1
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Liu L, Sun P, Zhang W. A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics. Brief Bioinform 2024; 25:bbae376. [PMID: 39082645 PMCID: PMC11289681 DOI: 10.1093/bib/bbae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/26/2024] [Accepted: 07/17/2024] [Indexed: 08/03/2024] Open
Abstract
3'UTR-APAs have been extensively studied, but intronic polyadenylations (IPAs) remain largely unexplored. We characterized the profiles of 22 260 IPAs in 9679 patient samples across 32 cancer types from the Cancer Genome Atlas cohort. By comparing tumor and paired normal tissues, we identified 180 ~ 4645 dysregulated IPAs in 132 ~ 2249 genes in each of 690 patient tumors from 22 cancer types that showed consistent patterns within individual cancer types. We selected 2741 genes that showed consistently patterns across cancer types, including 1834 pan-cancer tumor-enriched and 907 tumor-depleted IPA genes; the former were amply represented in the functional pathways such as deoxyribonucleic acid damage repair. Expression of IPA isoforms was associated with tumor mutation burden and patient characteristics (e.g. sex, race, cancer stages, and subtypes) in cancer-specific and feature-specific manners, and could be a more accurate prognostic marker than gene expression (summary of all isoforms). In summary, our study reveals the roles and the clinical relevance of tumor-associated IPAs.
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Affiliation(s)
- Liang Liu
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
- Center for Cancer Genomics and Precision Oncology, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Medical Center Blvd, Winston-Salem, NC 27157, United States
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157, United States
- Center for Cancer Genomics and Precision Oncology, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Medical Center Blvd, Winston-Salem, NC 27157, United States
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2
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Nahalka J. 1-L Transcription of SARS-CoV-2 Spike Protein S1 Subunit. Int J Mol Sci 2024; 25:4440. [PMID: 38674024 PMCID: PMC11049929 DOI: 10.3390/ijms25084440] [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: 02/29/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic prompted rapid research on SARS-CoV-2 pathogenicity. Consequently, new data can be used to advance the molecular understanding of SARS-CoV-2 infection. The present bioinformatics study discusses the "spikeopathy" at the molecular level and focuses on the possible post-transcriptional regulation of the SARS-CoV-2 spike protein S1 subunit in the host cell/tissue. A theoretical protein-RNA recognition code was used to check the compatibility of the SARS-CoV-2 spike protein S1 subunit with mRNAs in the human transcriptome (1-L transcription). The principle for this method is elucidated on the defined RNA binding protein GEMIN5 (gem nuclear organelle-associated protein 5) and RNU2-1 (U2 spliceosomal RNA). Using the method described here, it was shown that 45% of the genes/proteins identified by 1-L transcription of the SARS-CoV-2 spike protein S1 subunit are directly linked to COVID-19, 39% are indirectly linked to COVID-19, and 16% cannot currently be associated with COVID-19. The identified genes/proteins are associated with stroke, diabetes, and cardiac injury.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia;
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
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3
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Yuemaierabola A, Guo J, Sun L, Yeerkenbieke B, Liu F, Ye D, Zhai X, Guo W, Cao Y. Comprehensive analysis of CPSF4-related alternative splice genes in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:13955-13971. [PMID: 37542549 PMCID: PMC10590311 DOI: 10.1007/s00432-023-05178-z] [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: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND An important stage in controlling gene expression is RNA alternative splicing (AS), and aberrant AS can trigger the development and spread of malignancies, including hepatocellular carcinoma (HCC). A crucial component of AS is cleavage and polyadenylation-specific factor 4 (CPSF4), a component of the CPSF complex, but it is unclear how CPSF4-related AS molecules describe immune cell infiltration in the total tumor microenvironment (TME). METHODS Using RNA-sequencing data and clinical data from TCGA-LIHC from the Cancer Genome Atlas (TCGA) database, the AS genes with differential expression were found. The univariate Cox analysis, KM analysis, and Spearman analysis were used to identify the AS genes related to prognosis. Screening of key AS genes that are highly correlated with CPSF4. Key genes were screened using Cox regression analysis and stepwise regression analysis, and prognosis prediction models and the topography of TME cell infiltration were thoroughly analyzed. RESULTS A model consisting of seven AS genes (STMN1, CLSPN, MDK, RNFT2, PRR11, RNF157, GHR) was constructed that was aimed to predict prognostic condition. The outcomes of the HCC samples in the high-risk group were considerably worse than those in the lower risk group (p < 0.0001), and different risk patient groups were formed. According to the calibration curves and the area under the ROC curve (AUC) values for survival at 1, 2, and 3 years, the clinical nomogram performs well in predicting survival in HCC patients. These values were 0.76, 0.70, and 0.69, respectively. Moreover, prognostic signature was markedly related to immune infiltration and immune checkpoint genes expression. CONCLUSION By shedding light on the function of CPSF4 and the seven AS genes in the formation and progression of HCC, this research analysis contributes to the development of more useful prognostic, diagnostic, and possibly therapeutic biomarkers.
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Affiliation(s)
- Anwaier Yuemaierabola
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Jun Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Lili Sun
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Buerlan Yeerkenbieke
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Fuzhong Liu
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Dilinaer Ye
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Xiaoyi Zhai
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Wenjia Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China.
| | - Yan Cao
- Cancer Hospital of Xinjiang Uygur Autonomous Region (Affiliated Cancer Hospital of Xinjiang Medical University), Urumqi, 830011, China.
