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Yan Y, Yu C, Xie B, Zhou H, Zhang C, Tian L. Characterization and Early Response of the DEAD Gene Family to Heat Stress in Tomato. PLANTS (BASEL, SWITZERLAND) 2025; 14:1172. [PMID: 40284060 PMCID: PMC12030476 DOI: 10.3390/plants14081172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 03/31/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025]
Abstract
The DEAD-box RNA helicase family, acting as a critical regulator in RNA metabolism, plays a vital role in plant growth, development, and adaptation to various stresses. Although a number of DEAD proteins have been reported to participate in heat stress response in several species, the response of DEAD-box RNA helicases to heat stress has not been comprehensively analyzed in tomato. In this study, 42 SlDEAD genes were identified from the tomato genome. Evolutionary analysis of DEAD family genes across different plant species reveals that DEAD family genes can be segregated into five groups. A comprehensive analysis of their physicochemical properties, gene structure, chromosome location, and conserved motifs unveils diversity among the members of the SlDEAD family. An investigation into the subcellular localization of seven SlDEAD proteins indicates that SlDEAD7, SlDEAD14, and SlDEAD26 are located in the endoplasmic reticulum, and SlDEAD40 is located in the endoplasmic reticulum and nucleus, whereas SlDEAD17, SlDEAD25, and SlDEAD35 are located in the chloroplast. The expression of 37 out of 42 SlDEAD genes was responsive to heat stress induction. During the early stage of high-temperature treatment, they exhibited five distinct expression patterns. These findings contribute to a deeper comprehension of the evolution, expansion complexity, and function of SlDEAD genes and provide insights into the potential role of SlDEAD genes in tomato tolerance to heat stress.
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Affiliation(s)
- Yanyan Yan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (C.Y.); (B.X.); (H.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou 311300, China
| | - Chao Yu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (C.Y.); (B.X.); (H.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou 311300, China
| | - Bolun Xie
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (C.Y.); (B.X.); (H.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Zhou
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (C.Y.); (B.X.); (H.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou 311300, China
| | - Caiyu Zhang
- Institute of Agricultural Experiment Station of Changxing Substation, Zhejiang University, Hangzhou 310058, China;
| | - Li Tian
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China; (Y.Y.); (C.Y.); (B.X.); (H.Z.)
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou 311300, China
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Boo SH, Shin MK, Hwang HJ, Hwang H, Chang S, Kim T, Baek D, Kim YK. Circular RNAs trigger nonsense-mediated mRNA decay. Mol Cell 2024; 84:4862-4877.e7. [PMID: 39667933 DOI: 10.1016/j.molcel.2024.11.022] [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: 08/29/2023] [Revised: 08/13/2024] [Accepted: 11/15/2024] [Indexed: 12/14/2024]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs produced predominantly through a back-splicing process. They play regulatory roles in various biological and physiological processes; however, the molecular mechanisms by which circRNAs operate remain unclear. Herein, we demonstrate that circRNAs facilitate rapid mRNA degradation through RNA-RNA interactions between circRNAs and the 3' untranslated regions (3' UTRs) of mRNAs. This interaction positions the exon-junction complexes (EJCs), deposited onto circRNAs by back-splicing, near the 3' UTRs of the mRNAs, thereby leading to EJC-dependent nonsense-mediated mRNA decay (NMD), a process we describe as circRNA-induced NMD (circNMD). Our transcriptomic analysis reveals hundreds of potential circNMD candidates, and the biological importance of circNMD in cellular apoptosis is validated. We also demonstrate that exogenously expressed circRNAs designed to interact with the 3' UTRs of endogenous mRNAs significantly downregulate the mRNA levels. Collectively, our observations provide compelling molecular evidence for circNMD and its potential therapeutic application in selective mRNA downregulation.
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Affiliation(s)
- Sung Ho Boo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyeonseo Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunwoo Chang
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Republic of Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
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3
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Patel MZ, Jiang Y, Kakumani PK. Somatic piRNA and PIWI-mediated post-transcriptional gene regulation in stem cells and disease. Front Cell Dev Biol 2024; 12:1495035. [PMID: 39717847 PMCID: PMC11663942 DOI: 10.3389/fcell.2024.1495035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 11/25/2024] [Indexed: 12/25/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that bind to the PIWI subclass of the Argonaute protein family and are essential for maintaining germline integrity. Initially discovered in Drosophila, PIWI proteins safeguard piRNAs, forming ribonucleoprotein (RNP) complexes, crucial for regulating gene expression and genome stability, by suppressing transposable elements (TEs). Recent insights revealed that piRNAs and PIWI proteins, known for their roles in germline maintenance, significantly influence mRNA stability, translation and retrotransposon silencing in both stem cells and bodily tissues. In the current review, we explore the multifaceted roles of piRNAs and PIWI proteins in numerous biological contexts, emphasizing their involvement in stem cell maintenance, differentiation, and the development of human diseases. Additionally, we discussed the up-and-coming animal models, beyond the classical fruit fly and earthworm systems, for studying piRNA-PIWIs in self-renewal and cell differentiation. Further, our review offers new insights and discusses the emerging roles of piRNA-dependent and independent functions of PIWI proteins in the soma, especially the mRNA regulation at the post-transcriptional level, governing stem cell characteristics, tumor development, and cardiovascular and neurodegenerative diseases.
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Affiliation(s)
| | | | - Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
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4
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Shin MK, Chang J, Park J, Lee HJ, Woo JS, Kim YK. Nonsense-mediated mRNA decay of mRNAs encoding a signal peptide occurs primarily after mRNA targeting to the endoplasmic reticulum. Mol Cells 2024; 47:100049. [PMID: 38513766 PMCID: PMC11016901 DOI: 10.1016/j.mocell.2024.100049] [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: 02/20/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024] Open
Abstract
Translation of messenger ribonucleic acids (mRNAs) encoding integral membrane proteins or secreted proteins occurs on the surface of the endoplasmic reticulum (ER). When a nascent signal peptide is synthesized from the mRNAs, the ribosome-nascent chain complex (RNC) is recognized by the signal recognition particle (SRP) and then transported to the surface of the ER. The appropriate targeting of the RNC-SRP complex to the ER is monitored by a quality control pathway, a nuclear cap-binding complex (CBC)-ensured translational repression of RNC-SRP (CENTRE). In this study, using ribosome profiling of CBC-associated and eukaryotic translation initiation factor 4E-associated mRNAs, we reveal that, at the transcriptomic level, CENTRE is in charge of the translational repression of the CBC-RNC-SRP until the complex is specifically transported to the ER. We also find that CENTRE inhibits the nonsense-mediated mRNA decay (NMD) of mRNAs within the CBC-RNC-SRP. The NMD occurs only after the CBC-RNC-SRP is targeted to the ER and after eukaryotic translation initiation factor 4E replaces CBC. Our data indicate dual surveillance for properly targeting mRNAs encoding integral membrane or secretory proteins to the ER. CENTRE blocks gene expression at the translation level before the CBC-RNC-SRP delivery to the ER, and NMD monitors mRNA quality after its delivery to the ER.
