1
|
Zheng ZM. RNA therapy is shining for genetic diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102042. [PMID: 37876533 PMCID: PMC10590990 DOI: 10.1016/j.omtn.2023.102042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| |
Collapse
|
2
|
Yandrapally S, Sarkar S, Banerjee S. HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing. J Virol 2023; 97:e0104423. [PMID: 37905837 PMCID: PMC10688328 DOI: 10.1128/jvi.01044-23] [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: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE HIV-infected host cells impose varied degrees of regulation on viral replication, from very high to abortive. Proliferation of HIV in astrocytes is limited when compared to immune cells, such as CD4+ T lymphocytes. Understanding such differential regulation is one of the key questions in the field as these cells permit HIV persistence and rebound viremia, challenging HIV treatment and clinical cure. This study focuses on understanding the molecular mechanism behind such cell-specific disparities. We show that one of the key mechanisms is the regulation of heterogenous nuclear ribonucleoprotein A2, a host factor involved in alternative splicing and RNA processing, by HIV-1 Tat in CD4+ T lymphocytes, not observed in astrocytes. This regulation causes an increase in the levels of unspliced/partially spliced viral RNA and nuclear export of Rev-RNA complexes which results in high viral propagation in CD4+ T lymphocytes. The study reveals a new mechanism imposed by HIV on host cells that determines the fate of infection.
Collapse
Affiliation(s)
- Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Satarupa Sarkar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| |
Collapse
|
3
|
Li R, Gao S, Chen H, Zhang X, Yang X, Zhao J, Wang Z. Virus usurps alternative splicing to clear the decks for infection. Virol J 2023; 20:131. [PMID: 37340420 DOI: 10.1186/s12985-023-02098-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Since invasion, there will be a tug-of-war between host and virus to scramble cellular resources, for either restraining or facilitating infection. Alternative splicing (AS) is a conserved and critical mechanism of processing pre-mRNA into mRNAs to increase protein diversity in eukaryotes. Notably, this kind of post-transcriptional regulatory mechanism has gained appreciation since it is widely involved in virus infection. Here, we highlight the important roles of AS in regulating viral protein expression and how virus in turn hijacks AS to antagonize host immune response. This review will widen the understandings of host-virus interactions, be meaningful to innovatively elucidate viral pathogenesis, and provide novel targets for developing antiviral drugs in the future.
Collapse
Affiliation(s)
- Ruixue Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Shenyan Gao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Huayuan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, People's Republic of China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Zeng Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China.
| |
Collapse
|
4
|
Kelsall E, Harris C, Sen T, Hatton D, Dunn S, Gibson S. Interplay of heavy chain introns influences efficient transcript splicing and affects product quality of recombinant biotherapeutic antibodies from CHO cells. MAbs 2023; 15:2242548. [PMID: 37555672 PMCID: PMC10413919 DOI: 10.1080/19420862.2023.2242548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Introns are included in genes encoding therapeutic proteins for their well-documented function of boosting expression. However, mis-splicing of introns in recombinant immunoglobulin (IgG) heavy chain (HC) transcripts can produce amino acid sequence product variants. These variants can affect product quality; therefore, purification process optimization may be needed to remove them, or if they cannot be removed, then in-depth characterization must be carried out to understand their effects on biological activity. In this study, HC transgene engineering approaches were investigated and were successful in significantly reducing the previously identified IgG HC splice variants to <0.5%. Subsequently, a comprehensive evaluation was conducted to understand the influence of the different introns in the HC genes on the expression of recombinant biotherapeutic antibodies. The data revealed an unexpected cooperation between specific introns for efficient splicing, where intron retention led to significant reductions in IgG expression of up to 75% for some intron combinations. Furthermore, it was shown that HC introns could be fully removed without significantly affecting productivity. This work paves the way for future biotherapeutic antibody transgene design with regard to inclusion of HC introns. By removing unnecessary introns, transgene mRNA transcript will no longer be mis-spliced, thereby eliminating HC splice variants and improving antibody product quality.
Collapse
Affiliation(s)
- Emma Kelsall
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Claire Harris
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Titash Sen
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Diane Hatton
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Sarah Dunn
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Suzanne Gibson
- Cell Culture and Fermentation Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| |
Collapse
|
5
|
Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2022; 39:6965022. [PMID: 36579860 PMCID: PMC9831059 DOI: 10.1093/bioinformatics/btac846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. RESULTS Here, we propose Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection. AVAILABILITY AND IMPLEMENTATION The Spycone package is available as a PyPI package. The source code of Spycone is available under the GPLv3 license at https://github.com/yollct/spycone and the documentation at https://spycone.readthedocs.io/en/latest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Chit Tong Lio
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg 22607, Germany,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig 38106, Germany,Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig 38106, Germany
| | | | - Olga Tsoy
- To whom correspondence should be addressed.
| |
Collapse
|
6
|
Monoclonal Antibody Sequence Variants Disguised as Fragments: Identification, Characterization, and Their Removal by Purification Process Optimization. J Pharm Sci 2022; 111:3009-3016. [PMID: 35940243 DOI: 10.1016/j.xphs.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022]
Abstract
During early stage development of a therapeutic IgG1 monoclonal antibody, high levels of low molecular weight (LMW) peaks were observed by high performance size-exclusion chromatography and capillary electrophoresis. Further characterization of the LMW peak enriched HPSEC fractions using reversed phase liquid chromatography coupled to mass spectrometry showed these LMW species were 47 kDa and 50 kDa in size. However, the measured masses could not be matched to any fragments resulting from peptide bond hydrolysis. To identify these unknown LMW species, molecular characterization methods were employed, including high-throughput sequencing of RNA. Transcriptomic analysis revealed the LMW species were generated by mis-splicing events in the heavy chain transcript, which produced truncated heavy chain products that assembled with the light chain to mimic the appearance of fragments identified by routine purity assays. In an effort to improve product quality, an optimized purification process was developed. Characterization of the process intermediates confirmed removal of both LMW species by the optimized process. Our study demonstrates that deep-dive analytical characterization of biotherapeutics is critical to ensure product quality and inform process development. Transcriptomic analysis tools can help identify the cause of unknown species, and plays a key role in product and process characterization.
Collapse
|
7
|
Zhang S, Mao M, Lv Y, Yang Y, He W, Song Y, Wang Y, Yang Y, Al Abo M, Freedman JA, Patierno SR, Wang Y, Wang Z. A widespread length-dependent splicing dysregulation in cancer. SCIENCE ADVANCES 2022; 8:eabn9232. [PMID: 35977015 PMCID: PMC9385142 DOI: 10.1126/sciadv.abn9232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Dysregulation of alternative splicing is a key molecular hallmark of cancer. However, the common features and underlying mechanisms remain unclear. Here, we report an intriguing length-dependent splicing regulation in cancers. By systematically analyzing the transcriptome of thousands of cancer patients, we found that short exons are more likely to be mis-spliced and preferentially excluded in cancers. Compared to other exons, cancer-associated short exons (CASEs) are more conserved and likely to encode in-frame low-complexity peptides, with functional enrichment in GTPase regulators and cell adhesion. We developed a CASE-based panel as reliable cancer stratification markers and strong predictors for survival, which is clinically useful because the detection of short exon splicing is practical. Mechanistically, mis-splicing of CASEs is regulated by elevated transcription and alteration of certain RNA binding proteins in cancers. Our findings uncover a common feature of cancer-specific splicing dysregulation with important clinical implications in cancer diagnosis and therapies.
Collapse
Affiliation(s)
- Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuesheng Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yingqun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Tech University, Shanghai 200031, China
| | - Weijing He
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A. Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Steven R. Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
8
|
Majerciak V, Alvarado-Hernandez B, Lobanov A, Cam M, Zheng ZM. Genome-wide regulation of KSHV RNA splicing by viral RNA-binding protein ORF57. PLoS Pathog 2022; 18:e1010311. [PMID: 35834586 PMCID: PMC9321434 DOI: 10.1371/journal.ppat.1010311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/26/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023] Open
Abstract
RNA splicing plays an essential role in the expression of eukaryotic genes. We previously showed that KSHV ORF57 is a viral splicing factor promoting viral lytic gene expression. In this report, we compared the splicing profile of viral RNAs in BCBL-1 cells carrying a wild-type (WT) versus the cells containing an ORF57 knock-out (57KO) KSHV genome during viral lytic infection. Our analyses of viral RNA splice junctions from RNA-seq identified 269 RNA splicing events in the WT and 255 in the 57KO genome, including the splicing events spanning large parts of the viral genome and the production of vIRF4 circRNAs. No circRNA was detectable from the PAN region. We found that the 57KO alters the RNA splicing efficiency of targeted viral RNAs. Two most susceptible RNAs to ORF57 splicing regulation are the K15 RNA with eight exons and seven introns and the bicistronic RNA encoding both viral thymidylate synthase (ORF70) and membrane-associated E3-ubiquitin ligase (K3). ORF57 inhibits splicing of both K15 introns 1 and 2. ORF70/K3 RNA bears two introns, of which the first intron is within the ORF70 coding region as an alternative intron and the second intron in the intergenic region between the ORF70 and K3 as a constitutive intron. In the WT cells expressing ORF57, most ORF70/K3 transcripts retain the first intron to maintain an intact ORF70 coding region. In contrast, in the 57KO cells, the first intron is substantially spliced out. Using a minigene comprising of ORF70/K3 locus, we further confirmed ORF57 regulation of ORF70/K3 RNA splicing, independently of other viral factors. By monitoring protein expression, we showed that ORF57-mediated retention of the first intron leads to the expression of full-length ORF70 protein. The absence of ORF57 promotes the first intron splicing and expression of K3 protein. Altogether, we conclude that ORF57 regulates alternative splicing of ORF70/K3 bicistronic RNA to control K3-mediated immune evasion and ORF70 participation of viral DNA replication in viral lytic infection.