- Nursing School of Xinjiang Medical University, Urumqi, 830011, China.
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4
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Ntini E, Budach S, Vang Ørom UA, Marsico A. Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. Cell Syst 2023; 14:906-922.e6. [PMID: 37857083 DOI: 10.1016/j.cels.2023.09.005] [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: 10/30/2022] [Revised: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.
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Affiliation(s)
- Evgenia Ntini
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Institute of Molecular Biology and Biotechnology, IMBB-FORTH, 70013 Heraklio, Greece.
| | - Stefan Budach
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany
| | - Ulf A Vang Ørom
- Aarhus University, Department of Molecular Biology and Genetics, 8000 Aarhus, Denmark
| | - Annalisa Marsico
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Computational Health Center, Helmholtz Center Munich, Munich, Germany.
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5
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Huang Y, Ji H, Dong J, Wang X, He Z, Cheng Z, Zhu Q. CPSF3 Promotes Pre-mRNA Splicing and Prevents CircRNA Cyclization in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:4057. [PMID: 37627085 PMCID: PMC10452738 DOI: 10.3390/cancers15164057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
CircRNAs are crucial in tumorigenesis and metastasis, and are comprehensively downregulated in hepatocellular carcinoma (HCC). Previous studies demonstrated that the back-splicing of circRNAs was closely related to 3'-end splicing. As a core executor of 3'-end cleavage, we hypothesized that CPSF3 modulated circRNA circularization. Clinical data were analyzed to establish the prognostic correlations. Cytological experiments were performed to determine the role of CPSF3 in HCC. A fluorescent reporter was employed to explore the back-splicing mechanism. The circRNAs regulated by CPSF3 were screened by RNA-seq and validated by PCR, and changes in downstream pathways were explored by molecular experiments. Finally, the safety and efficacy of the CPSF3 inhibitor JTE-607 were verified both in vitro and in vivo. The results showed that CPSF3 was highly expressed in HCC cells, promoting their proliferation and migration, and that a high CPSF3 level was predictive of a poor prognosis. A mechanistic study revealed that CPSF3 enhanced RNA cleavage, thereby reducing circRNAs, and increasing linear mRNAs. Furthermore, inhibition of CPSF3 by JET-607 suppressed the proliferation of HCC cells. Our findings indicate that the increase of CPSF3 in HCC promotes the shift of pre-mRNA from circRNA to linear mRNA, leading to uncontrolled cell proliferation. JTE-607 exerted a therapeutic effect on HCC by blocking CPSF3.
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Affiliation(s)
- Ying Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Haofei Ji
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Jiani Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Xueying Wang
- China National Intellectual Property Administration, Beijing 100088, China;
| | - Zhilin He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
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6
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Vlasenok M, Margasyuk S, Pervouchine DD. Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation. NAR Genom Bioinform 2023; 5:lqad051. [PMID: 37260513 PMCID: PMC10227441 DOI: 10.1093/nargab/lqad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are two crucial steps in the post-transcriptional regulation of eukaryotic gene expression. Protocols capturing and sequencing RNA 3'-ends have uncovered widespread intronic polyadenylation (IPA) in normal and disease conditions, where it is currently attributed to stochastic variations in the pre-mRNA processing. Here, we took advantage of the massive amount of RNA-seq data generated by the Genotype Tissue Expression project (GTEx) to simultaneously identify and match tissue-specific expression of intronic polyadenylation sites with tissue-specific splicing. A combination of computational methods including the analysis of short reads with non-templated adenines revealed that APA events are more abundant in introns than in exons. While the rate of IPA in composite terminal exons and skipped terminal exons expectedly correlates with splicing, we observed a considerable fraction of IPA events that lack AS support and attributed them to spliced polyadenylated introns (SPI). We hypothesize that SPIs represent transient byproducts of a dynamic coupling between APA and AS, in which the spliceosome removes the intron while it is being cleaved and polyadenylated. These findings indicate that cotranscriptional pre-mRNA splicing could serve as a rescue mechanism to suppress premature transcription termination at intronic polyadenylation sites.
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Affiliation(s)
- Maria Vlasenok
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Sergey Margasyuk
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Dmitri D Pervouchine
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
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7
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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8
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CPSF6-mediated XBP1 3'UTR shortening attenuates cisplatin-induced ER stress and elevates chemo-resistance in lung adenocarcinoma. Drug Resist Updat 2023; 68:100933. [PMID: 36821972 DOI: 10.1016/j.drup.2023.100933] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/28/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Alternative polyadenylation (APA) is a widespread mechanism generating RNA molecules with alternative 3' ends. Herein, we discovered that TargetScan includes a novel XBP1 transcript with a longer 3' untranslated region (UTR) (XBP1-UL) than that included in NCBI. XBP1-UL exhibited a lowered level in blood samples from lung adenocarcinoma (LUAD) patients and in those after DDP treatment. Consistently, XBP1-UL was reduced in A549 cells compared to normal BEAS-2B cells, as well as in DDP-treated/resistant A549 cells relative to controls. Moreover, due to decreased usage of the distal polyadenylation site (PAS) in 3'UTR, XBP1-UL level was lowered in A549 cells and decreased further in DDP-resistant A549 (A549/DDP) cells. Importantly, use of the distal PAS (dPAS) and XBP1-UL level were gradually reduced in A549 cells under increasing concentrations of DDP, which was attributed to DDP-induced endoplasmic reticulum (ER) stress. Furthermore, XBP1 transcripts with shorter 3'UTR (XBP1-US) were more stable and presented stronger potentiation on DDP resistance. The choice of proximal PAS (pPAS) was attributed to CPSF6 elevation, which was caused by BRCA1-distrupted R-loop accumulation in CPSF6 5'end. DDP-induced nuclear LINC00221 also facilitated CPSF6-induced pPAS choice in the pre-XBP1 3'end. Finally, we found that unlike the unspliced XBP1 protein (XBP1-u), the spliced form XBP1-s retarded p53 degradation to facilitate DNA damage repair of LUAD cells. The current study provides new insights into tumor progression and DDP resistance in LUAD, which may contribute to improved LUAD treatment.