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Affiliation(s)
- Min-Kyung Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joori Park
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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Allikka Parambil S, Li D, Zelko M, Poulet A, van Wolfswinkel J. piRNA generation is associated with the pioneer round of translation in stem cells. Nucleic Acids Res 2024; 52:2590-2608. [PMID: 38142432 PMCID: PMC10954484 DOI: 10.1093/nar/gkad1212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023] Open
Abstract
Much insight has been gained on how stem cells maintain genomic integrity, but less attention has been paid to how they maintain their transcriptome. Here, we report that the PIWI protein SMEDWI-1 plays a role in the filtering of dysfunctional transcripts from the transcriptome of planarian stem cells. SMEDWI-1 accomplishes this through association with the ribosomes during the pioneer round of translation, and processing of poorly translated transcripts into piRNAs. This results in the removal of such transcripts from the cytoplasmic pool and at the same time creates a dynamic pool of small RNAs for post-transcriptional surveillance through the piRNA pathway. Loss of SMEDWI-1 results in elevated levels of several non-coding transcripts, including rRNAs, snRNAs and pseudogene mRNAs, while reducing levels of several coding transcripts. In the absence of SMEDWI-1, stem cell colonies are delayed in their expansion and a higher fraction of descendants exit the stem cell state, indicating that this transcriptomic sanitation mediated by SMEDWI-1 is essential to maintain stem cell health. This study presents a new model for the function of PIWI proteins in stem cell maintenance, that complements their role in transposon repression, and proposes a new biogenesis pathway for piRNAs in stem cells.
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Affiliation(s)
- Sudheesh Allikka Parambil
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Danyan Li
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Michael Zelko
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
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6
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Huang GW, Yang TQ, Chen QQ, Liu XM, Xie LH, Huang W, Chen XL, Geng YQ, Gu J. circular RNA circ-231 promotes protein biogenesis of TPI1 and PRDX6 through mediating the interaction of eIF4A3 with STAU1 to facilitate unwinding of secondary structure in 5' UTR, enhancing progression of human esophageal squamous cell carcinoma (ESCC). J Cancer 2024; 15:2518-2537. [PMID: 38577609 PMCID: PMC10988296 DOI: 10.7150/jca.92578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024] Open
Abstract
Background: The nuclear cap-binding complex (CBC)-dependent translation (CT) is an important initial translation pathway for 5'-cap-dependent translation in normal mammal cells. Eukaryotic translation initiation factor 4A-III (eIF4A3), as an RNA helicase, is recruited to CT complex and enhances CT efficiency through participating in unwinding of secondary structure in the 5' UTR. However, the detailed mechanism for eIF4A3 implicated in unwinding of secondary structure in the 5' UTR in normal mammal cells is still unclear. Specially, we need to investigate whether the kind of mechanism in normal mammal cells extrapolates to cancer cells, e.g. ESCC, and further interrogate whether and how the mechanism triggers malignant phenotype of ESCC, which are important for identifying a potential therapeutic target for patients with ESCC. Methods: Bioinformatics analysis, RNA immunoprecipitation and RNA pulldown assays were performed to detect the interaction of circular RNA circ-231 with eIF4A3. In vitro and in vivo assays were performed to detect biological roles of circ-231 in ESCC. RNA immunoprecipitation, RNA pulldown, mass spectrometry analysis and co-immunoprecipitation assays were used to measure the interaction of circ-231, eIF4A3 and STAU1 in HEK293T and ESCC. In vitro EGFP reporter and 5' UTR of mRNA pulldown assays were performed to probe for the binding of circ-231, eIF4A3 and STAU1 to secondary structure of 5' UTR. Results: RNA immunoprecipitation assays showed that circ-231 interacted with eIF4A3 in HEK293T and ESCC. Further study confirmed that circ-231 orchestrated with eIF4A3 to control protein expression of TPI1 and PRDX6, but not for mRNA transcripts. The in-depth mechanism study uncovered that both circ-231 and eIF4A3 were involved in unwinding of secondary structure in 5' UTR of TPI1 and PRDX6. More importantly, circ-231 promoted the interaction between eIF4A3 and STAU1. Intriguingly, both circ-231 and eIF4A3 were dependent on STAU1 binding to secondary structure in 5' UTR. Biological function assays revealed that circ-231 promoted the migration and proliferation of ESCC via TPI1 and PRDX6. In ESCC, the up-regulated expression of circ-231 was observed and patients with ESCC characterized by higher expression of circ-231 have concurrent lymph node metastasis, compared with control. Conclusions: Our data unravels the detailed mechanism by which STAU1 binds to secondary structure in 5' UTR of mRNAs and recruits eIF4A3 through interacting with circ-231 and thereby eIF4A3 is implicated in unwinding of secondary structure, which is common to HEK293T and ESCC. However, importantly, our data reveals that circ-231 promotes migration and proliferation of ESCC and the up-regulated circ-231 greatly correlates with tumor lymph node metastasis, insinuating that circ-231 could be a therapeutic target and an indicator of risk of lymph node metastasis for patients with ESCC.