Collapse
Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute, NIH, Frederick, Maryland, Unites States of America
- * E-mail: (VM); (Z-MZ)
| | - Beatriz Alvarado-Hernandez
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute, NIH, Frederick, Maryland, Unites States of America
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, NIH, Bethesda, Maryland, Unites States of America
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, NIH, Bethesda, Maryland, Unites States of America
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute, NIH, Frederick, Maryland, Unites States of America
- * E-mail: (VM); (Z-MZ)
| |
Collapse
|
9
|
Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
Collapse
|
10
|
Zhou Y, Ng DY, Richards AM, Wang P. Loss of full-length pumilio 1 abrogates miRNA-221-induced gene p27 silencing-mediated cell proliferation in the heart. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:456-470. [PMID: 35036057 PMCID: PMC8728526 DOI: 10.1016/j.omtn.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022]
Abstract
Upregulated expression of microRNA (miR)-221 is associated with downregulation of p27 and subsequent increased cell proliferation in a variety of human cancers. It is unknown whether miR-221 mimics could trigger neoplastic cellular proliferation. In vitro, we demonstrated miR-221 significantly downregulates the expression of P27 and increases proliferation of H9c2 and cardiac fibroblasts. The knockdown of PUM1 but not PUM2 abolished such effects by miR-221, as verified by RT-qPCR and western blot, direct binding of p27 3′ UTR by luciferase reporter assay and cell proliferation by Ki67. In vivo expression of P27 in the rat liver, heart, kidney, spleen, and muscle were not affected by miR-221 at 1 and 4 mg/kg and concurrently full-length (FL) PUM1 (140 kDa) was not detected. Instead, isoforms of 105 and 90 kDa were observed and generated through alternative RNA slicing verified by cDNA cloning and sequencing and cathepsin K cleavage confirmed by studies with the inhibitor odanacatib. This is the first study to address the possible pro-proliferative effects of miR-221 mimic therapeutics in cardiovascular applications. Loss of FL PUM1 expression is a key factor abrogating miR-221-mediated p27 regulation, although other concurrent mechanisms cannot be excluded. Our findings provide essential insights into the context-dependent nature of miRNA functionality.
Collapse
|
11
|
El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
Collapse
Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
12
|
Brant AC, Menezes AN, Felix SP, Almeida LM, Moreira MAM. Preferential expression of a HPV genotype in invasive cervical carcinomas infected by multiple genotypes. Genomics 2020; 112:2942-2948. [PMID: 32437850 DOI: 10.1016/j.ygeno.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/17/2020] [Accepted: 05/07/2020] [Indexed: 12/24/2022]
Abstract
Multiple infections by HPV genotypes are frequently detected in HPV+ cervical lesions but the interaction between each viral genotype during carcinogenesis is poorly understood. Here we carried out a comprehensive study to characterize the multiple HPV expression and integration by RNA-seq analyses of 19 invasive cervical carcinomas coinfected by several HPV genotypes. Analysis of tumor DNA by a hybridization assay indicated multiple infections ranging from 2 to 6 different HPV genotypes. RNA-seq analysis showed that a single HPV genotype was preferentially expressed. Finally, the search for HPV/human chimeric transcripts indicated integration from preferentially expressed genotypes. In conclusion, the present study indicated that, in invasive cervical carcinomas infected by multiple HPV genotypes, one HPV was preferentially expressed, supporting the hypothesis that a single HPV genotype was associated with cancer development.
Collapse
Affiliation(s)
- A C Brant
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil; Post-Graduate Program in Genetics, Universidade Federal do Rio de Janeiro (UFRJ), Brazil
| | - A N Menezes
- Cancer Genetics and Evolution Laboratory, Cancer Research UK, Institute of Genetics & Molecular Medicine, The University of Edinburgh, UK
| | - S P Felix
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - L M Almeida
- Department of Population Research, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - M A M Moreira
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
| |
Collapse
|
13
|
Yuan L, Hu F, Zhang Y, Meng L, An T, Chen Y, Zhang X. Identification and functional analysis of a novel splice variant of AC3-33 in breast cancer. Exp Ther Med 2019; 19:183-191. [PMID: 31853289 PMCID: PMC6909594 DOI: 10.3892/etm.2019.8212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 09/10/2019] [Indexed: 01/20/2023] Open
Abstract
Alternative RNA splicing plays a key role in regulating gene function and influencing protein expression diversity. In the present study, an AC-33 transcript variant (NCBI Reference Sequence: NM_001308229.1), splice variant (sv)AC3-33, was successfully cloned from the MCF-7 breast cancer cell line by reverse transcription PCR using primers based on expressed sequence tags. The aim of the present study was to investigate the structure and function of svAC3-33. svAC3-33 has an open reading frame of 1,825 base pairs, lacks AC3-33 exon 2 and is encoded by 294 amino acids. svAC3-33 is localized within the cytoplasm. The Cell Counting Kit-8 and EdU detection of cell proliferation assays showed that svAC3-33 inhibited MCF-7 cell proliferation. Similarly, svAC3-33 knockdown by RNA interference was shown to have the opposite effect by repressing the cell cycle progression of breast cancer cells. Furthermore, the data indicated that svAC3-33 may upregulate the expression of p21. The present study provides evidence that the increased expression of svAC3-33 may inhibit the activity of the transcription factor AP-1. The luciferase reporter gene assay detected a downregulation of the expression of c-Jun, but not c-Fos, which in turn affected cell proliferation. In conclusion, these results indicated a function for svAC3-33 in inhibiting the cell proliferation of MCF-7 cells by regulating the AP-1 signaling pathway.
Collapse
Affiliation(s)
- Lu Yuan
- College of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Fen Hu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Yunfeng Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, Hebei 063000, P.R. China
| | - Lijun Meng
- Department of Environmental and Chemical Engineering, Tangshan College, Tangshan, Hebei 063000, P.R. China
| | - Tianyang An
- College of Jitang, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Yajing Chen
- College of Pharmacy, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Xiujun Zhang
- College of Psychology, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| |
Collapse
|
14
|
Zappaterra M, Luise D, Zambonelli P, Mele M, Serra A, Costa LN, Davoli R. Association study between backfat fatty acid composition and SNPs in candidate genes highlights the effect of FASN polymorphism in large white pigs. Meat Sci 2019; 156:75-84. [DOI: 10.1016/j.meatsci.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
|
15
|
Tang S, Patel A, Krause PR. Hidden regulation of herpes simplex virus 1 pre-mRNA splicing and polyadenylation by virally encoded immediate early gene ICP27. PLoS Pathog 2019; 15:e1007884. [PMID: 31206552 PMCID: PMC6597130 DOI: 10.1371/journal.ppat.1007884] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/03/2019] [Indexed: 12/23/2022] Open
Abstract
In contrast to human cells, very few HSV-1 genes are known to be spliced, although the same pre-mRNA processing machinery is shared. Here, through global analysis of splice junctions in cells infected with HSV-1 and an HSV-1 mutant virus with deletion of infectious cell culture protein 27 (ICP27), one of two viral immediate early (IE) genes essential for viral replication, we identify hundreds of novel alternative splice junctions mapping to both previously known HSV-1 spliced genes and previously unknown spliced genes, the majority of which alter the coding potential of viral genes. Quantitative and qualitative splicing efficiency analysis of these novel alternatively spliced genes based on RNA-Seq and RT-PCR reveals that splicing at these novel splice sites is efficient only when ICP27 is absent; while in wildtype HSV-1 infected cells, the splicing of these novel splice junctions is largely silenced in a gene/sequence specific manner, suggesting that ICP27 not only promotes accumulation of ICP27 targeted transcripts but also ensures correctness of the functional coding sequences through inhibition of alternative splicing. Furthermore, ICP27 toggles expression of ICP34.5, the major viral neurovirulence factor, through inhibition of splicing and activation of a proximal polyadenylation signal (PAS) in the newly identified intron, revealing a novel regulatory mechanism for expression of a viral gene. Thus, through the viral IE protein ICP27, HSV-1 co-opts both splicing and polyadenylation machinery to achieve optimal viral gene expression during lytic infection. On the other hand, during latent infection when ICP27 is absent, HSV-1 likely takes advantages of host splicing machinery to restrict expression of randomly activated antigenic viral genes to achieve immune evasion. Little is known regarding to how HSV, a large DNA virus and known to contain very few spliced genes, escapes host pre-mRNA splicing machinery. Here, by establishing a high throughput splice junction identification platform and quantitative analysis method to assess splicing efficiency based on high throughput data, we find that HSV-1 encodes hundreds of previously unknown alternative splice junctions; however, splicing of these novel spliced genes is largely silenced in wild-type HSV-1 infected cells, explaining why only very few spliced genes have been previously identified in HSV-1. Moreover, ICP27 is required for splicing inhibition and 3’ end formation of ICP34.5, the major viral neurovirulence factor and also the major target of latently expressed viral miRNAs. These findings not only fundamentally change the view of HSV gene structure, but also reveal a mechanism by which HSV employs host splicing and polyadenylation machineries to achieve optimal gene expression during acute infection and may also contribute to immune evasion during latency when ICP27 is not expressed.