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9
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Alles J, Legnini I, Pacelli M, Rajewsky N. Rapid nuclear deadenylation of mammalian messenger RNA. iScience 2022; 26:105878. [PMID: 36691625 PMCID: PMC9860345 DOI: 10.1016/j.isci.2022.105878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened after transcription. Our data suggests that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs retain long poly(A) tails. Modeling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggests that nuclear deadenylation might be a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
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Affiliation(s)
- Jonathan Alles
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany
| | - Ivano Legnini
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Maddalena Pacelli
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany,Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany,Corresponding author
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10
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Peng S, Guo D, Guo Y, Zhao H, Mei J, Han Y, Guan R, Wang T, Song T, Sun K, Liu Y, Mao T, Chang H, Xue J, Cai Y, Chen D, Wang S. CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 is an RNA-binding protein controlling plant immunity via an RNA processing complex. THE PLANT CELL 2022; 34:1724-1744. [PMID: 35137215 PMCID: PMC9048907 DOI: 10.1093/plcell/koac037] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/27/2022] [Indexed: 06/01/2023]
Abstract
Plant innate immunity is capable of combating diverse and ever evolving pathogens. The plasticity of innate immunity could be boosted by RNA processing. Arabidopsis thaliana CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 (CPR5), a key negative immune regulator, is a component of the nuclear pore complex. Here we further identified CPR5 as a component of RNA processing complexes. Through genetic screening, we found that RNA splicing activator NineTeen Complex and RNA polyadenylation factor CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, coordinately function downstream of CPR5 to activate plant immunity. CPR5 and these two regulators form a complex that is localized in nuclear speckles, an RNA processing organelle. Intriguingly, we found that CPR5 is an RNA-binding protein belonging to the Transformer 2 (Tra2) subfamily of the serine/arginine-rich family. The RNA recognition motif of CPR5 protein binds the Tra2-targeted RNA sequence in vitro and is functionally replaceable by those of Tra2 subfamily proteins. In planta, it binds RNAs of CPR5-regulated alternatively spliced genes (ASGs) identified by RNA-seq. ARGONAUTE 1 (AGO1) is one of the ASGs and, consistent with this, the ago1 mutant suppresses the cpr5 phenotype. These findings reveal that CPR5 is an RNA-binding protein linking RNA processing with plant immunity.
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Affiliation(s)
| | | | | | - Heyu Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jun Mei
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yakun Han
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Rui Guan
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tianhua Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Teng Song
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Keke Sun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yunhan Liu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ting Mao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Huan Chang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingshi Xue
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Hubei, Wuhan 430075, China
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11
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Vijayakumar A, Park A, Steitz JA. Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells. Front Immunol 2022; 13:828665. [PMID: 35222412 PMCID: PMC8866245 DOI: 10.3389/fimmu.2022.828665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic mRNA 3´-end processing is a multi-step process beginning with pre-mRNA transcript cleavage followed by poly(A) tail addition. Closely coupled to transcription termination, 3´-end processing is a critical step in the regulation of gene expression, and disruption of 3´-end processing is known to affect mature mRNA levels. Various viral proteins interfere with the 3´-end processing machinery, causing read-through transcription and altered levels of mature transcripts through inhibition of cleavage and polyadenylation. Thus, disruption of 3´-end processing contributes to widespread host shutoff, including suppression of the antiviral response. Additionally, observed features of read-through transcripts such as decreased polyadenylation, nuclear retention, and decreased translation suggest that viruses may utilize these mechanisms to modulate host protein production and dominate cellular machinery. The degree to which the effects of read-through transcript production are harnessed by viruses and host cells remains unclear, but existing research highlights the importance of host 3´-end processing modulation during viral infection.