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Affiliation(s)
- Guo-Wei Huang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Ti-Qun Yang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Qian-Qian Chen
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Xing-Mu Liu
- Department of Surgery, Second Affiliated Hospital, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Ling-Hui Xie
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Wei Huang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Xue-Ling Chen
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Yi-Qun Geng
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Jiang Gu
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
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Chang J, Shin MK, Park J, Hwang HJ, Locker N, Ahn J, Kim D, Baek D, Park Y, Lee Y, Boo SH, Kim HI, Kim YK. An interaction between eIF4A3 and eIF3g drives the internal initiation of translation. Nucleic Acids Res 2023; 51:10950-10969. [PMID: 37811880 PMCID: PMC10639049 DOI: 10.1093/nar/gkad763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
An RNA structure or modified RNA sequences can provide a platform for ribosome loading and internal translation initiation. The functional significance of internal translation has recently been highlighted by the discovery that a subset of circular RNAs (circRNAs) is internally translated. However, the molecular mechanisms underlying the internal initiation of translation in circRNAs remain unclear. Here, we identify eIF3g (a subunit of eIF3 complex) as a binding partner of eIF4A3, a core component of the exon-junction complex (EJC) that is deposited onto spliced mRNAs and plays multiple roles in the regulation of gene expression. The direct interaction between eIF4A3-eIF3g serves as a molecular linker between the eIF4A3 and eIF3 complex, thereby facilitating internal ribosomal entry. Protein synthesis from in vitro-synthesized circRNA demonstrates eIF4A3-driven internal translation, which relies on the eIF4A3-eIF3g interaction. Furthermore, our transcriptome-wide analysis shows that efficient polysomal association of endogenous circRNAs requires eIF4A3. Notably, a subset of endogenous circRNAs can express a full-length intact protein, such as β-catenin, in an eIF4A3-dependent manner. Collectively, our results expand the understanding of the protein-coding potential of the human transcriptome, including circRNAs.
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Affiliation(s)
- Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyung Shin
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Nicolas Locker
- Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7HX, UK
| | - Junhak Ahn
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Doyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonkyoung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ho Boo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyeong-In Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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8
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Lin HH, Chang CY, Huang YR, Shen CH, Wu YC, Chang KL, Lee YC, Lin YC, Ting WC, Chien HJ, Zheng YF, Lai CC, Hsiao KY. Exon Junction Complex Mediates the Cap-Independent Translation of Circular RNA. Mol Cancer Res 2023; 21:1220-1233. [PMID: 37527157 DOI: 10.1158/1541-7786.mcr-22-0877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/22/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Evidence that circular RNAs (circRNA) serve as protein template is accumulating. However, how the cap-independent translation is controlled remains largely uncharacterized. Here, we show that the presence of intron and thus splicing promote cap-independent translation. By acquiring the exon junction complex (EJC) after splicing, the interaction between circRNA and ribosomes was promoted, thereby facilitating translation. Prevention of splicing by treatment with spliceosome inhibitor or mutating splicing signal hindered cap-independent translation of circRNA. Moreover, EJC-tethering using Cas13 technology reconstituted EJC-dependent circRNA translation. Finally, the level of a coding circRNA from succinate dehydrogenase assembly factor 2 (circSDHAF2) was found to be elevated in the tumorous tissues from patients with colorectal cancer, and shown to be critical in tumorigenesis of colorectal cancer in both cell and murine models. These findings reveal that EJC-dependent control of circSDHAF2 translation is involved in the regulation of oncogenic pathways. IMPLICATIONS EJC-mediated cap-independent translation of circRNA is implicated in the tumorigenesis of colorectal cancer.
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Affiliation(s)
- Hui-Hsuan Lin
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chiu-Yuan Chang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ren Huang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Che-Hung Shen
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Yu-Chen Wu
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kai-Li Chang
- Department of Physiology, National Cheng Kung University, Tainan, Taiwan
| | - Yueh-Chun Lee
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ya-Chi Lin
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Wen-Chien Ting
- Division of Colorectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Han-Ju Chien
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Yi-Feng Zheng
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kuei-Yang Hsiao
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Doctoral Program in Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung
- Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung
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9
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Jung I, Kim YK. Exon Junction Complex Is a Molecular Compass of N 6-Methyladenosine Modification. Mol Cells 2023; 46:589-591. [PMID: 37853685 PMCID: PMC10590705 DOI: 10.14348/molcells.2023.0101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 10/20/2023] Open
Affiliation(s)
- Inhong Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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10
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Zheng B, Chen X, Ling Q, Cheng Q, Ye S. Role and therapeutic potential of DEAD-box RNA helicase family in colorectal cancer. Front Oncol 2023; 13:1278282. [PMID: 38023215 PMCID: PMC10654640 DOI: 10.3389/fonc.2023.1278282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed and the second cancer-related death worldwide, leading to more than 0.9 million deaths every year. Unfortunately, this disease is changing rapidly to a younger age, and in a more advanced stage when diagnosed. The DEAD-box RNA helicase proteins are the largest family of RNA helicases so far. They regulate almost every aspect of RNA physiological processes, including RNA transcription, editing, splicing and transport. Aberrant expression and critical roles of the DEAD-box RNA helicase proteins have been found in CRC. In this review, we first summarize the protein structure, cellular distribution, and diverse biological functions of DEAD-box RNA helicases. Then, we discuss the distinct roles of DEAD-box RNA helicase family in CRC and describe the cellular mechanism of actions based on recent studies, with an aim to provide future strategies for the treatment of CRC.
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Affiliation(s)
- Bichun Zheng
- Department of Anorectal Surgery, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
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11
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Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
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Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
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12
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Ming J, Wang C. N7-Methylguanosine-Related lncRNAs: Integrated Analysis Associated With Prognosis and Progression in Clear Cell Renal Cell Carcinoma. Front Genet 2022; 13:871899. [PMID: 35495133 PMCID: PMC9043611 DOI: 10.3389/fgene.2022.871899] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/29/2022] [Indexed: 01/07/2023] Open
Abstract
N7-Methylguanosine (m7G) and long non-coding RNAs (lncRNAs) have been widely reported to play an important role in cancer. However, there is little known about the relationship between m7G-related lncRNAs and clear cell renal cell carcinoma (ccRCC). To find new potential biomarkers and construct an m7G-related lncRNA prognostic signature for ccRCC, we retrieved transcriptome data and clinical data from The Cancer Genome Atlas (TCGA), and divided the entire set into train set and test set with the ratio of 1:1 randomly. The m7G-related lncRNAs were identified by Pearson correlation analysis (|coefficients| > 0.4, and p < 0.001). Then we performed the univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct a 12 m7G-related lncRNA prognostic signature. Next, principal component analysis (PCA), the Kaplan–Meier method, time-dependent receiver operating characteristics (ROC) were made to verify and evaluate the risk signature. A nomogram based on the risk signature and clinical parameters was developed and showed high accuracy and reliability for predicting the overall survival (OS). Functional enrichment analysis (GO, KEGG and GSEA) was used to investigate the potential biological pathways. We also performed the analysis of tumor mutation burden (TMB), immunological analysis including immune scores, immune cell infiltration (ICI), immune function, tumor immune escape (TIE) and immunotherapeutic drug in our study. In conclusion, using the 12 m7G-related lncRNA risk signature as a prognostic indicator may offer us insight into the oncogenesis and treatment response prediction of ccRCC.