Collapse
Affiliation(s)
- Shuang Tang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (ST); (PRK)
| | - Amita Patel
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Philip R. Krause
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (ST); (PRK)
| |
Collapse
|
16
|
Jia R, Ajiro M, Yu L, McCoy P, Zheng ZM. Oncogenic splicing factor SRSF3 regulates ILF3 alternative splicing to promote cancer cell proliferation and transformation. RNA (NEW YORK, N.Y.) 2019; 25:630-644. [PMID: 30796096 PMCID: PMC6467003 DOI: 10.1261/rna.068619.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/28/2023]
Abstract
Alternative RNA splicing is an important focus in molecular and clinical oncology. We report here that SRSF3 regulates alternative RNA splicing of interleukin enhancer binding factor 3 (ILF3) and production of this double-strand RNA-binding protein. An increased coexpression of ILF3 isoforms and SRSF3 was found in various types of cancers. ILF3 isoform-1 and isoform-2 promote cell proliferation and transformation. Tumor cells with reduced SRSF3 expression produce aberrant isoform-5 and -7 of ILF3. By binding to RNA sequence motifs, SRSF3 regulates the production of various ILF3 isoforms by exclusion/inclusion of ILF3 exon 18 or by selection of an alternative 3' splice site within exon 18. ILF3 isoform-5 and isoform-7 suppress tumor cell proliferation and the isoform-7 induces cell apoptosis. Our data indicate that ILF3 isoform-1 and isoform-2 are two critical factors for cell proliferation and transformation. The increased SRSF3 expression in cancer cells plays an important role in maintaining the steady status of ILF3 isoform-1 and isoform-2.
Collapse
Affiliation(s)
- Rong Jia
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Ke Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Masahiko Ajiro
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Lulu Yu
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Philip McCoy
- Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| |
Collapse
|
17
|
Paget-Bailly P, Meznad K, Bruyère D, Perrard J, Herfs M, Jung AC, Mougin C, Prétet JL, Baguet A. Comparative RNA sequencing reveals that HPV16 E6 abrogates the effect of E6*I on ROS metabolism. Sci Rep 2019; 9:5938. [PMID: 30976051 PMCID: PMC6459911 DOI: 10.1038/s41598-019-42393-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/27/2019] [Indexed: 01/16/2023] Open
Abstract
High-risk Human Papillomavirus infections are responsible for anogenital and oropharyngeal cancers. Alternative splicing is an important mechanism controlling HPV16 gene expression. Modulation in the splice pattern leads to polycistronic HPV16 early transcripts encoding a full length E6 oncoprotein or truncated E6 proteins, commonly named E6*. Spliced E6*I transcripts are the most abundant RNAs produced in HPV-related cancers. To date, the biological function of the E6*I isoform remains controversial. In this study, we identified, by RNA sequencing, cellular targets deregulated by E6*I, among which genes related to ROS metabolism. Concomitantly, E6*I-overexpressing cells display high levels of ROS. However, co-overexpression of both E6 and E6*I has no effect on ROS production. In HPV16-infected cells expressing different E6/E6*I levels, we show that the newly identified targets CCL2 and RAC2 are increased by E6*I but decreased by E6 expression, suggesting that E6 abrogates the effect of E6*I. Taken together, these data support the idea that E6*I acts independently of E6 to increase ROS production and that E6 has the ability to counteract the effects of E6*I. This asks the question of how E6*I can be considered separately of E6 in the natural history of HPV16 infection.
Collapse
Affiliation(s)
- Philippe Paget-Bailly
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France.,Université Bourgogne Franche Comté, Besançon, France
| | - Koceila Meznad
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France.,Université Bourgogne Franche Comté, Besançon, France
| | - Diane Bruyère
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Jérôme Perrard
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France.,Université Bourgogne Franche Comté, Besançon, France
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Alain C Jung
- Université de Strasbourg, Inserm, UMR_S1113, Centre de lutte contre le cancer Paul STRAUSS, Strasbourg, France
| | - Christiane Mougin
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France.,Université Bourgogne Franche Comté, Besançon, France.,Centre Hospitalier Régional Universitaire, CNR HPV, 3 Bvd Alexandre Fleming, Besançon, France
| | - Jean-Luc Prétet
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France.,Université Bourgogne Franche Comté, Besançon, France.,Centre Hospitalier Régional Universitaire, CNR HPV, 3 Bvd Alexandre Fleming, Besançon, France
| | - Aurélie Baguet
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, UFR Santé, 19 rue Ambroise Paré, Besançon, France. .,Université Bourgogne Franche Comté, Besançon, France.
| |
Collapse
|
18
|
Brant AC, Majerciak V, Moreira MAM, Zheng ZM. HPV18 Utilizes Two Alternative Branch Sites for E6*I Splicing to Produce E7 Protein. Virol Sin 2019; 34:211-221. [PMID: 30945125 PMCID: PMC6513837 DOI: 10.1007/s12250-019-00098-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
Human papillomavirus 18 (HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6E7 pre-mRNA. The E6 ORF region in the bicistronic E6E7 pre-mRNA contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6*I RNA for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences (BPS) upstream of its 3′ splice site, with an identical heptamer AACUAAC, for E6*I splicing. One heptamer has a branch site adenosine (underlined) at nt 384 and the other at nt 388. E6*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6*I splicing prefers the 3′ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant RNA splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.
Collapse
Affiliation(s)
- Ayslan Castro Brant
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA.,Genetics Post-Graduation Program, Rio de Janeiro Federal University, Rio de Janeiro, Brazil.,Genetics Program, Nacional Cancer Institute, INCA, Rio de Janeiro, 20231-050, Brazil
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | | | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA.
| |
Collapse
|
19
|
Abstract
Hepcidin is a main regulator of iron metabolism, of which abnormal expression affects intestinal absorption and reticuloendothelial sequestration of iron by interacting with ferroportin. It is also noted that abnormal iron accumulation is one of the key factors to facilitate promotion and progression of cancer including hepatoma. In this study, we firstly revealed that a new alternative HAMP transcript was found in hepatoma-derived cell line HLF, which was identical to the wild-type preprohepcidin sequence except lacking of an internal 60 bases. In addition to HLF, most of hepatoma-derived cell lines have significant copy numbers of variant-type hepcidin mRNA by a copy-based-digital PCR. Furthermore, the copy number of hepcidin mRNA variant was significantly higher in serum exosomes of hepatocellular carcinoma patients. The quantification of exosomal hepcidin mRNA variant may serve as a potential new biomarker for HCC diagnosis.
Collapse
Affiliation(s)
- Katsunori Sasaki
- Division of Gastroenterological Surgery II, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Yutaka Kohgo
- Department of Gastroenterology, International University of Health and Welfare Hospital, Nasushiobara, Japan
| | - Takaaki Ohtake
- Department of Gastroenterology, International University of Health and Welfare Hospital, Nasushiobara, Japan
| |
Collapse
|
20
|
Brant AC, Menezes AN, Felix SP, de Almeida LM, Sammeth M, Moreira MAM. Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive study in invasive cervical cancer. Genomics 2018; 111:1853-1861. [PMID: 30552977 DOI: 10.1016/j.ygeno.2018.12.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022]
Abstract
Scarce data are available on the expression of papillomavirus genome and the frequency of alternatively spliced E6E7 mRNAs in invasive cervical cancer. We carried out a comprehensive characterization of HPV expression by RNA-Seq analysis in 22 invasive cervical cancer with HPV16 or HPV18, characterizing the presence of integrated/episomal viral DNA, the integration sites in human genome and the proportion of alternative splicing products of E6 and E7 genes. The expression patterns suggested the presence of episomal and/or integrated viral DNA, with integration detected in most tumors, frequently occurring within human genes in HPV18+ and in intergenic regions in HPV16+ tumors. Alternative splicing of E6E7 transcripts showed E6*I as the most frequent isoform for both viral types, followed by E6*II and E6/E7 (unspliced) transcripts in HPV16+, and by E6/E7 in HPV18+ tumors. Previously described E6*VI and E6*V transcript isoforms for HPV16, and E6*X for HPV18, were rare or not detected.