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Affiliation(s)
- Aarthi Vijayakumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Annsea Park
- Department of Immunobiology, Yale University, New Haven, CT, United States
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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12
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CPSF4 regulates circRNA formation and microRNA mediated gene silencing in hepatocellular carcinoma. Oncogene 2021; 40:4338-4351. [PMID: 34103682 DOI: 10.1038/s41388-021-01867-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 11/08/2022]
Abstract
CircRNAs play essential roles in various physiological processes and involves in many diseases, in particular cancer. Global downregulation of circRNA expression has been observed in hepatocellular carcinoma (HCC) in many studies. Previous studies revealed that the pre-mRNA 3' end processing complex participates in circRNA cyclization and plays an important role in HCC tumorigenesis. Therefore, we explored the role of CPSF4, for 3' end formation and cleavage, in circRNA formation. Clinical research has shown that CPSF4 expression is upregulated in HCC and that high expression of CPSF4 is associated with poor prognosis in HCC patients. Mechanistic studies have demonstrated that CPSF4 reduces the levels of circRNAs, which possess a polyadenylation signal sequence and this decrease in circRNAs reduces the accumulation of miRNA and disrupts the miRNA-mediated gene silencing in HCC. Experiments in cell culture and xenograft mouse models showed that CPSF4 promotes the proliferation of HCC cells and enhances tumorigenicity. Moreover, CPSF4 antagonizes the tumor suppressor effect of its downstream circRNA in HCC. In summary, CPSF4 acts as an oncogene in HCC through circRNA inhibition and disruption of miRNA-mediated gene silencing.
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Li N, Jiang S, Fu R, Lv J, Yao J, Mai J, Hua X, Chen H, Liu J, Lu M. Cleavage and polyadenylation-specific factor 3 induces cell cycle arrest via PI3K/Akt/GSK-3β signaling pathways and predicts a negative prognosis in hepatocellular carcinoma. Biomark Med 2021; 15:347-358. [PMID: 33666519 DOI: 10.2217/bmm-2021-0039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Recent studies have shown that cleavage and polyadenylation-specific factor 3 (CPSF3) is a promising antitumor therapeutic target, but its potential role in hepatocellular carcinoma (HCC) has not been reported. Materials & methods: We explored the expression pattern of CPSF3 in HCC through bioinformatics analysis, quantitative polymerase chain reaction (qPCR) and western blot. The potential role of CPSF3 as a biomarker for HCC was evaluated by Kaplan-Meier analysis. Next, changes in HCC cell lines in the CPSF3 knockdown model group and the control group were assessed by Cell Counting Kit-8, clonal formation, flow cytometry and EdU staining. Western blot detected changes in protein levels of the PI3K/Akt/GSK-3β axis of two HCC cell lines in the knockdown group and the control group. Results: The results showed that the transcription and protein levels of CPSF3 were significantly higher in HCC tissues than in adjacent normal tissues (p < 0.05). The HCC cohort with increased expression of CPSF3 is associated with advanced stage and differentiation and predicts poorer prognosis (p < 0.05). CPSF3 knockdown significantly inhibited proliferation and clone formation of HepG2 and SMMC-7721 cell lines. Flow cytometry analysis showed G1-S cell cycle arrest in the CPSF3 knockdown group, and the results of EdU staining were consistent with this. Compared with the control group, p-Akt and cyclin D1 were decreased, and GSK-3β was increased in the knockdown group. Conclusion: CPSF3 may be a potential diagnostic biomarker and candidate therapeutic target for HCC.
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Affiliation(s)
- Ning Li
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Shaotao Jiang
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Rongdang Fu
- Department of Hepatic Surgery, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, 528000, China
| | - Jin Lv
- Department of Pathology, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, 528000, China
| | - Jiyou Yao
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Jialuo Mai
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Xuefeng Hua
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Huan Chen
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Jie Liu
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Minqiang Lu
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
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Ashraf U, Benoit-Pilven C, Navratil V, Ligneau C, Fournier G, Munier S, Sismeiro O, Coppée JY, Lacroix V, Naffakh N. Influenza virus infection induces widespread alterations of host cell splicing. NAR Genom Bioinform 2020; 2:lqaa095. [PMID: 33575639 PMCID: PMC7680258 DOI: 10.1093/nargab/lqaa095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/24/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).
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Affiliation(s)
- Usama Ashraf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 75013 Paris, France
| | - Clara Benoit-Pilven
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, 69675 Bron, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 69622 Villeurbanne, France
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, 91057 Évry, France
| | - Cécile Ligneau
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Guillaume Fournier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Sandie Munier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Vincent Lacroix
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
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15
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Price AM, Hayer KE, McIntyre ABR, Gokhale NS, Abebe JS, Della Fera AN, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Direct RNA sequencing reveals m 6A modifications on adenovirus RNA are necessary for efficient splicing. Nat Commun 2020; 11:6016. [PMID: 33243990 PMCID: PMC7691994 DOI: 10.1038/s41467-020-19787-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, 10065, USA
- Department of Molecular Life Sciences, University of Zurich, 8006, Zurich, Switzerland
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Immunology, University of Washington, Seattle, WA, 98115, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Biological Sciences Graduate Group, University of Maryland, College Park, MD, 20742, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10017, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA.