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13
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Ho CH, Paolantoni C, Bawankar P, Tang Z, Brown S, Roignant J, Treisman JE. An exon junction complex-independent function of Barentsz in neuromuscular synapse growth. EMBO Rep 2022; 23:e53231. [PMID: 34726300 PMCID: PMC8728599 DOI: 10.15252/embr.202153231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
The exon junction complex controls the translation, degradation, and localization of spliced mRNAs, and three of its core subunits also play a role in splicing. Here, we show that a fourth subunit, Barentsz, has distinct functions within and separate from the exon junction complex in Drosophila neuromuscular development. The distribution of mitochondria in larval muscles requires Barentsz as well as other exon junction complex subunits and is not rescued by a Barentsz transgene in which residues required for binding to the core subunit eIF4AIII are mutated. In contrast, interactions with the exon junction complex are not required for Barentsz to promote the growth of neuromuscular synapses. We find that the Activin ligand Dawdle shows reduced expression in barentsz mutants and acts downstream of Barentsz to control synapse growth. Both barentsz and dawdle are required in motor neurons, muscles, and glia for normal synapse growth, and exogenous Dawdle can rescue synapse growth in the absence of barentsz. These results identify a biological function for Barentsz that is independent of the exon junction complex.
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Affiliation(s)
- Cheuk Hei Ho
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Praveen Bawankar
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Zuojian Tang
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
Computational Biology at Ridgefield US, Global Computational Biology and Digital ScienceBoehringer IngelheimRidgefieldCTUSA
| | - Stuart Brown
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
ExxonMobil Corporate Strategic ResearchAnnandaleNJUSA
| | - Jean‐Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Jessica E Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
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14
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Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
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Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
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15
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Park J, Chang J, Hwang HJ, Jeong K, Lee HJ, Ha H, Park Y, Lim C, Woo JS, Kim YK. The pioneer round of translation ensures proper targeting of ER and mitochondrial proteins. Nucleic Acids Res 2021; 49:12517-12534. [PMID: 34850140 PMCID: PMC8643669 DOI: 10.1093/nar/gkab1098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The pioneer (or first) round of translation of newly synthesized mRNAs is largely mediated by a nuclear cap-binding complex (CBC). In a transcriptome-wide analysis of polysome-associated and CBC-bound transcripts, we identify RN7SL1, a noncoding RNA component of a signal recognition particle (SRP), as an interaction partner of the CBC. The direct CBC–SRP interaction safeguards against abnormal expression of polypeptides from a ribosome–nascent chain complex (RNC)–SRP complex until the latter is properly delivered to the endoplasmic reticulum. Failure of this surveillance causes abnormal expression of misfolded proteins at inappropriate intracellular locations, leading to a cytosolic stress response. This surveillance pathway also blocks protein synthesis through RNC–SRP misassembled on an mRNA encoding a mitochondrial protein. Thus, our results reveal a surveillance pathway in which pioneer translation ensures proper targeting of endoplasmic reticulum and mitochondrial proteins.
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Affiliation(s)
- Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Chunghun Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae-Sung Woo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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16
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eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy. Cell Death Differ 2021; 28:3344-3356. [PMID: 34158631 PMCID: PMC8630043 DOI: 10.1038/s41418-021-00822-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
During autophagy, the coordinated actions of autophagosomes and lysosomes result in the controlled removal of damaged intracellular organelles and superfluous substrates. The evolutionary conservation of this process and its requirement for maintaining cellular homeostasis emphasizes the need to better dissect the pathways governing its molecular regulation. In our previously performed high-content screen, we assessed the effect of 1530 RNA-binding proteins on autophagy. Among the top regulators, we identified the eukaryotic translation initiation factor 4A-3 (eIF4A3). Here we show that depletion of eIF4A3 leads to a potent increase in autophagosome and lysosome biogenesis and an enhanced autophagic flux. This is mediated by the key autophagy transcription factor, TFEB, which becomes dephosphorylated and translocates from the cytoplasm to the nucleus where it elicits an integrated transcriptional response. We further identified an exon-skipping event in the transcript encoding for the direct TFEB kinase, GSK3B, which leads to a reduction in GSK3B expression and activity. Through analysis of TCGA data, we found a significant upregulation of eIF4A3 expression across several cancer types and confirmed the potential relevance of this newly identified signaling axis in human tumors. Hence, our data suggest a previously unrecognized role for eIF4A3 as a gatekeeper of autophagy through the control of TFEB activation, revealing a new mechanism for autophagy regulation.
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17
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Hemolymph Ecdysteroid Titer Affects Maternal mRNAs during Bombyx mori Oogenesis. INSECTS 2021; 12:insects12110969. [PMID: 34821770 PMCID: PMC8622876 DOI: 10.3390/insects12110969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/02/2023]
Abstract
Simple Summary Both maternal genes and ecdysteroids play important roles during embryonic development. In this study, we aimed to characterize the dynamic landscape of maternal mRNAs and the relationship between maternal genes and ecdysteroids during silkworm oogenesis. For the first time, we determined the start of the accumulation of maternal mRNAs in the ovary at the wandering stage during the larval period. We detected the developmental expression profiles of each gene in the ovary or ovariole. We finally confirmed the role of 20-hydroxyecdysone in regulating maternal gene expression. Taken together, our findings expand the understanding of insect oogenesis and provide a perspective on the embryonic development of the silkworm. Abstract Silkworm larval–pupal metamorphosis and the first half of pupal–adult development occur during oogenesis from previtellogenesis to vitellogenesis and include two peaks of the hemolymph ecdysteroid titer. Moreover, a rise in 20-hydroxyecdysone titer in early pupae can trigger the first major transition from previtellogenesis to vitellogenesis in silkworm oogenesis. In this study, we first investigated the expression patterns of 66 maternal genes in the ovary at the wandering stage. We then examined the developmental expression profiles in six time-series samples of ovaries or ovarioles by reverse transcription–quantitative PCR. We found that the transcripts of 22 maternal genes were regulated by 20-hydroxyecdysone in the isolated abdomens of the pupae following a single injection of 20-hydroxyecdysone. This study is the first to determine the relationship between 20-hydroxyecdysone and maternal genes during silkworm oogenesis. These findings provide a basis for further research into the embryonic development of Bombyx mori.