Collapse
Affiliation(s)
- Ayslan C Brant
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil; Post-Graduate Program in Genetics, Universidade Federal do Rio de Janeiro (UFRJ), Brazil
| | - Albert N Menezes
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Shayany P Felix
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Liz M de Almeida
- Department of Population Research, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
| | - Michael Sammeth
- Department of Bioinformatics, Transcriptomics and Functional Genomics, Federal University of Rio de Janeiro (UFRJ), Brazil.
| | - Miguel A M Moreira
- Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
| |
Collapse
|
21
|
Abstract
This chapter is the first one to introduce the detection of viral RNA splicing as a new tool for clinical diagnosis of virus infections. These include various infections caused by influenza viruses, human immunodeficiency viruses (HIV), human T-cell leukemia viruses (HTLV), Torque teno viruses (TTV), parvoviruses, adenoviruses, hepatitis B virus, polyomaviruses, herpesviruses, and papillomaviruses. Detection of viral RNA splicing for active viral gene expression in a clinical sample is a nucleic acid-based detection. The interpretation of the detected viral RNA splicing results is straightforward without concern for carry-over DNA contamination, because the spliced RNA is smaller than its corresponding DNA template. Although many methods can be used, a simple method to detect viral RNA splicing is reverse transcription-polymerase chain reaction (RT-PCR). In principle, the detection of spliced RNA transcripts by RT-PCR depends on amplicon selection and primer design. The most common approach is the amplification over the intron regions by a set of primers in flanking exons. A larger product than the predicted size of smaller, spliced RNA is in general an unspliced RNA or contaminating viral genomic DNA. A spliced mRNA always gives a smaller RT-PCR product than its unspliced RNA due to removal of intron sequences by RNA splicing. The contaminating viral DNA can be determined by a minus RT amplification (PCR). Alternatively, specific amplification of a spliced RNA can be obtained by using an exon-exon junction primer because the sequence at exon-exon junction is not present in the unspliced RNA nor in viral genomic DNA.
Collapse
|
22
|
Morel A, Baguet A, Perrard J, Demeret C, Jacquin E, Guenat D, Mougin C, Prétet JL. 5azadC treatment upregulates miR-375 level and represses HPV16 E6 expression. Oncotarget 2018; 8:46163-46176. [PMID: 28521287 PMCID: PMC5542257 DOI: 10.18632/oncotarget.17575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 04/10/2017] [Indexed: 01/06/2023] Open
Abstract
High-risk human papillomaviruses are the etiological agents of cervical cancer and HPV16 is the most oncogenic genotype. Immortalization and transformation of infected cells requires the overexpression of the two viral oncoproteins E6 and E7 following HPV DNA integration into the host cell genome. Integration often leads to the loss of the E2 open reading frame and the corresponding protein can no longer act as a transcriptional repressor on p97 promoter. Recently, it has been proposed that long control region methylation also contributes to the regulation of E6/E7 expression. To determine which epigenetic mechanism is involved in HPV16 early gene regulation, 5-aza-2′-deoxycytidine was used to demethylate Ca Ski and SiHa cell DNA. Decreased expression of E6 mRNA and protein levels was observed in both cell lines in an E2-independent manner. E6 repression was accompanied by neither a modification of the main cellular transcription factor expression involved in long control region regulation, nor by a modification of the E6 mRNA splicing pattern. In contrast, a pronounced upregulation of miR-375, known to destabilize HPV16 early viral mRNA, was observed. Finally, the use of miR-375 inhibitor definitively proved the involvement of miR-375 in E6 repression. These results highlight that cellular DNA methylation modulates HPV16 early gene expression and support a role for epigenetic events in high-risk HPV associated-carcinogenesis.
Collapse
Affiliation(s)
- Adrien Morel
- EA3181, Université Bourgogne Franche-Comté, LabEx LipSTIC ANR-11-LABX-0021, Besançon, France
| | - Aurélie Baguet
- EA3181, Université Bourgogne Franche-Comté, LabEx LipSTIC ANR-11-LABX-0021, Besançon, France
| | - Jérôme Perrard
- EA3181, Université Bourgogne Franche-Comté, LabEx LipSTIC ANR-11-LABX-0021, Besançon, France
| | - Caroline Demeret
- Département de Virologie, Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, CNRS UMR 3569, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Elise Jacquin
- Signalling Department, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - David Guenat
- Centre Hospitalier Régional Universitaire, Besançon, France.,Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Christiane Mougin
- EA3181, Université Bourgogne Franche-Comté, LabEx LipSTIC ANR-11-LABX-0021, Besançon, France.,Centre Hospitalier Régional Universitaire, Besançon, France
| | - Jean-Luc Prétet
- EA3181, Université Bourgogne Franche-Comté, LabEx LipSTIC ANR-11-LABX-0021, Besançon, France.,Centre Hospitalier Régional Universitaire, Besançon, France
| |
Collapse
|
23
|
Zhang Z, Cao W, Edery I. The SR protein B52/SRp55 regulates splicing of the period thermosensitive intron and mid-day siesta in Drosophila. Sci Rep 2018; 8:1872. [PMID: 29382842 PMCID: PMC5789894 DOI: 10.1038/s41598-017-18167-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/06/2017] [Indexed: 11/24/2022] Open
Abstract
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as temperature increases, an adaptive response that aims to minimize the deleterious effects from exposure to heat. This temperature-dependent plasticity in mid-day sleep levels is partly based on the thermal sensitive splicing of an intron in the 3′ untranslated region (UTR) of the circadian clock gene termed period (per). In this study, we evaluated a possible role for the serine/arginine-rich (SR) splicing factors in the regulation of dmpi8 splicing efficiency and mid-day siesta. Using a Drosophila cell culture assay we show that B52/SRp55 increases dmpi8 splicing efficiency, whereas other SR proteins have little to no effect. The magnitude of the stimulatory effect of B52 on dmpi8 splicing efficiency is modulated by natural variation in single nucleotide polymorphisms (SNPs) in the per 3′ UTR that correlate with B52 binding levels. Down-regulating B52 expression in clock neurons increases mid-day siesta and reduces dmpi8 splicing efficiency. Our results establish a novel role for SR proteins in sleep and suggest that polymorphisms in the per 3′ UTR contribute to natural variation in sleep behavior by modulating the binding efficiencies of SR proteins.
Collapse
Affiliation(s)
- Zhichao Zhang
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.,Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Huimin Road 211#, Chengdu, Sichuan Province, 611130, P. R. China
| | - Weihuan Cao
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.,Human Genetics Institute of New Jersey, Nelson Biology Laboratories, 604 Allison Road, Piscataway, NJ, 08854, USA
| | - Isaac Edery
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.
| |
Collapse
|
24
|
Xue XY, Majerciak V, Uberoi A, Kim BH, Gotte D, Chen X, Cam M, Lambert PF, Zheng ZM. The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues. PLoS Pathog 2017; 13:e1006715. [PMID: 29176795 PMCID: PMC5720830 DOI: 10.1371/journal.ppat.1006715] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/07/2017] [Accepted: 10/25/2017] [Indexed: 12/17/2022] Open
Abstract
Mouse papillomavirus type 1 (MmuPV1) provides, for the first time, the opportunity to study infection and pathogenesis of papillomaviruses in the context of laboratory mice. In this report, we define the transcriptome of MmuPV1 genome present in papillomas arising in experimentally infected mice using a combination of RNA-seq, PacBio Iso-seq, 5’ RACE, 3’ RACE, primer-walking RT-PCR, RNase protection, Northern blot and in situ hybridization analyses. We demonstrate that the MmuPV1 genome is transcribed unidirectionally from five major promoters (P) or transcription start sites (TSS) and polyadenylates its transcripts at two major polyadenylation (pA) sites. We designate the P7503, P360 and P859 as “early” promoters because they give rise to transcripts mostly utilizing the polyadenylation signal at nt 3844 and therefore can only encode early genes, and P7107 and P533 as “late” promoters because they give rise to transcripts utilizing polyadenylation signals at either nt 3844 or nt 7047, the latter being able to encode late, capsid proteins. MmuPV1 genome contains five splice donor sites and three acceptor sites that produce thirty-six RNA isoforms deduced to express seven predicted early gene products (E6, E7, E1, E1^M1, E1^M2, E2 and E8^E2) and three predicted late gene products (E1^E4, L2 and L1). The majority of the viral early transcripts are spliced once from nt 757 to 3139, while viral late transcripts, which are predicted to encode L1, are spliced twice, first from nt 7243 to either nt 3139 (P7107) or nt 757 to 3139 (P533) and second from nt 3431 to nt 5372. Thirteen of these viral transcripts were detectable by Northern blot analysis, with the P533-derived late E1^E4 transcripts being the most abundant. The late transcripts could be detected in highly differentiated keratinocytes of MmuPV1-infected tissues as early as ten days after MmuPV1 inoculation and correlated with detection of L1 protein and viral DNA amplification. In mature warts, detection of L1 was also found in more poorly differentiated cells, as previously reported. Subclinical infections were also observed. The comprehensive transcription map of MmuPV1 generated in this study provides further evidence that MmuPV1 is similar to high-risk cutaneous beta human papillomaviruses. The knowledge revealed will facilitate the use of MmuPV1 as an animal virus model for understanding of human papillomavirus gene expression, pathogenesis and immunology. Papillomavirus (PV) infections lead to development of both benign warts and cancers. Because PVs are epitheliotropic and species specific, it has been extremely challenging to study PV infection in the context of a naturally occurring infection in a tractable laboratory animal. The recent discovery of the papillomavirus, MmuPV1, that infects laboratory mice, provides an important new animal model system for understanding the pathogenesis of papillomavirus-associated diseases. By using state of the art RNA-seq to provide deep sequencing analysis of what regions of the viral genome are transcribed and PacBio Iso-seq that produces longer reads to define the complete sequences of individual transcripts in combination with several conventional technologies to confirm transcription starts sites, splice sites, and polyadenylation sites, we provide the first detailed description of the MmuPV1 transcript map using RNA from MmuPV1-induced mouse warts. This study reveals the presence of mRNA transcripts capable of coding for ten protein products in the MmuPV1 genome and leads to correctly re-assigning the E1^E4, L2 and L1 coding regions. We were able to detect individual transcripts from the infected wart tissues by RT-PCR, Northern blot and RNA ISH, to define the temporal onset of productive viral infection and to ectopically express a predicted viral protein for functional studies. The constructed MmuPV1 transcript map provides a foundation to advance our understanding of papillomavirus biology and pathogenesis.