| | - Matthew D Weitzman
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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16
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Jia Q, Nie H, Yu P, Xie B, Wang C, Yang F, Wei G, Ni T. HNRNPA1-mediated 3' UTR length changes of HN1 contributes to cancer- and senescence-associated phenotypes. Aging (Albany NY) 2020; 11:4407-4437. [PMID: 31257225 PMCID: PMC6660030 DOI: 10.18632/aging.102060] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/24/2019] [Indexed: 01/10/2023]
Abstract
Cellular senescence has been regarded as a mechanism of tumor suppression. Studying the regulation of gene expression at various levels in cell senescence will shed light on cancer therapy. Alternative polyadenylation (APA) regulates gene expression by altering 3′ untranslated regions (3′ UTR) and plays important roles in diverse biological processes. However, whether APA of a specific gene functions in both cancer and senescence remains unclear. Here, we discovered that 3′ UTR of HN1 (or JPT1) showed shortening in cancers and lengthening in senescence, correlated well with its high expression in cancer cells and low expression in senescent cells, respectively. HN1 transcripts with longer 3′ UTR were less stable and produced less protein. Down-regulation of HN1 induced senescence-associated phenotypes in both normal and cancer cells. Patients with higher HN1 expression had lower survival rates in various carcinomas. Interestingly, down-regulating the splicing factor HNRNPA1 induced 3′ UTR lengthening of HN1 and senescence-associated phenotypes, which could be partially reversed by overexpressing HN1. Together, we revealed for the first time that HNRNPA1-mediated APA of HN1 contributed to cancer- and senescence-related phenotypes. Given senescence is a cancer prevention mechanism, our discovery indicates the HNRNPA1-HN1 axis as a potential target for cancer treatment.
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Affiliation(s)
- Qi Jia
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
| | - Peng Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Baiyun Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, P.R. China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
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17
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Tamaddon M, Shokri G, Hosseini Rad SMA, Rad I, Emami Razavi À, Kouhkan F. Involved microRNAs in alternative polyadenylation intervene in breast cancer via regulation of cleavage factor "CFIm25". Sci Rep 2020; 10:11608. [PMID: 32665581 PMCID: PMC7360588 DOI: 10.1038/s41598-020-68406-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 06/24/2020] [Indexed: 12/22/2022] Open
Abstract
Cleavage factor “CFIm25”, as a key repressor at proximal poly (A) site, negatively correlates to cell proliferation and tumorigenicity in various cancers. Hence, understanding CFIm25 mechanism of action in breast cancer would be a great benefit. To this aim four steps were designed. First, potential miRNAs that target 3′-UTR of CFIm25 mRNA, retrieved from Targetscan web server. Second, screened miRNAs were profiled in 100 breast cancer and 100 normal adjacent samples. Third, miRNAs that their expression was inversely correlated to the CFIm25, overexpressed in MDA-MB-231 cell line, and their effect on proliferation and migration monitored via MTT and wound healing assays, respectively. Fourth, interaction of miRNAs of interest with 3′-UTR of CFIm25 confirmed via luciferase assay and western blot. Our results indicate that CFIm25 considerably down-regulates in human breast cancer tissue. qRT-PCR assay, luciferase test, and western blotting confirm that CFIm25 itself could be directly regulated by oncomiRs such as miR-23, -24, -27, -135, -182 and -374. Besides, according to MTT and wound healing assays of cell lines, CFIm25 knockdown intensifies cell growth, proliferation and migration. Our results also confirm indirect impact of CFIm25 on regulation of mRNA’s 3′–UTR length, which then control corresponding miRNAs’ action. miRNAs directly control CFIm25 expression level, which then tunes expression of the oncogenes and tumor proliferation. Therefore, regulation of CFIm25 expression level via miRNAs is expected to improve treatment responses in breast cancer.
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Affiliation(s)
- Mona Tamaddon
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Gelareh Shokri
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | | | - Iman Rad
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Àmirnader Emami Razavi
- Ìran National Tumor Bank, Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Kouhkan
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran.
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18
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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19
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Iijima Y, Tanaka M, Suzuki S, Hauser D, Tanaka M, Okada C, Ito M, Ayukawa N, Sato Y, Ohtsuka M, Scheiffele P, Iijima T. SAM68-Specific Splicing Is Required for Proper Selection of Alternative 3' UTR Isoforms in the Nervous System. iScience 2019; 22:318-335. [PMID: 31805436 PMCID: PMC6909182 DOI: 10.1016/j.isci.2019.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
Neuronal alternative splicing is a core mechanism for functional diversification. We previously found that STAR family proteins (SAM68, SLM1, SLM2) regulate spatiotemporal alternative splicing in the nervous system. However, the whole aspect of alternative splicing programs by STARs remains unclear. Here, we performed a transcriptomic analysis using SAM68 knockout and SAM68/SLM1 double-knockout midbrains. We revealed different alternative splicing activity between SAM68 and SLM1; SAM68 preferentially targets alternative 3′ UTR exons. SAM68 knockout causes a long-to-short isoform switch of a number of neuronal targets through the alteration in alternative last exon (ALE) selection or alternative polyadenylation. The altered ALE usage of a novel target, interleukin 1 receptor accessory protein (Il1rap), results in remarkable conversion from a membrane-bound type to a secreted type in Sam68KO brains. Proper ALE selection is necessary for IL1RAP neuronal function. Thus the SAM68-specific splicing program provides a mechanism for neuronal selection of alternative 3′ UTR isoforms. SAM68 and the related protein SLM1 exhibit distinct alternative splicing activity SAM68 specifically controls 3′ UTR selection of multiple neuronal genes Proper 3′ UTR selection is necessary for IL1RAP neuronal function Neuronal expression of SAM68 requires proper 3′ UTR selection in the nervous system