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18
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Ho JJD, Cunningham TA, Manara P, Coughlin CA, Arumov A, Roberts ER, Osteen A, Kumar P, Bilbao D, Krieger JR, Lee S, Schatz JH. Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome. Cell Rep 2021; 37:109806. [PMID: 34644561 PMCID: PMC8558842 DOI: 10.1016/j.celrep.2021.109806] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
Tactical disruption of protein synthesis is an attractive therapeutic strategy, with the first-in-class eIF4A-targeting compound zotatifin in clinical evaluation for cancer and COVID-19. The full cellular impact and mechanisms of these potent molecules are undefined at a proteomic level. Here, we report mass spectrometry analysis of translational reprogramming by rocaglates, cap-dependent initiation disruptors that include zotatifin. We find effects to be far more complex than simple “translational inhibition” as currently defined. Translatome analysis by TMT-pSILAC (tandem mass tag-pulse stable isotope labeling with amino acids in cell culture mass spectrometry) reveals myriad upregulated proteins that drive hitherto unrecognized cytotoxic mechanisms, including GEF-H1-mediated anti-survival RHOA/JNK activation. Surprisingly, these responses are not replicated by eIF4A silencing, indicating a broader translational adaptation than currently understood. Translation machinery analysis by MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) identifies rocaglate-specific dependence on specific translation factors including eEF1ε1 that drive translatome remodeling. Our proteome-level interrogation reveals that the complete cellular response to these historical “translation inhibitors” is mediated by comprehensive translational landscape remodeling. Tactical protein synthesis inhibition is actively pursued as a cancer therapy that bypasses signaling redundancies limiting current strategies. Ho et al. show that rocaglates, first identified as inhibitors of eIF4A activity, globally reprogram cellular translation at both protein synthesis machinery and translatome levels, inducing cytotoxicity through anti-survival GEF-H1/RHOA/JNK signaling.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Tyler A Cunningham
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Paola Manara
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Caroline A Coughlin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Artavazd Arumov
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Evan R Roberts
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ashanti Osteen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Preet Kumar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | - Stephen Lee
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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19
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Park Y, Park J, Hwang HJ, Kim L, Jeong K, Song HK, Rufener SC, Mühlemann O, Kim YK. Translation mediated by the nuclear cap-binding complex is confined to the perinuclear region via a CTIF-DDX19B interaction. Nucleic Acids Res 2021; 49:8261-8276. [PMID: 34232997 PMCID: PMC8373075 DOI: 10.1093/nar/gkab579] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 06/08/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Newly synthesized mRNA is translated during its export through the nuclear pore complex, when its 5′-cap structure is still bound by the nuclear cap-binding complex (CBC), a heterodimer of cap-binding protein (CBP) 80 and CBP20. Despite its critical role in mRNA surveillance, the mechanism by which CBC-dependent translation (CT) is regulated remains unknown. Here, we demonstrate that the CT initiation factor (CTIF) is tethered in a translationally incompetent manner to the perinuclear region by the DEAD-box helicase 19B (DDX19B). DDX19B hands over CTIF to CBP80, which is associated with the 5′-cap of a newly exported mRNA. The resulting CBP80–CTIF complex then initiates CT in the perinuclear region. We also show that impeding the interaction between CTIF and DDX19B leads to uncontrolled CT throughout the cytosol, consequently dysregulating nonsense-mediated mRNA decay. Altogether, our data provide molecular evidence supporting the importance of tight control of local translation in the perinuclear region.
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Affiliation(s)
- Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Leehyeon Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Kyu Song
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Simone C Rufener
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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20
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García-de-Gracia F, Gaete-Argel A, Riquelme-Barrios S, Pereira-Montecinos C, Rojas-Araya B, Aguilera P, Oyarzún-Arrau A, Rojas-Fuentes C, Acevedo ML, Chnaiderman J, Valiente-Echeverría F, Toro-Ascuy D, Soto-Rifo R. CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev. RNA Biol 2021; 18:745-758. [PMID: 33103564 PMCID: PMC8078705 DOI: 10.1080/15476286.2020.1832375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Translation initiation of the human immunodeficiency virus type-1 (HIV-1) full-length RNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the full-length RNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF inhibits HIV-1 and HIV-2 Gag synthesis from the full-length RNA. Our results indicate that CTIF associates with HIV-1 Rev through its N-terminal domain and is recruited onto the full-length RNA ribonucleoprotein complex in order to interfere with Gag synthesis. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that Rev interferes with the association of CTIF with CBP80 indicating that CTIF and Rev compete for the CBC subunit.
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Affiliation(s)
- Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Camila Pereira-Montecinos
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Bárbara Rojas-Araya
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Paulina Aguilera
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aarón Oyarzún-Arrau
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Cecilia Rojas-Fuentes
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Mónica L. Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jonás Chnaiderman
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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21
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The exon junction complex core factor eIF4A3 is a key regulator of HPV16 gene expression. Biosci Rep 2021; 41:228142. [PMID: 33760064 PMCID: PMC8026852 DOI: 10.1042/bsr20203488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
High-risk human papillomavirus (hrHPVs), particularly HPV16 and HPV18, are the etiologic factors of ano-genital cancers and some head and neck squamous cell carcinomas (HNSCCs). Viral E6 and E7 oncoproteins, controlled at both transcriptional and post-transcriptional levels, drive hrHPVs-induced carcinogenesis. In the present study, we investigated the implication of the DEAD-box helicase eukaryotic translation initiation factor 4A3 (eIF4A3,) an Exon Junction Complex factor, in the regulation of HPV16 gene expression. Our data revealed that the depletion of the factor eIF4A3 up-regulated E7 oncoprotein levels. We also showed that the inhibition of the nonsense-mediated RNA decay (NMD) pathway, resulted in the up-regulation of E7 at both RNA and protein levels. We therefore proposed that HPV16 transcripts might present different susceptibilities to NMD and that this pathway could play a key role in the levels of expression of these viral oncoproteins during the development of HPV-related cancers.
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22
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Bage MG, Almohammed R, Cowling VH, Pisliakov A. A novel RNA pol II CTD interaction site on the mRNA capping enzyme is essential for its allosteric activation. Nucleic Acids Res 2021; 49:3109-3126. [PMID: 33684220 PMCID: PMC8034621 DOI: 10.1093/nar/gkab130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/12/2022] Open
Abstract
Recruitment of the mRNA capping enzyme (CE/RNGTT) to the site of transcription is essential for the formation of the 5' mRNA cap, which in turn ensures efficient transcription, splicing, polyadenylation, nuclear export and translation of mRNA in eukaryotic cells. The CE GTase is recruited and activated by the Serine-5 phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. Through the use of molecular dynamics simulations and enhanced sampling techniques, we provide a systematic and detailed characterization of the human CE-CTD interface, describing the effect of the CTD phosphorylation state, length and orientation on this interaction. Our computational analyses identify novel CTD interaction sites on the human CE GTase surface and quantify their relative contributions to CTD binding. We also identify, for the first time, allosteric connections between the CE GTase active site and the CTD binding sites, allowing us to propose a mechanism for allosteric activation. Through binding and activity assays we validate the novel CTD binding sites and show that the CDS2 site is essential for CE GTase activity stimulation. Comparison of the novel sites with cocrystal structures of the CE-CTD complex in different eukaryotic taxa reveals that this interface is considerably more conserved than previous structures have indicated.