Collapse
Affiliation(s)
- Xiang-Yang Xue
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, NCI/NIH, Frederick, Maryland, United States of America
- Department of Microbiology and Immunology, Wenzhou Medical University, Zhejiang, China
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, NCI/NIH, Frederick, Maryland, United States of America
| | - Aayushi Uberoi
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Bong-Hyun Kim
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, Maryland, United States of America
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland, United States of America
| | - Deanna Gotte
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, NCI/NIH, Frederick, Maryland, United States of America
| | - Xiongfong Chen
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, Maryland, United States of America
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland, United States of America
| | - Maggie Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI/NIH, Bethesda, Maryland, United States of America
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, NCI/NIH, Frederick, Maryland, United States of America
- * E-mail:
| |
Collapse
|
25
|
RNA splicing in human disease and in the clinic. Clin Sci (Lond) 2017; 131:355-368. [PMID: 28202748 DOI: 10.1042/cs20160211] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 01/12/2023]
Abstract
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism. Furthermore, even when a mutation is correctly identified as affecting the splicing process, there still remains the difficulty of providing an exact evaluation of the potential impact on disease onset, severity and duration. In this review, we provide a brief overview of splicing diagnostic methodologies, from in silico bioinformatics approaches to wet lab in vitro and in vivo systems to evaluate splicing efficiencies. In particular, we provide an overview of how the latest developments in high-throughput sequencing can be applied to the clinic, and are already changing clinical approaches.
Collapse
|
26
|
Deka B, Singh KK. Multifaceted Regulation of Gene Expression by the Apoptosis- and Splicing-Associated Protein Complex and Its Components. Int J Biol Sci 2017; 13:545-560. [PMID: 28539829 PMCID: PMC5441173 DOI: 10.7150/ijbs.18649] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/24/2017] [Indexed: 11/24/2022] Open
Abstract
The differential deposition of RNA-binding proteins (RBPs) on pre-mRNA mediates the processes of gene expression. One of the complexes containing RBPs that play a crucial part in RNA metabolism is the apoptosis-and splicing-associated protein (ASAP) complex. In this review, we present a summary of the structure of ASAP complex and its localization. Also, we discuss the findings by different groups on various functions of the subunits of the ASAP complex in RNA metabolism. The subunits of the ASAP complex are RNPS1, Acinus and SAP18. Originally, the ASAP complex was thought to link RNA processing with apoptosis. Further studies have shown the role of these components in RNA metabolism of cells, including transcription, splicing, translation and nonsense-mediated mRNA decay (NMD). In transcription, RNPS1 is involved in preventing the formation of R-loop, while Acinus and SAP18 suppress transcription with the help of histone deacetylase. On the one hand, individual components of the ASAP complex, namely RNPS1 and Acinus act as splicing activators, whereas on the other hand, in-vitro assay shows that the ASAP complex behaves as splicing repressor. In addition, the individual members of the ASAP complex associates with the exon junction complex (EJC) to play roles in splicing and translation. RNPS1 increases the translation efficiency by participating in the 3'end processing and polysome association of mRNAs. Similarly, during NMD RNPS1 aids in the recruitment of decay factors by interacting with EJC.
Collapse
Affiliation(s)
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| |
Collapse
|
27
|
Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements. J Virol 2016; 90:9138-52. [PMID: 27489271 DOI: 10.1128/jvi.00965-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/25/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Human papillomavirus 18 (HPV18) is the second most common oncogenic HPV type associated with cervical, anogenital, and oropharyngeal cancers. Like other oncogenic HPVs, HPV18 encodes two major (one early and one late) polycistronic pre-mRNAs that are regulated by alternative RNA splicing to produce a repertoire of viral transcripts for the expression of individual viral genes. However, RNA cis-regulatory elements and trans-acting factors contributing to HPV18 alternative RNA splicing remain unknown. In this study, an exonic splicing enhancer (ESE) in the nucleotide (nt) 3520 to 3550 region in the HPV18 genome was identified and characterized for promotion of HPV18 929^3434 splicing and E1^E4 production through interaction with SRSF3, a host oncogenic splicing factor differentially expressed in epithelial cells and keratinocytes. Introduction of point mutations in the SRSF3-binding site or knockdown of SRSF3 expression in cells reduces 929^3434 splicing and E1^E4 production but activates other, minor 929^3465 and 929^3506 splicing. Knockdown of SRSF3 expression also enhances the expression of E2 and L1 mRNAs. An exonic splicing silencer (ESS) in the HPV18 nt 612 to 639 region was identified as being inhibitory to the 233^416 splicing of HPV18 E6E7 pre-mRNAs via binding to hnRNP A1, a well-characterized, abundantly and ubiquitously expressed RNA-binding protein. Introduction of point mutations into the hnRNP A1-binding site or knockdown of hnRNP A1 expression promoted 233^416 splicing and reduced E6 expression. These data provide the first evidence that the alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host trans-acting splicing factors. IMPORTANCE Expression of HPV18 genes is regulated by alternative RNA splicing of viral polycistronic pre-mRNAs to produce a repertoire of viral early and late transcripts. RNA cis elements and trans-acting factors contributing to HPV18 alternative RNA splicing have been discovered in this study for the first time. The identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnRNP A1, and regulates E6 and E7 expression of the early E6E7 polycistronic pre-mRNA. The identified ESE at the E1^E4 ORF promotes HPV18 929^3434 splicing of both viral early and late pre-mRNAs and E1^E4 production through interaction with SRSF3. This study provides important observations on how alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host splicing factors and offers potential therapeutic targets to overcome HPV-related cancer.
Collapse
|
28
|
Liu J, Sun Y, Yang C, Zhang Y, Jiang Q, Huang J, Ju Z, Wang X, Zhong J, Wang C. Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls. PLoS One 2016; 11:e0162730. [PMID: 27669152 PMCID: PMC5036895 DOI: 10.1371/journal.pone.0162730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Inner centromere protein (INCENP) plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC). To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs) g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE) motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P < 0.05). Bulls with H11H11 and H2H10 exhibited higher initial sperm motility than those with H2H2 (P < 0.05). The expression levels of INCENP in bulls with H1H12 and H11H11 were significantly higher than those in bulls with H9H12 (P < 0.05), as determined by qRT-PCR. Findings suggest that g.19970 A>G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.
Collapse
Affiliation(s)
- Juan Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- College of Agronomic Sciences in Shandong Agricultural University, Taian, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- * E-mail:
| |
Collapse
|
29
|
A selective splicing variant of hepcidin mRNA in hepatocellular carcinoma cell lines. Biochem Biophys Res Commun 2016; 476:501-507. [DOI: 10.1016/j.bbrc.2016.05.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
|
30
|
Ajiro M, Zheng ZM. Vemurafenib-resistant BRAF selects alternative branch points different from its wild-type BRAF in intron 8 for RNA splicing. Cell Biosci 2015; 5:70. [PMID: 26697165 PMCID: PMC4687071 DOI: 10.1186/s13578-015-0061-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022] Open
Abstract
One mechanism of resistance of the melanoma-associated BRAF kinase to its small molecule inhibitor vemurafenib is by point mutations in its intron 8 resulting in exons 4–8 skipping. In this report, we carried out in vitro BRAF RNA splicing assays and lariat RT-PCR to map the intron 8 branch points in wild-type and BRAF mutants. We identify multiple branch points (BP) in intron 8 of both wild-type (wt) and vemurafenib-resistant BRAF RNA. In wt BRAF, BPs are located at -29A, -28A and -26A, whereas in a vemurafenib-resistant BRAF splicing mutant, BPs map to -22A, -18A and -15A, proximal to the intron 8 3′ splice site. This finding of a distal-to-proximal shift of the branch point sequence in BRAF splicing in response to point-mutations in intron 8 provides insight into the regulation of BRAF alternative splicing upon vemurafenib resistance.
Collapse
Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 USA
| |
Collapse
|
31
|
Majerciak V, Zheng ZM. Alternative RNA splicing of KSHV ORF57 produces two different RNA isoforms. Virology 2015; 488:81-7. [PMID: 26609938 DOI: 10.1016/j.virol.2015.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/17/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
In lytically infected B cells Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 gene encodes two RNA isoforms by alternative splicing of its pre-mRNA, which contains a small, constitutive intron in its 5' half and a large, suboptimal intron in its 3's half. The RNA1 isoform encodes full-length ORF57 and is a major isoform derived from splicing of the constitutive small intron, but retaining the suboptimal large intron as the coding region. A small fraction (<5%) of ORF57 RNA undergoes double splicing to produce a smaller non-coding RNA2 due to lack of a translational termination codon. Both RNAs are cleaved and polyadenylated at the same cleavage site CS83636. The insertion of ORF57 RNA1 into a restriction cutting site in certain mammalian expression vectors activates splicing of the subopitmal intron and produces a truncated ORF57 protein.