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Affiliation(s)
- Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - David Hauser
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Masayuki Tanaka
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Chisa Okada
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Masatoshi Ito
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yuji Sato
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Peter Scheiffele
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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20
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Ning Y, Liu W, Guan X, Xie X, Zhang Y. CPSF3 is a promising prognostic biomarker and predicts recurrence of non-small cell lung cancer. Oncol Lett 2019; 18:2835-2844. [PMID: 31452762 PMCID: PMC6704296 DOI: 10.3892/ol.2019.10659] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 05/17/2019] [Indexed: 12/04/2022] Open
Abstract
Cleavage polyadenylation specificity factor (CPSF) is the core component of the 3′-end processing complex, which determines the site of 3′-end cleavage interactions of specific sequence elements within pre-mRNAs. The present study revealed that all members of the CPSF complex were overexpressed in lung cancer tissue from The Cancer Genome Atlas (TCGA) Lung Cancer Cohort compared with normal lung tissue. Analysis of overall survival and recurrence-free survival verified that only CPSF3 was associated with prognosis and recurrence of lung adenocarcinoma (LUAD), and thus could be a promising biomarker. Additionally, receiver operating characteristic curve analysis revealed that CPSF3 may function as a diagnostic biomarker to distinguish between two histological subtypes of non-small cell lung cancer. Furthermore, analysis of the association of CPSF3 expression with clinicopathological parameters indicated that CPSF3 was associated with smoking history, tumor diameter, lymph node metastasis, clinical stage and radiation therapy in LUAD. Additionally, analysis of the DNA methylation data of the TCGA-LUAD Cohort revealed that CPSF3 DNA CpG sites (cg12057242 and cg25739938) were generally hypomethylated in LUAD compared with normal lung tissue. Correlation analysis identified the CPSF3 DNA CpG site cg25739938 to be negatively correlated with CPSF3 expression, while no correlation was identified with cg12057242. In addition, correlation analysis demonstrated that the overexpression of CPSF3 was correlated with CPSF3 DNA copy number variants (CNAs). The findings indicate that abnormal expression of CPSF3 may be caused by DNA CNAs; and DNA hypermethylation and function may be a promising diagnostic and prognostic indicator for LUAD.
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Affiliation(s)
- Yue Ning
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 511436, P.R. China
| | - Wanxia Liu
- Center for Transforming Medicine, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Xiaoying Guan
- Department of Experimental Nuclear Medicine and Radiology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 511436, P.R. China
| | - Xiaobin Xie
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 511436, P.R. China
| | - Yajie Zhang
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 511436, P.R. China
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The Nonstructural NS1 Protein of Influenza Viruses Modulates TP53 Splicing through Host Factor CPSF4. J Virol 2019; 93:JVI.02168-18. [PMID: 30651364 DOI: 10.1128/jvi.02168-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) are known to modulate and "hijack" several cellular host mechanisms, including gene splicing and RNA maturation machineries. These modulations alter host cellular responses and enable an optimal expression of viral products throughout infection. The interplay between the host protein p53 and IAV, in particular through the viral nonstructural protein NS1, has been shown to be supportive for IAV replication. However, it remains unknown whether alternatively spliced isoforms of p53, known to modulate p53 transcriptional activity, are affected by IAV infection and contribute to IAV replication. Using a TP53 minigene, which mimics intron 9 alternative splicing, we have shown here that the NS1 protein of IAV changes the expression pattern of p53 isoforms. Our results demonstrate that CPSF4 (cellular protein cleavage and polyadenylation specificity factor 4) independently and the interaction between NS1 and CPSF4 modulate the alternative splicing of TP53 transcripts, which may result in the differential activation of p53-responsive genes. Finally, we report that CPSF4 and most likely beta and gamma spliced p53 isoforms affect both viral replication and IAV-associated type I interferon secretion. All together, our data show that cellular p53 and CPSF4 factors, both interacting with viral NS1, have a crucial role during IAV replication that allows IAV to interact with and alter the expression of alternatively spliced p53 isoforms in order to regulate the cellular innate response, especially via type I interferon secretion, and perform efficient viral replication.IMPORTANCE Influenza A viruses (IAV) constitute a major public health issue, causing illness and death in high-risk populations during seasonal epidemics or pandemics. IAV are known to modulate cellular pathways to promote their replication and avoid immune restriction via the targeting of several cellular proteins. One of these proteins, p53, is a master regulator involved in a large panel of biological processes, including cell cycle arrest, apoptosis, or senescence. This "cellular gatekeeper" is also involved in the control of viral infections, and viruses have developed a wide diversity of mechanisms to modulate/hijack p53 functions to achieve an optimal replication in their hosts. Our group and others have previously shown that p53 activity is finely modulated by different multilevel mechanisms during IAV infection. Here, we characterized IAV nonstructural protein NS1 and the cellular factor CPSF4 as major partners involved in the IAV-induced modulation of the TP53 alternative splicing that was associated with a strong modulation of p53 activity and notably the p53-mediated antiviral response.