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Affiliation(s)
- Marcus G Bage
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rajaei Almohammed
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Andrei V Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
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23
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Zhu Y, Ren C, Yang L. Effect of eukaryotic translation initiation factor 4A3 in malignant tumors. Oncol Lett 2021; 21:358. [PMID: 33747215 PMCID: PMC7967930 DOI: 10.3892/ol.2021.12619] [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: 08/11/2020] [Accepted: 02/19/2021] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic translation initiation factor 4A3 (EIF4A3), a key component of the exon junction complex, is widely involved in RNA splicing and nonsense-mediated mRNA decay. EIF4A3 has also been reported to be involved in cell cycle regulation and apoptosis. Thus, EIF4A3 may serve as a pivotal regulatory factor involved in the occurrence and development of multiple diseases. Previous studies have demonstrated that EIF4A3 is mutated in neuromuscular degenerative lesions and is differentially expressed in several tumors, serving as a non-coding RNA binding protein to regulate its expression. In addition, studies have reported that inhibiting EIF4A3 can prevent tumor cell proliferation, thus, several researchers are trying to design and synthesize potent and selective EIF4A3 inhibitors. The present review summarizes the function of EIF4A3 in cell cycle and discusses it underlying molecular mechanisms that contribute to the occurrence of malignant diseases. In addition, EIF4A3 selective inhibitors, and bioinformatics analyses performed to analyze the expression and mutations of EIF4A3 in gynecological tumors and breast cancer, are also discussed.
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Affiliation(s)
- Yuanhang Zhu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Chenchen Ren
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Li Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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24
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Mateu-Regué À, Nielsen FC, Christiansen J. Cytoplasmic mRNPs revisited: Singletons and condensates. Bioessays 2020; 42:e2000097. [PMID: 33145808 DOI: 10.1002/bies.202000097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/04/2020] [Indexed: 01/01/2023]
Abstract
Cytoplasmic messenger ribonucleoprotein particles (mRNPs) represent the cellular transcriptome, and recent data have challenged our current understanding of their architecture, transport, and complexity before translation. Pre-translational mRNPs are composed of a single transcript, whereas P-bodies and stress granules are condensates. Both pre-translational mRNPs and actively translating mRNPs seem to adopt a linear rather than a closed-loop configuration. Moreover, assembly of pre-translational mRNPs in physical RNA regulons is an unlikely event, and co-regulated translation may occur locally following extracellular cues. We envisage a stochastic mRNP transport mechanism where translational repression of single mRNPs-in combination with microtubule-mediated cytoplasmic streaming and docking events-are prerequisites for local translation, rather than direct transport.
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Affiliation(s)
| | | | - Jan Christiansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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25
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Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol 2020; 17:1239-1251. [PMID: 32496897 PMCID: PMC7549709 DOI: 10.1080/15476286.2020.1766179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Translation initiation is a critical facet of gene expression with important impacts that underlie cellular responses to stresses and environmental cues. Its dysregulation in many diseases position this process as an important area for the development of new therapeutics. The gateway translation factor eIF4E is typically considered responsible for ‘global’ or ‘canonical’ m7G cap-dependent translation. However, eIF4E impacts translation of specific transcripts rather than the entire translatome. There are many alternative cap-dependent translation mechanisms that also contribute to the translation capacity of the cell. We review the diversity of these, juxtaposing more recently identified mechanisms with eIF4E-dependent modalities. We also explore the multiplicity of functions played by translation factors, both within and outside protein synthesis, and discuss how these differentially contribute to their ultimate physiological impacts. For comparison, we discuss some modalities for cap-independent translation. In all, this review highlights the diverse mechanisms that engage and control translation in eukaryotes.
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Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
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26
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Singh G, Fritz SE, Seufzer B, Boris-Lawrie K. The mRNA encoding the JUND tumor suppressor detains nuclear RNA-binding proteins to assemble polysomes that are unaffected by mTOR. J Biol Chem 2020; 295:7763-7773. [PMID: 32312751 DOI: 10.1074/jbc.ra119.012005] [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: 11/27/2019] [Revised: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
One long-standing knowledge gap is the role of nuclear proteins in mRNA translation. Nuclear RNA helicase A (DHX9/RHA) is necessary for the translation of the mRNAs of JUND (JunD proto-oncogene AP-1 transcription factor subunit) and HIV-1 genes, and nuclear cap-binding protein 1 (NCBP1)/CBP80 is a component of HIV-1 polysomes. The protein kinase mTOR activates canonical messenger ribonucleoproteins by post-translationally down-regulating the eIF4E inhibitory protein 4E-BP1. We posited here that NCBP1 and DHX9/RHA (RHA) support a translation pathway of JUND RNA that is independent of mTOR. We present evidence from reciprocal immunoprecipitation experiments indicating that NCBP1 and RHA both are components of messenger ribonucleoproteins in several cell types. Moreover, tandem affinity and RT-quantitative PCR results revealed that JUND mRNA is a component of a previously unknown ribonucleoprotein complex. Results from the tandem IP indicated that another component of the JUND-containing ribonucleoprotein complex is NCBP3, a recently identified ortholog of NCBP2/CBP20. We also found that NCBP1, NCBP3, and RHA, but not NCBP2, are components of JUND-containing polysomes. Mutational analysis uncovered two dsRNA-binding domains of RHA that are necessary to tether JUND-NCBP1/NCBP3 to polysomes. We also found that JUND translation is unaffected by inhibition of mTOR, unless RHA was down-regulated by siRNA. These findings uncover a noncanonical cap-binding complex consisting of NCBP1/NCBP3 and RHA substitutes for the eukaryotic translation initiation factors 4E and 4G and activates mTOR-independent translation of the mRNA encoding the tumor suppressor JUND.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sarah E Fritz
- Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Bradley Seufzer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108 .,Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
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27
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eIF4A3 Phosphorylation by CDKs Affects NMD during the Cell Cycle. Cell Rep 2020; 26:2126-2139.e9. [PMID: 30784594 DOI: 10.1016/j.celrep.2019.01.101] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/16/2018] [Accepted: 01/25/2019] [Indexed: 12/24/2022] Open
Abstract
Exon junction complexes (EJCs) loaded onto spliced mRNAs during splicing serve as molecular markers for various post-transcriptional gene-regulatory processes, including nonsense-mediated mRNA decay (NMD). Although the composition and structure of EJCs are well characterized, the mechanism regulating EJC deposition remains unknown. Here we find that threonine 163 (T163) within the RNA-binding motif of eIF4A3 (a core EJC component) is phosphorylated by cyclin-dependent protein kinases 1 and 2 in a cell cycle-dependent manner. T163 phosphorylation hinders binding of eIF4A3 to spliced mRNAs and other EJC components. Instead, it promotes association of eIF4A3 with CWC22, which guides eIF4A3 to an active spliceosome. These molecular events ensure the fidelity of specific deposition of the EJC ∼20-24 nt upstream of an exon-exon junction. Accordingly, NMD is affected by T163 phosphorylation. Collectively, our data provide evidence that T163 phosphorylation affects EJC formation and, consequently, NMD efficiency in a cell cycle-dependent manner.