Collapse
Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, 21702 MD, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, 21702 MD, USA.
| |
Collapse
|
32
|
Abstract
In this article, advances in designing polymeric nanoparticles for targeted cancer gene therapy are reviewed. Characterization and evaluation of biomaterials, targeting ligands, and transcriptional elements are each discussed. Advances in biomaterials have driven improvements to nanoparticle stability and tissue targeting, conjugation of ligands to the surface of polymeric nanoparticles enable binding to specific cancer cells, and the design of transcriptional elements has enabled selective DNA expression specific to the cancer cells. Together, these features have improved the performance of polymeric nanoparticles as targeted non-viral gene delivery vectors to treat cancer. As polymeric nanoparticles can be designed to be biodegradable, non-toxic, and to have reduced immunogenicity and tumorigenicity compared to viral platforms, they have significant potential for clinical use. Results of polymeric gene therapy in clinical trials and future directions for the engineering of nanoparticle systems for targeted cancer gene therapy are also presented.
Collapse
Affiliation(s)
- Jayoung Kim
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David R. Wilson
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Camila G. Zamboni
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jordan J. Green
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
33
|
Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. Mol Ecol 2015; 24:3093-106. [PMID: 25930165 PMCID: PMC4480654 DOI: 10.1111/mec.13221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 02/06/2023]
Abstract
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the ‘edges’ of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.
Collapse
Affiliation(s)
- Stephen J Bush
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Paula X Kover
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| |
Collapse
|
34
|
Cooper AR, Lill GR, Gschweng EH, Kohn DB. Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter. Nucleic Acids Res 2014; 43:682-90. [PMID: 25520191 PMCID: PMC4288199 DOI: 10.1093/nar/gku1312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lentiviral vectors almost universally use heterologous internal promoters to express transgenes. One of the most commonly used promoter fragments is a 1.2-kb sequence from the human ubiquitin C (UBC) gene, encompassing the promoter, some enhancers, first exon, first intron and a small part of the second exon of UBC. Because splicing can occur after transcription of the vector genome during vector production, we investigated whether the intron within the UBC promoter fragment is faithfully transmitted to target cells. Genetic analysis revealed that more than 80% of proviral forms lack the intron of the UBC promoter. The human elongation factor 1 alpha (EEF1A1) promoter fragment intron was not lost during lentiviral packaging, and this difference between the UBC and EEF1A1 promoter introns was conferred by promoter exonic sequences. UBC promoter intron loss caused a 4-fold reduction in transgene expression. Movement of the expression cassette to the opposite strand prevented intron loss and restored full expression. This increase in expression was mostly due to non-classical enhancer activity within the intron, and movement of putative intronic enhancer sequences to multiple promoter-proximal sites actually repressed expression. Reversal of the UBC promoter also prevented intron loss and restored full expression in bidirectional lentiviral vectors.
Collapse
Affiliation(s)
- Aaron R Cooper
- Molecular Biology Interdepartmental PhD Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Georgia R Lill
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric H Gschweng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B Kohn
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA 90095, USA Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
35
|
Poddar S, Eul J, Patzel V. Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing? Comput Struct Biotechnol J 2014; 10:51-7. [PMID: 25210599 PMCID: PMC4151871 DOI: 10.1016/j.csbj.2014.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly transforming 100 kDa super T antigen. Sequences of other viruses including HIV-1 and the human adenovirus type 5 were reported to be involved in heterologous trans-splicing towards cellular or viral sequences but the meaning of these events remains unclear. We computationally and experimentally investigated molecular features associated with viral RNA trans-splicing and identified a common pattern: Viral RNA trans-splicing occurs between strong cryptic or regular viral splice sites and strong regular or cryptic splice sites of the trans-splice partner sequences. The majority of these splice sites are supported by exonic splice enhancers. Splice sites that could compete with the trans-splicing sites for cis-splice reactions are weaker or inexistent. Finally, all but one of the trans-splice reactions seem to be facilitated by one or more complementary binding domains of 11 to 16 nucleotides in length which, however occur with a statistical probability close to one for the given length of the involved sequences. The chimeric RNAs generated via heterologous viral RNA trans-splicing either did not lead to fusion proteins or led to proteins of unknown function. Our data suggest that distinct viral RNAs are highly susceptible to trans-splicing and that heterologous viral trans-splicing, unlike homologous SV40 trans-splicing, represents a chance event.
Collapse
Affiliation(s)
- Sushmita Poddar
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| | - Joachim Eul
- INEIDFO GmbH, Weserstrasse 23, 12045 Berlin, Germany
| | - Volker Patzel
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore
| |
Collapse
|
36
|
Guzeloglu-Kayisli O, Lalioti MD, Babayev E, Torrealday S, Karakaya C, Seli E. Human embryonic poly(A)-binding protein (EPAB) alternative splicing is differentially regulated in human oocytes and embryos. Mol Hum Reprod 2013; 20:59-65. [PMID: 24002949 DOI: 10.1093/molehr/gat061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Oocyte maturation is associated with suppression of transcriptional activity. Consequently, gene expression during oocyte maturation, fertilization and early embryo development, until zygotic genome activation (ZGA) is primarily regulated by translational activation of maternally derived mRNAs. Embryonic poly(A)-binding protein (EPAB) is the predominant poly(A)-binding protein in Xenopus, mouse and human oocytes and early embryos prior to ZGA. EPAB plays a key role in polyadenylation-dependent translational activation of mRNAs by stabilizing polyadenylated mRNAs and by stimulating their translation. Epab-knockout female mice are sterile, fail to generate mature oocytes and display impaired cumulus expansion and ovulation. Consistent with its role during gametogenesis and early embryo development, Xenopus and mouse Epab mRNA is expressed exclusively in oocytes and early embryos, and is undetectable following ZGA or in somatic tissues. Herein, we demonstrate that although EPAB is expressed in human somatic tissues, its transcripts largely consist of an alternatively spliced form lacking the first 58 bp of exon 8, which leads to the formation of a premature stop codon 6 amino acids downstream on exon 8, and omission of the functionally critical poly(A)-binding domain. Moreover, 8-cell and blastocyst stage human embryos also express only the alternatively spliced form of EPAB. On the other hand, the full-length form of EPAB mRNA is exclusively expressed in oocytes. In conclusion, in contrast with the transcriptional regulation in Xenopus and mouse, oocyte- and early embryo-specific expression of EPAB in human is regulated by a post-transcriptional mechanism.
Collapse
Affiliation(s)
- Ozlem Guzeloglu-Kayisli
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 310 Cedar Street, LSOG 304B, New Haven, CT 06520-8063, USA
| | | | | | | | | | | |
Collapse
|
37
|
Corbo C, Orrù S, Salvatore F. SRp20: an overview of its role in human diseases. Biochem Biophys Res Commun 2013; 436:1-5. [PMID: 23685143 DOI: 10.1016/j.bbrc.2013.05.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 10/26/2022]
Abstract
Alternative splicing in mRNA maturation has emerged as a major field of study also because of its implications in various diseases. The SR proteins play an important role in the regulation of this process. Evidence indicates that SRp20 (SFSR3), the smallest member of the SR protein family, is involved in numerous biological processes. Here we review the state-of-the-art of knowledge about the SR proteins, in particular SRp20, in terms of its function and misregulation in human diseases including cancer also in view of its potential as a therapeutic target.
Collapse
|
38
|
Regulation of human papillomavirus gene expression by splicing and polyadenylation. Nat Rev Microbiol 2013; 11:239-51. [DOI: 10.1038/nrmicro2984] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
39
|
Tang YW, Stratton CW. Detection of Viral RNA Splicing in Diagnostic Virology. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2013. [PMCID: PMC7120143 DOI: 10.1007/978-1-4614-3970-7_38] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10065 New York USA
| | - Charles W. Stratton
- Vanderbilt Clinic, Clinical Microbiology Laboratory, Vanderbilt University Medical Center, 22nd Avenue 1301, Nashville, 37232-5310 Tennessee USA
| |
Collapse
|
40
|
Ajiro M, Jia R, Zhang L, Liu X, Zheng ZM. Intron definition and a branch site adenosine at nt 385 control RNA splicing of HPV16 E6*I and E7 expression. PLoS One 2012; 7:e46412. [PMID: 23056301 PMCID: PMC3464268 DOI: 10.1371/journal.pone.0046412] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
HPV16 E6 and E7, two viral oncogenes, are expressed from a single bicistronic pre-mRNA. In this report, we provide the evidence that the bicistronic pre-mRNA intron 1 contains three 5' splice sites (5' ss) and three 3' splice sites (3' ss) normally used in HPV16(+) cervical cancer and its derived cell lines. The choice of two novel alternative 5' ss (nt 221 5' ss and nt 191 5' ss) produces two novel isoforms of E6E7 mRNAs (E6*V and E6*VI). The nt 226 5' ss and nt 409 3' ss is preferentially selected over the other splice sites crossing over the intron to excise a minimal length of the intron in RNA splicing. We identified AACAAAC as the preferred branch point sequence (BPS) and an adenosine at nt 385 (underlined) in the BPS as a branch site to dictate the selection of the nt 409 3' ss for E6*I splicing and E7 expression. Introduction of point mutations into the mapped BPS led to reduced U2 binding to the BPS and thereby inhibition of the second step of E6E7 splicing at the nt 409 3' ss. Importantly, the E6E7 bicistronic RNA with a mutant BPS and inefficient splicing makes little or no E7 and the resulted E6 with mutations of (91)QYNK(94) to (91)PSFW(94) displays attenuate activity on p53 degradation. Together, our data provide structural basis of the E6E7 intron 1 for better understanding of how viral E6 and E7 expression is regulated by alternative RNA splicing. This study elucidates for the first time a mapped branch point in HPV16 genome involved in viral oncogene expression.