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Abstract
In eukaryotes, the separation of translation from transcription by the nuclear envelope enables mRNA modifications such as capping, splicing, and polyadenylation. These modifications are mediated by a spectrum of ribonuclear proteins that associate with preRNA transcripts, coordinating the different steps and coupling them to nuclear export, ensuring that only mature transcripts reach the cytoplasmic translation machinery. Although the components of this machinery have been identified and considerable functional insight has been achieved, a number of questions remain outstanding about mRNA nuclear export and how it is integrated into the nuclear phase of the gene expression pathway. Nuclear export factors mediate mRNA transit through nuclear pores to the cytoplasm, after which these factors are removed from the mRNA, preventing transcripts from returning to the nucleus. However, as outlined in this review, several aspects of the mechanism by which transport factor binding and release are mediated remain unclear, as are the roles of accessory nuclear components in these processes. Moreover, the mechanisms by which completion of mRNA splicing and polyadenylation are recognized, together with how they are coordinated with nuclear export, also remain only partially characterized. One attractive hypothesis is that dissociating poly(A) polymerase from the cleavage and polyadenylation machinery could signal completion of mRNA maturation and thereby provide a mechanism for initiating nuclear export. The impressive array of genetic, molecular, cellular, and structural data that has been generated about these systems now provides many of the tools needed to define the precise mechanisms involved in these processes and how they are integrated.
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Affiliation(s)
- Murray Stewart
- From the MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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23
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Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I. Influenza virus infection causes global RNAPII termination defects. Nat Struct Mol Biol 2018; 25:885-893. [PMID: 30177761 PMCID: PMC10754036 DOI: 10.1038/s41594-018-0124-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/09/2018] [Indexed: 12/23/2022]
Abstract
Viral infection perturbs host cells and can be used to uncover regulatory mechanisms controlling cellular responses and susceptibility to infections. Using cell biological, biochemical, and genetic tools, we reveal that influenza A virus (IAV) infection induces global transcriptional defects at the 3' ends of active host genes and RNA polymerase II (RNAPII) run-through into extragenic regions. Deregulated RNAPII leads to expression of aberrant RNAs (3' extensions and host-gene fusions) that ultimately cause global transcriptional downregulation of physiological transcripts, an effect influencing antiviral response and virulence. This phenomenon occurs with multiple strains of IAV, is dependent on influenza NS1 protein, and can be modulated by SUMOylation of an intrinsically disordered region (IDR) of NS1 expressed by the 1918 pandemic IAV strain. Our data identify a strategy used by IAV to suppress host gene expression and indicate that polymorphisms in IDRs of viral proteins can affect the outcome of an infection.
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Affiliation(s)
- Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nacho Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judd Hultquist
- Department of Medicine (Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Jimenez-Morales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Yixuan Ma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Fenouil
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Teresa Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Ayllon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sweta Ravisankar
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Bahareh Haddad
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Diana Low
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY, USA
| | - Massimo Squatrito
- Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid, Spain
| | - Dalila Pinto
- Department of Psychiatry, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimaada Allette
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minji Byun
- Department of Medicine, Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Laird Smith
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Terrence Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a mutation that expands the polyglutamine (CAG) repeat in exon 1 of the huntingtin (HTT) gene. Wild-type HTT protein interacts with other proteins to protect cells against toxic stimuli, mediate vesicle transport and endocytosis, and modulate synaptic activity. Mutant HTT protein disrupts autophagy, vesicle transport, neurotransmitter signaling, and mitochondrial function. Although many of the activities of wild-type HTT protein and the toxicities of mutant HTT protein are characterized, less is known about the activities of HTT mRNA. Most putative HD therapies aim to target mutant HTT mRNA before it is translated into the protein. Therefore, it is imperative to learn as much as we can about how cells handle both wild-type and mutant HTT mRNA so that effective therapies can be designed. Here, we review the structure of wild-type and mutant HTT mRNA, with emphasis on their alternatively polyadenylated or spliced isoforms. We then consider the abundance of HTT mRNA isoforms in HD and discuss the potential implications of these findings. Evidence in the review should be used to guide future research aimed at developing mRNA-lowering therapies for HD.
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Affiliation(s)
- Lindsay Romo
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Emily S. Mohn
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Neil Aronin
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
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25
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Huang C, Shi J, Guo Y, Huang W, Huang S, Ming S, Wu X, Zhang R, Ding J, Zhao W, Jia J, Huang X, Xiang AP, Shi Y, Yao C. A snoRNA modulates mRNA 3' end processing and regulates the expression of a subset of mRNAs. Nucleic Acids Res 2017; 45:8647-8660. [PMID: 28911119 PMCID: PMC5587809 DOI: 10.1093/nar/gkx651] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/15/2017] [Indexed: 01/08/2023] Open
Abstract
mRNA 3′ end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3′ processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3′ processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF). We have functionally characterized one of these snoRNAs and our results demonstrated that the U/A-rich SNORD50A inhibits mRNA 3′ processing by blocking the Fip1-poly(A) site (PAS) interaction. Consistently, SNORD50A depletion altered the Fip1–RNA interaction landscape and changed the alternative polyadenylation (APA) profiles and/or transcript levels of a subset of genes. Taken together, our data revealed a novel function for snoRNAs and provided the first evidence that non-coding RNAs may play an important role in regulating mRNA 3′ processing.