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28
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Lin Y, Liang R, Mao Y, Ye J, Mai R, Gao X, Liu Z, Wainwright T, Li Q, Luo M, Ge L, Li Y, Zou D. Comprehensive analysis of biological networks and the eukaryotic initiation factor 4A-3 gene as pivotal in hepatocellular carcinoma. J Cell Biochem 2020; 121:4094-4107. [PMID: 31898336 DOI: 10.1002/jcb.29596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022]
Abstract
Eukaryotic initiation factor 4A-3 (EIF4A3) is a core component of the exon junction complex (EJC). Abnormalities in EIF4A3 are associated with carcinogenesis. The present study aimed to determine the biological role of EIF4A3 in hepatocellular carcinoma (HCC). Our study is based on the analysis of HCC sequencing data from public databases. We first used the Gene Expression Profiling Interactive Analysis tool and ONCOMINE to analyze the EIF4A3 expression, and the results were validated in human clinical tissues by a quantitative real-time polymerase chain reaction, Western blot, and immunohistochemical. Then, we used cBioPortal to identify EIF4A3 alterations and function networks. Finally, we created a network of genes that were positively correlated with EIF4A3 using LinkedOmics, and analyzed this network using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. For the genes identified, we also analyzed the relevant kinase and transcription factor target networks as well as the protein-protein interaction networks. Our results show that EIF4A3 was overexpressed in HCC tissues in comparison with normal tissues, and high EIF4A3 expression was significantly associated with poor prognosis. Analysis of the functional networks of genes that were co-occurring with EIF4A3 amplification revealed connections with several chemokine signaling pathways. Furthermore, genes that positively correlated with EIF4A3 were mainly related to cell cycle and spliceosome pathways, several cell cycle regulatory kinases, and tumor-associated transcription factors. Finally, crosslinking-immunoprecipitation and high-throughput sequencing (CLIP-seq) data showed that EIF4A3 protein binds to multiple exon regions of the cell cycle regulatory genes cyclin-dependent kinases 1 and 2 and transcription factor E2F1. Our study unveils potential biological networks in HCC and the pivotal role of EIF4A3 as a bridging protein, highlighting the need for an in-depth study of EIF4A3 in carcinogenesis.
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Affiliation(s)
- Yan Lin
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Rong Liang
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Jiazhou Ye
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Rongyun Mai
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xing Gao
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ziyu Liu
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Taylor Wainwright
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Qian Li
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Min Luo
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lianying Ge
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Department of Endoscopy, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yongqiang Li
- Department of Medical Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Donghua Zou
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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29
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Abstract
BACKGROUND RNA-binding proteins (RBPs) are crucial in modulating RNA metabolism in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Although previous studies on the conservation of RBP targets have been carried out in lower eukaryotes such as yeast, relatively little is known about the extent of conservation of the binding sites of RBPs across mammalian species. RESULTS In this study, we employ CLIP-seq datasets for 60 human RBPs and demonstrate that most binding sites for a third of these RBPs are conserved in at least 50% of the studied vertebrate species. Across the studied RBPs, binding sites were found to exhibit a median conservation of 58%, ~ 20% higher than random genomic locations, suggesting a significantly higher preservation of RBP-RNA interaction networks across vertebrates. RBP binding sites were highly conserved across primates with weak conservation profiles in birds and fishes. We also note that phylogenetic relationship between members of an RBP family does not explain the extent of conservation of their binding sites across species. Multivariate analysis to uncover features contributing to differences in the extents of conservation of binding sites across RBPs revealed RBP expression level and number of post-transcriptional targets to be the most prominent factors. Examination of the location of binding sites at the gene level confirmed that binding sites occurring on the 3' region of a gene are highly conserved across species with 90% of the RBPs exhibiting a significantly higher conservation of binding sites in 3' regions of a gene than those occurring in the 5'. Gene set enrichment analysis on the extent of conservation of binding sites to identify significantly associated human phenotypes revealed an enrichment for multiple developmental abnormalities. CONCLUSIONS Our results suggest that binding sites of human RBPs are highly conserved across primates with weak conservation profiles in lower vertebrates and evolutionary relationship between members of an RBP family does not explain the extent of conservation of their binding sites. Expression level and number of targets of an RBP are important factors contributing to the differences in the extent of conservation of binding sites. RBP binding sites on 3' ends of a gene are the most conserved across species. Phenotypic analysis on the extent of conservation of binding sites revealed the importance of lineage-specific developmental events in post-transcriptional regulatory network evolution.