Collapse
Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Rong Jia
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lifang Zhang
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Xuefeng Liu
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
41
|
Liu TY, Chen CY, Juan CC, Au LC. Coding region of adiponectin contains a silent intron reactivated by the adjacent intervening sequence of vector. Plasmid 2012; 69:67-71. [PMID: 22982979 DOI: 10.1016/j.plasmid.2012.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 10/27/2022]
Abstract
Precise splicing pre-mRNA into correct mRNA is a tightly orchestrated process involving both cis and trans factors. However, the regulatory mechanism underlying alternative splicing remain elusive. An alternative splicing was revealed by comparing RT-PCR products (cDNA) of human adiponectin gene (ADPN) genes and sequencing the corresponding cDNA recovered from CHO-K1 cells transfected with a pIRES-neo vector carrying the cDNA. We determined that an 88-nt sequence in the original cDNA was missing from the adiponectin mRNA isolated from the transfected cells. After analyzing the flanking sequences and context of the 88-nt fragment, we discovered that it does have a typical intron configuration containing the splicing donor and acceptor, polypyrimidine tract, and branch site. A point mutation at the acceptor site (AG→TG) abolishes this splicing site indicating that it is a bona fide intron. The intron splicing defaulted again when the adjacent intervening sequence (IVS) of pIRES-neo was deleted or adiponectin 3'-UTR was present. We found that 3'-UTR segment contained several splicing silencers and IVS contained high density of splicing enhancers. It explained the reactivation of this silent intron. Our results elicited the possibility that a 3'-UTR-free cDNA may reactivate an otherwise silent intron in the coding region as it is cloned for expression in mammalian cells.
Collapse
Affiliation(s)
- Tzu-Ying Liu
- Department of Physiology, National Yang-Ming University, Taipei 11221, Taiwan, ROC
| | | | | | | |
Collapse
|
42
|
Anderson SL, Liu B, Qiu J, Sturm AJ, Schwartz JA, Peters AJ, Sullivan KA, Rubin BY. Nutraceutical-mediated restoration of wild-type levels of IKBKAP-encoded IKAP protein in familial dysautonomia-derived cells. Mol Nutr Food Res 2012; 56:570-9. [PMID: 22495984 DOI: 10.1002/mnfr.201100670] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SCOPE The reported ability to modulate the production of the wild-type transcript in cells bearing the splice-altering familial dysautonomia (FD)-causing mutation in the IKBKAP gene prompted an evaluation of the impact of commonly consumed nutraceuticals on the splicing of this transcript. METHODS AND RESULTS Screening efforts revealed the ability of the isoflavones, genistein, and daidzein, to impact splicing and increase the production of the wild-type, exon-20-containing, transcript, and the full-length IKBKAP-encoded IΚB kinase complex associated protein(IKAP) in FD-derived cells. Genistein was also found to impact splicing in neuronal cells, a cell type profoundly impacted by FD. The simultaneous exposure of FD-derived cells to genistein and epigallocatechin gallate (EGCG) resulted in the almost exclusive production of the exon-20-containing transcript and the production of wild-type amounts of IKAP protein. CONCLUSION This study represents the first demonstration that the isoflavones, genistein and daidzein, possess splice-altering capabilities and that simultaneous treatment with genistein and EGCG reverses the splice-altering impact of the FD-causing mutation. These findings support the clinical evaluation of the therapeutic impact of the combined administration of these two commonly consumed nutraceuticals on this patient population and suggest a broader evaluation of the impact of these nutraceuticals on the in vivo RNA splicing process.
Collapse
Affiliation(s)
- Sylvia L Anderson
- Laboratory for Familial Dysautonomia Research, Department of Biological Sciences, Fordham University, Bronx, NY10458, USA
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Wong J, Garner B, Halliday GM, Kwok JBJ. Srp20 regulates TrkB pre-mRNA splicing to generate TrkB-Shc transcripts with implications for Alzheimer's disease. J Neurochem 2012; 123:159-71. [PMID: 22788679 DOI: 10.1111/j.1471-4159.2012.07873.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Previously, we reported elevated levels of the neuron-specific tropomyosin receptor kinase B (TrkB) transcript, TrkB- sarc homology containing (Shc) in the hippocampus of Alzheimer's disease (AD) brains. In this study, we determined how TrkB-Shc transcripts are increased in AD. Utilizing a TrkB minigene transiently transfected into SHSY5Y cells, we found increased exon 19 inclusion in TrkB minigene transcripts (to generate TrkB-Shc) following cellular exposure to amyloid beta 1-42 (Αβ(42)). As this suggested altered TrkB pre-mRNA splicing in AD, we conducted an in silico screening for putative splice regulatory protein-binding sites in the intron/exon splice regulatory regions of exons 18 and 19 of the TrkB gene and then assessed their gene expression profiles using a microarray database of control/AD post-mortem human hippocampal brain tissue. We found significant changes in serine/arginine protein 20 (Srp20) gene expression in AD cases and confirmed this using a second cohort of control/AD. In vitro, we found increased Srp20 mRNA levels in SHSY5Y cells treated with Αβ(42) fibrils. Moreover, Srp20 over-expression was found to increase exon 19 inclusion in TrkB minigene transcripts and ratio of endogenous TrkB-Shc:TrkB-TK+ mRNA expression. Conversely, Srp20 expression knockdown produced the opposite effects. Our findings suggest that dysregulation of factors regulating TrkB pre-mRNA splicing may contribute to gene expression changes that occur in AD.
Collapse
Affiliation(s)
- Jenny Wong
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia.
| | | | | | | |
Collapse
|
44
|
Tang Y, Horikawa I, Ajiro M, Robles AI, Fujita K, Mondal AM, Stauffer JK, Zheng ZM, Harris CC. Downregulation of splicing factor SRSF3 induces p53β, an alternatively spliced isoform of p53 that promotes cellular senescence. Oncogene 2012; 32:2792-8. [PMID: 22777358 DOI: 10.1038/onc.2012.288] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most human pre-mRNA transcripts are alternatively spliced, but the significance and fine-tuning of alternative splicing in different biological processes is only starting to be understood. SRSF3 (SRp20) is a member of a highly conserved family of splicing factors that have critical roles in key biological processes, including tumor progression. Here, we show that SRSF3 regulates cellular senescence, a p53-mediated process to suppress tumorigenesis, through TP53 alternative splicing. Downregulation of SRSF3 was observed in normal human fibroblasts undergoing replicative senescence, and was associated with the upregulation of p53β, an alternatively spliced isoform of p53 that promotes p53-mediated senescence. Knockdown of SRSF3 by short interfering RNA (siRNA) in early-passage fibroblasts induced senescence, which was associated with elevated expression of p53β at mRNA and protein levels. Knockdown of p53 partially rescued SRSF3-knockdown-induced senescence, suggesting that SRSF3 acts on p53-mediated cellular senescence. RNA pulldown assays demonstrated that SRSF3 binds to an alternatively spliced exon uniquely included in p53β mRNA through the consensus SRSF3-binding sequences. RNA crosslinking and immunoprecipitation assays (CLIP) also showed that SRSF3 in vivo binds to endogenous p53 pre-mRNA at the region containing the p53β-unique exon. Splicing assays using a transfected TP53 minigene in combination with siRNA knockdown of SRSF3 showed that SRSF3 functions to inhibit the inclusion of the p53β-unique exon in splicing of p53 pre-mRNA. These data suggest that downregulation of SRSF3 represents an endogenous mechanism for cellular senescence that directly regulates the TP53 alternative splicing to generate p53β. This study uncovers the role for general splicing machinery in tumorigenesis, and suggests that SRSF3 is a direct regulator of p53.
Collapse
Affiliation(s)
- Y Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4258, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Ding S, Shi J, Qian W, Iqbal K, Grundke-Iqbal I, Gong CX, Liu F. Regulation of alternative splicing of tau exon 10 by 9G8 and Dyrk1A. Neurobiol Aging 2012; 33:1389-99. [PMID: 21215488 PMCID: PMC3085640 DOI: 10.1016/j.neurobiolaging.2010.11.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 08/23/2010] [Accepted: 11/21/2010] [Indexed: 12/19/2022]
Abstract
Adult human brain expresses 6 isoforms of tau protein as a result of alternative splicing. Alternative splicing of exon 10 (E10) leads to tau isoforms containing either 3 (3R-tau) or 4 (4R-tau) microtubule-binding repeats. Imbalance in the 3R-tau/4R-tau ratio causes neurofibrillary degeneration and dementia. Here, we demonstrated that the dual-specificity tyrosine phosphorylation-regulated kinase 1A (Dyrk1A) interacted with the splicing factor 9G8 and phosphorylated it at several serine residues. Dyrk1A itself promoted tau E10 inclusion, whereas 9G8 inhibited E10 inclusion, and these actions were variable depending on the cell types. Coexpression of Dyrk1A and 9G8 led to their translocation from the nucleus to the cytoplasm and suppressed their ability to regulate tau exon 10 splicing. This action is probably due to their interaction-induced translocation from the nucleus, where the regulation of tau E10 splicing occurs, to the cytoplasm. These findings provide novel insights into the molecular mechanism of the regulation of tau E10 splicing and further our understanding of the neurodegeneration caused by dysregulation of tau E10 splicing.
