclear intracellular compartment in PC12 cells and primary neurons, leading to a change in neurotrophin receptor expression. Overall, this study demonstrates the existence of novel Kidins220/ARMS splice isoforms with unique properties, revealing additional complexity in the functional regulation of neurotrophin receptors, and potentially other signalling pathways involved in neuronal and cardiovascular development.
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Affiliation(s)
- Nathalie Schmieg
- Molecular Neuropathobiology Laboratory, Sobell Department of Motor Neuroscience & Movement Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
- The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, United Kingdom
| | - Claire Thomas
- The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, United Kingdom
| | - Arisa Yabe
- The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, United Kingdom
| | - David S. Lynch
- Molecular Neuropathobiology Laboratory, Sobell Department of Motor Neuroscience & Movement Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
- Leonard Wolfson Centre for Experimental Neurology, University College London, 8 Queen Anne Street, London W1G 9LD, United Kingdom
| | - Teresa Iglesias
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), C/ Arturo Duperier, 4, Madrid 28029, Spain
- CIBERNED (ISCIII), C/ Valderrebollo 5, Madrid 28031, Spain
| | - Probir Chakravarty
- The Francis Crick Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, United Kingdom
| | - Giampietro Schiavo
- Molecular Neuropathobiology Laboratory, Sobell Department of Motor Neuroscience & Movement Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
- * E-mail:
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Saji N, Kawarai T, Miyamoto R, Sato T, Morino H, Orlacchio A, Oki R, Kimura K, Kaji R. Exome sequencing identifies a novel intronic mutation in ENG that causes recurrence of pulmonary arteriovenous malformations. J Neurol Sci 2015; 352:29-33. [PMID: 25868896 DOI: 10.1016/j.jns.2015.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/16/2015] [Accepted: 02/03/2015] [Indexed: 11/16/2022]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) occasionally can be discovered in patients with cerebrovascular disease. Pulmonary arteriovenous malformation (PAVM) is one of the complications in HHT and occasionally is causative for life-threatening embolic stroke. Several genetic defects have been reported in patients with HHT. The broad spectrum of phenotype and intrafamilial phenotype variations, including age-at-onset of vascular events, often make an early diagnosis difficult. We present here a Japanese family with a novel intronic heterozygous mutation of ENG, which was identified using whole exome sequencing (WES). The intronic mutation, IVS3+4delAGTG, results in in-frame deletion of exon 3 and would produce a shorter ENG protein lacking the extracellular forty-seven amino acid sequences, which is located within the orphan domain. Our findings highlight the importance of the domain for the downstream signaling pathway of transforming growth factor-beta and bone morphogenesis protein superfamily receptors. Considering the phenotype variations and the available treatment for vascular complications, an early diagnosis using genetic testing, including WES, should be considered for individuals at risk of HHT.
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Affiliation(s)
- Naoki Saji
- Department of Stroke Medicine, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan.
| | - Toshitaka Kawarai
- Department of Clinical Neuroscience, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan.
| | - Ryosuke Miyamoto
- Department of Clinical Neuroscience, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan.
| | - Takahiro Sato
- Department of Stroke Medicine, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan.
| | - Hiroyuki Morino
- Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan..
| | - Antonio Orlacchio
- Laboratorio di Neurogenetica, CERC-IRCCS Santa Lucia, Rome, Italy; Dipartimento di Medicina dei Sistemi, Università di Roma "Tor Vergata", Rome, Italy.
| | - Ryosuke Oki
- Department of Clinical Neuroscience, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan.
| | - Kazumi Kimura
- Department of Stroke Medicine, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan.
| | - Ryuji Kaji
- Department of Clinical Neuroscience, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan.
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Di Santo MC, Ilina N, Pagano EA, Sozzi GO. A Japanese plum α-l-arabinofuranosidase/β-D-xylosidase gene is developmentally regulated by alternative splicing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:173-183. [PMID: 25576002 DOI: 10.1016/j.plantsci.2014.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 06/04/2023]
Abstract
A full-length cDNA clone named PsARF/XYL was obtained from Prunus salicina Lindl., and determined to encode a putative α-l-arabinofuranosidase/β-d-xylosidase belonging to glycoside hydrolase (GH, EC 3.2.1.-) family 3. Two related PsARF/XYL cDNAs were amplified, one from a fully-spliced transcript (PsARF/XYLa) and another one from an intron-retained transcript (PsARF/XYLb). The protein deduced from PsARF/XYLb is a truncated peptide at C-terminus that conserves the active-site amino acid sequence. High levels of PsARF/XYLa and PsARF/XYLb transcripts are detectable in several plant tissues. PsARF/XYLb transcripts accumulate progressively during the phase of exponential fruit growth but they become barely noticeable during on-tree ripening, or after a 6-h exposure of preclimacteric full-size plums to ethylene. In contrast, PsARF/XYLa is expressed throughout fruit development, and transcript accumulation parallels the climacteric rise in ethylene production during ripening. PsARF/XYLa expression is strongly induced in preclimacteric full-size plums after a 6-h treatment with physiologically active concentrations of ethylene. These findings suggest that PsARF/XYL gene is post-transcriptionally regulated by alternative splicing during development and that ethylene may be involved in this regulation. The isolation of a partial cDNA clone, PsARF1, is also reported. It encodes a putative cell-wall α-l-arabinofuranosidase, and its transcription is rapidly inhibited by ethylene in mature green plums.
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Affiliation(s)
- M Carolina Di Santo
- Facultad de Agronomía, Universidad de Buenos Aires, Avenida San Martín 4453, C1417DSE Buenos Aires, Argentina.
| | - Natalia Ilina
- Facultad de Agronomía, Universidad de Buenos Aires, Avenida San Martín 4453, C1417DSE Buenos Aires, Argentina
| | - Eduardo A Pagano
- Facultad de Agronomía, Universidad de Buenos Aires, Avenida San Martín 4453, C1417DSE Buenos Aires, Argentina
| | - Gabriel O Sozzi
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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