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Affiliation(s)
- Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yibin Guo
- Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Weijun Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Siqi Ming
- Institute of Tuberculosis Control, Key laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xingui Wu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Rui Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Junjun Ding
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Wei Zhao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Jia
- Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xi Huang
- Institute of Tuberculosis Control, Key laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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26
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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27
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Gudde AEEG, van Kessel IDG, André LM, Wieringa B, Wansink DG. Trinucleotide-repeat expanded and normal DMPK transcripts contain unusually long poly(A) tails despite differential nuclear residence. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:740-749. [PMID: 28435090 DOI: 10.1016/j.bbagrm.2017.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/26/2017] [Accepted: 04/14/2017] [Indexed: 12/29/2022]
Abstract
In yeast and higher eukaryotes nuclear retention of transcripts may serve in control over RNA decay, nucleocytoplasmic transport and premature cytoplasmic appearance of mRNAs. Hyperadenylation of RNA is known to be associated with nuclear retention, but the cause-consequence relationship between hyperadenylation and regulation of RNA nuclear export is still unclear. We compared polyadenylation status between normal and expanded DMPK transcripts in muscle cells and tissues derived from unaffected individuals and patients with myotonic dystrophy type 1 (DM1). DM1 is an autosomal dominant disorder caused by (CTG)n repeat expansion in the DMPK gene. DM1 etiology is characterized by an almost complete block of nuclear export of DMPK transcripts carrying a long (CUG)n repeat, including aberrant sequestration of RNA-binding proteins. We show here by use of cell fractionation, RNA size separation and analysis of poly(A) tail length that a considerable fraction of transcripts from the normal DMPK allele is also retained in the nucleus (~30%). They carry poly(A) tails with an unusually broad length distribution, ranging between a few dozen to >500 adenosine residues. Remarkably, expanded DMPK (CUG)n transcripts from the mutant allele, almost exclusively nuclear, carry equally long poly(A) tails. Our findings thus suggest that nuclear retention may be a common feature of regulation of DMPK RNA expression. The typical forced nuclear residence of expanded DMPK transcripts affects this regulation in tissues of DM1 patients, but not through hyperadenylation.
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Affiliation(s)
- Anke E E G Gudde
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Ingeborg D G van Kessel
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Laurène M André
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Bé Wieringa
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G Wansink
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands.
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28
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Antosz W, Pfab A, Ehrnsberger HF, Holzinger P, Köllen K, Mortensen SA, Bruckmann A, Schubert T, Längst G, Griesenbeck J, Schubert V, Grasser M, Grasser KD. The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors. THE PLANT CELL 2017; 29:854-870. [PMID: 28351991 PMCID: PMC5435424 DOI: 10.1105/tpc.16.00735] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/22/2017] [Accepted: 03/26/2017] [Indexed: 05/03/2023]
Abstract
Transcript elongation factors (TEFs) are a heterogeneous group of proteins that control the efficiency of transcript elongation of subsets of genes by RNA polymerase II (RNAPII) in the chromatin context. Using reciprocal tagging in combination with affinity purification and mass spectrometry, we demonstrate that in Arabidopsis thaliana, the TEFs SPT4/SPT5, SPT6, FACT, PAF1-C, and TFIIS copurified with each other and with elongating RNAPII, while P-TEFb was not among the interactors. Additionally, NAP1 histone chaperones, ATP-dependent chromatin remodeling factors, and some histone-modifying enzymes including Elongator were repeatedly found associated with TEFs. Analysis of double mutant plants defective in different combinations of TEFs revealed genetic interactions between genes encoding subunits of PAF1-C, FACT, and TFIIS, resulting in synergistic/epistatic effects on plant growth/development. Analysis of subnuclear localization, gene expression, and chromatin association did not provide evidence for an involvement of the TEFs in transcription by RNAPI (or RNAPIII). Proteomics analyses also revealed multiple interactions between the transcript elongation complex and factors involved in mRNA splicing and polyadenylation, including an association of PAF1-C with the polyadenylation factor CstF. Therefore, the RNAPII transcript elongation complex represents a platform for interactions among different TEFs, as well as for coordinating ongoing transcription with mRNA processing.
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Affiliation(s)
- Wojciech Antosz
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Alexander Pfab
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Hans F Ehrnsberger
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Holzinger
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Karin Köllen
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Simon A Mortensen
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Schubert
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Gernot Längst
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
| | - Marion Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
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29
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Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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30
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Erson-Bensan AE. Alternative polyadenylation and RNA-binding proteins. J Mol Endocrinol 2016; 57:F29-34. [PMID: 27208003 DOI: 10.1530/jme-16-0070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022]
Abstract
Our understanding of the extent of microRNA-based gene regulation has expanded in an impressive pace over the past decade. Now, we are beginning to better appreciate the role of 3'-UTR (untranslated region) cis-elements which harbor not only microRNA but also RNA-binding protein (RBP) binding sites that have significant effect on the stability and translational rate of mRNAs. To add further complexity, alternative polyadenylation (APA) emerges as a widespread mechanism to regulate gene expression by producing shorter or longer mRNA isoforms that differ in the length of their 3'-UTRs or even coding sequences. Resulting shorter mRNA isoforms generally lack cis-elements where trans-acting factors bind, and hence are differentially regulated compared with the longer isoforms. This review focuses on the RBPs involved in APA regulation and their action mechanisms on APA-generated isoforms. A better understanding of the complex interactions between APA and RBPs is promising for mechanistic and clinical implications including biomarker discovery and new therapeutic approaches.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological SciencesOrta Dogu Teknik Universitesi (ODTU) (METU), Universiteler Mahallesi, Cankaya, Ankara, Turkey
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