Collapse
Affiliation(s)
- Shaohong Ding
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Jianhua Shi
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
| | - Wei Qian
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
| | - Inge Grundke-Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
| | - Cheng-Xin Gong
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
| | - Fei Liu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
| |
Collapse
|
46
|
Bowles KR, Brooks SP, Dunnett SB, Jones L. Gene expression and behaviour in mouse models of HD. Brain Res Bull 2012; 88:276-84. [PMID: 21854837 DOI: 10.1016/j.brainresbull.2011.07.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/27/2011] [Accepted: 07/31/2011] [Indexed: 01/09/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease, resulting in expansion of the CAG repeat in exon 1 of the HTT gene. The resulting mutant huntingtin protein has been implicated in the disruption of a variety of cellular functions, including transcription. Mouse models of HD have been central to the development of our understanding of gene expression changes in this disease, and are now beginning to elucidate the relationship between gene expression and behaviour. Here, we review current mouse models of HD and their characterisation in terms of gene expression. In addition, we look at how this can inform behaviours observed in mouse models of disease. The relationship between gene expression and behaviour in mouse models of HD is important, as this will further our knowledge of disease progression and its underlying molecular events, highlight new treatment targets, and potentially provide new biomarkers for therapeutic trials.
Collapse
Affiliation(s)
- K R Bowles
- Department of Psychological Medicine, MRC centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Wales, UK
| | | | | | | |
Collapse
|
47
|
Zhou B, Margariti A, Zeng L, Habi O, Xiao Q, Martin D, Wang G, Hu Y, Wang X, Xu Q. Splicing of histone deacetylase 7 modulates smooth muscle cell proliferation and neointima formation through nuclear β-catenin translocation. Arterioscler Thromb Vasc Biol 2012; 31:2676-84. [PMID: 21836063 DOI: 10.1161/atvbaha.111.230888] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Vascular smooth muscle cell (SMC) proliferation has an indispensable role in the pathogenesis of vascular disease, but the mechanism is not fully elucidated. The epigenetic enzyme histone deacetylase 7 (HDAC7) is involved in endothelial homeostasis and SMC differentiation and could have a role in SMC proliferation. In this study, we sought to examine the effect of 2 HDAC7 isoforms on SMC proliferation and neointima formation. METHODS AND RESULTS We demonstrated that overexpression of unspliced HDAC7 (HDAC7u) could suppress SMC proliferation through downregulation of cyclin D1 and cell cycle arrest, whereas spliced HDAC7 (HDAC7s) could not. Small interfering RNA (siRNA)-mediated knockdown of HDAC7 increased SMC proliferation and induced nuclear translocation of β-catenin. Additional experiments showed that only HDAC7u could bind to β-catenin and retain it in the cytoplasm. Reporter gene assay and reverse transcription polymerase chain reaction revealed a reduction of β-catenin activity in cells overexpressing HDAC7u but not HDAC7s. Deletion studies indicated that the C-terminal region of HDAC7u is responsible for the interaction with β-catenin. However, the addition of amino acids to the N terminus of HDAC7u disrupted the binding, further strengthening our hypothesis that HDAC7s does not interact with β-catenin. The growth factor platelet-derived growth factor-BB increased the splicing of HDAC7 while simultaneously decreasing the expression of HDAC7u. Importantly, in an animal model of femoral artery wire injury, we demonstrated that knockdown of HDAC7 by siRNA aggravates neointima formation in comparison with control siRNA. CONCLUSION Our findings demonstrate that splicing of HDAC7 modulates SMC proliferation and neointima formation through β-catenin nuclear translocation, which provides a potential therapeutic target in vascular disease.
Collapse
Affiliation(s)
- Boda Zhou
- Department of Physiology, Peking University, Beijing, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Drosophila Dynein intermediate chain gene, Dic61B, is required for spermatogenesis. PLoS One 2011; 6:e27822. [PMID: 22145020 PMCID: PMC3228723 DOI: 10.1371/journal.pone.0027822] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 10/26/2011] [Indexed: 11/19/2022] Open
Abstract
This study reports the identification and characterization of a novel gene, Dic61B, required for male fertility in Drosophila. Complementation mapping of a novel male sterile mutation, ms21, isolated in our lab revealed it to be allelic to CG7051 at 61B1 cytogenetic region, since two piggyBac insertion alleles, CG7051(c05439) and CG7051(f07138) failed to complement. CG7051 putatively encodes a Dynein intermediate chain. All three mutants, ms21, CG7051(c05439) and CG7051(f07138), exhibited absolute recessive male sterility with abnormally coiled sperm axonemes causing faulty sperm individualization as revealed by Phalloidin staining in Don Juan-GFP background. Sequencing of PCR amplicons uncovered two point mutations in ms21 allele and confirmed the piggyBac insertions in CG7051(c05439) and CG7051(f07138) alleles to be in 5'UTR and 4(th) exon of CG7051 respectively, excision of which reverted the male sterility. In situ hybridization to polytene chromosomes demonstrated CG7051 to be a single copy gene. RT-PCR of testis RNA revealed defective splicing of the CG7051 transcripts in mutants. Interestingly, expression of cytoplasmic dynein intermediate chain, α, β, γ tubulins and α-spectrin was normal in mutants while ultra structural studies revealed defects in the assembly of sperm axonemes. Bioinformatics further highlighted the homology of CG7051 to axonemal dynein intermediate chain of various organisms, including DNAI1 of humans, mutations in which lead to male sterility due to immotile sperms. Based on these observations we conclude that CG7051 encodes a novel axonemal dynein intermediate chain essential for male fertility in Drosophila and rename it as Dic61B. This is the first axonemal Dic gene of Drosophila to be characterized at molecular level and shown to be required for spermatogenesis.
Collapse
|
49
|
Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation. PLoS One 2011; 6:e25666. [PMID: 21991330 PMCID: PMC3185004 DOI: 10.1371/journal.pone.0025666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 09/08/2011] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The rapid increase in the availability of genome information has created considerable demand for both comparative and ab initio predictive bioinformatic analyses. The biology laid bare in the genomes of many organisms is often novel, presenting new challenges for bioinformatic interrogation. A paradigm for this is the collected genomes of the kinetoplastid parasites, a group which includes Trypanosoma brucei the causative agent of human African trypanosomiasis. These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes. METHODOLOGY/PRINCIPLE FINDINGS Here we utilise a Bayesian approach to identify local changes in nucleotide composition in the genome of T. brucei. We show that there are several elements which are found at the starts and ends of multicopy gene arrays and that there are compositional elements that are common to all intergenic regions. We also show that there is a composition-inversion element that occurs at the position of the trans-splice site. CONCLUSIONS/SIGNIFICANCE The nature of the elements discovered reinforces the hypothesis that context dependant RNA secondary structure has an important influence on gene expression regulation in Trypanosoma brucei.
Collapse
|
50
|
Construction of a full transcription map of human papillomavirus type 18 during productive viral infection. J Virol 2011; 85:8080-92. [PMID: 21680515 DOI: 10.1128/jvi.00670-11] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human papillomavirus type 18 (HPV18) is the second most common oncogenic HPV genotype, responsible for ∼15% of cervical cancers worldwide. In this study, we constructed a full HPV18 transcription map using HPV18-infected raft tissues derived from primary human vaginal or foreskin keratinocytes. By using 5' rapid amplification of cDNA ends (RACE), we mapped two HPV18 transcription start sites (TSS) for early transcripts at nucleotide (nt) 55 and nt 102 and the HPV18 late TSS frequently at nt 811, 765, or 829 within the E7 open reading frame (ORF) of the virus genome. HPV18 polyadenylation cleavage sites for early and late transcripts were mapped to nt 4270 and mainly to nt 7299 or 7307, respectively, by using 3' RACE. Although all early transcripts were cleaved exclusively at a single cleavage site, HPV18 late transcripts displayed the heterogeneity of 3' ends, with multiple minor cleavage sites for late RNA polyadenylation. HPV18 splice sites/splice junctions for both early and late transcripts were identified by 5' RACE and primer walking techniques. Five 5' splice sites (donor sites) and six 3' splice sites (acceptor sites) that are highly conserved in other papillomaviruses were identified in the HPV18 genome. HPV18 L1 mRNA translates a L1 protein of 507 amino acids (aa), smaller than the 568 aa residues previously predicted. Collectively, a full HPV18 transcription map constructed from this report will lead us to further understand HPV18 gene expression and virus oncogenesis.
Collapse
|