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Affiliation(s)
- Aarthi Ramakrishnan
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, 46202, USA. .,Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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30
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Jeong K, Ryu I, Park J, Hwang HJ, Ha H, Park Y, Oh ST, Kim YK. Staufen1 and UPF1 exert opposite actions on the replacement of the nuclear cap-binding complex by eIF4E at the 5' end of mRNAs. Nucleic Acids Res 2019; 47:9313-9328. [PMID: 31361897 PMCID: PMC6753478 DOI: 10.1093/nar/gkz643] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 01/31/2023] Open
Abstract
Newly synthesized mRNAs are exported from the nucleus to cytoplasm with a 5′-cap structure bound by the nuclear cap-binding complex (CBC). During or after export, the CBC should be properly replaced by cytoplasmic cap-binding protein eIF4E for efficient protein synthesis. Nonetheless, little is known about how the replacement takes place. Here, we show that double-stranded RNA-binding protein staufen1 (STAU1) promotes efficient replacement by facilitating an association between the CBC–importin α complex and importin β. Our transcriptome-wide analyses and artificial tethering experiments also reveal that the replacement occurs more efficiently when an mRNA associates with STAU1. This event is inhibited by a key nonsense-mediated mRNA decay factor, UPF1, which directly interacts with STAU1. Furthermore, we find that cellular apoptosis that is induced by ionizing radiation is accompanied by inhibition of the replacement via increased association between STAU1 and hyperphosphorylated UPF1. Altogether, our data highlight the functional importance of STAU1 and UPF1 in the course of the replacement of the CBC by eIF4E, adding a previously unappreciated layer of post-transcriptional gene regulation.
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Affiliation(s)
- Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Incheol Ryu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sang Taek Oh
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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31
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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32
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Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D, Wilson SA. Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Mol Cell 2019; 75:310-323.e8. [PMID: 31104896 PMCID: PMC6675937 DOI: 10.1016/j.molcel.2019.04.034] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 02/25/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5′ end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3′ end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5′ end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome. 5′ cap binding complex CBC acts as a transient landing pad for Alyref Alyref is deposited upstream of the exon-exon junction next to the EJC Alyref can be deposited on introns and regulate splicing Chtop is mainly deposited on 3′ UTRs and influences poly(A) site choices
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Affiliation(s)
- Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Llywelyn Griffith
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Catherine G Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David Sims
- MRC Computational Genomics Analysis and Training Programme (CGAT), MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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33
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Kim YK, Maquat LE. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA (NEW YORK, N.Y.) 2019; 25:407-422. [PMID: 30655309 PMCID: PMC6426291 DOI: 10.1261/rna.070136.118] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nonsense-mediated mRNA decay (NMD), which is arguably the best-characterized translation-dependent regulatory pathway in mammals, selectively degrades mRNAs as a means of post-transcriptional gene control. Control can be for the purpose of ensuring the quality of gene expression. Alternatively, control can facilitate the adaptation of cells to changes in their environment. The key to NMD, no matter what its purpose, is the ATP-dependent RNA helicase upstream frameshift 1 (UPF1), without which NMD fails to occur. However, UPF1 does much more than regulate NMD. As examples, UPF1 is engaged in functionally diverse mRNA decay pathways mediated by a variety of RNA-binding proteins that include staufen, stem-loop-binding protein, glucocorticoid receptor, and regnase 1. Moreover, UPF1 promotes tudor-staphylococcal/micrococcal-like nuclease-mediated microRNA decay. In this review, we first focus on how the NMD machinery recognizes an NMD target and triggers mRNA degradation. Next, we compare and contrast the mechanisms by which UPF1 functions in the decay of other mRNAs and also in microRNA decay. UPF1, as a protein polymath, engenders cells with the ability to shape their transcriptome in response to diverse biological and physiological needs.
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Affiliation(s)
- Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun 2019; 10:521. [PMID: 30705266 PMCID: PMC6355915 DOI: 10.1038/s41467-019-08381-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023] Open
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.
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Polyamines stimulate the CHSY1 synthesis through the unfolding of the RNA G-quadruplex at the 5'-untraslated region. Biochem J 2018; 475:3797-3812. [PMID: 30401686 DOI: 10.1042/bcj20180672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/04/2018] [Accepted: 11/05/2018] [Indexed: 01/20/2023]
Abstract
Glycosaminoglycans (GAGs), a group of structurally related acidic polysaccharides, are primarily found as glycan moieties of proteoglycans (PGs). Among these, chondroitin sulfate (CS) and dermatan sulfate, side chains of PGs, are widely distributed in animal kingdom and show structural variations, such as sulfation patterns and degree of epimerization, which are responsible for their physiological functions through interactions with growth factors, chemokines and adhesion molecules. However, structural changes in CS, particularly the ratio of 4-O-sulfation to 6-O-sulfation (4S/6S) and CS chain length that occur during the aging process, are not fully understood. We found that 4S/6S ratio and molecular weight of CS were decreased in polyamine-depleted cells. In addition, decreased levels of chondroitin synthase 1 (CHSY1) and chondroitin 4-O-sulfotransferase 2 proteins were also observed on polyamine depletion. Interestingly, the translation initiation of CHSY1 was suppressed by a highly structured sequence (positions -202 to -117 relative to the initiation codon) containing RNA G-quadruplex (G4) structures in 5'-untranslated region. The formation of the G4s was influenced by the neighboring sequences to the G4s and polyamine stimulation of CHSY1 synthesis disappeared when the formation of the G4s was inhibited by site-directed mutagenesis. These results suggest that the destabilization of G4 structures by polyamines stimulates CHSY1 synthesis and, at least in part, contribute to the maturation of CS chains.
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Gong P, Li J, He C. Exon junction complex (EJC) core genes play multiple developmental roles in Physalis floridana. PLANT MOLECULAR BIOLOGY 2018; 98:545-563. [PMID: 30426309 PMCID: PMC6280879 DOI: 10.1007/s11103-018-0795-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Molecular and functional characterization of four gene families of the Physalis exon junction complex (EJC) core improved our understanding of the evolution and function of EJC core genes in plants. The exon junction complex (EJC) plays significant roles in posttranscriptional regulation of genes in eukaryotes. However, its developmental roles in plants are poorly known. We characterized four EJC core genes from Physalis floridana that were named PFMAGO, PFY14, PFeIF4AIII and PFBTZ. They shared a similar phylogenetic topology and were expressed in all examined organs. PFMAGO, PFY14 and PFeIF4AIII were localized in both the nucleus and cytoplasm while PFBTZ was mainly localized in the cytoplasm. No protein homodimerization was observed, but they could form heterodimers excluding the PFY14-PFBTZ heterodimerization. Virus-induced gene silencing (VIGS) of PFMAGO or PFY14 aborted pollen development and resulted in low plant survival due to a leaf-blight-like phenotype in the shoot apex. Carpel functionality was also impaired in the PFY14 knockdowns, whereas pollen maturation was uniquely affected in PFBTZ-VIGS plants. Once PFeIF4AIII was strongly downregulated, plant survival was reduced via a decomposing root collar after flowering and Chinese lantern morphology was distorted. The expression of Physalis orthologous genes in the DYT1-TDF1-AMS-bHLH91 regulatory cascade that is associated with pollen maturation was significantly downregulated in PFMAGO-, PFY14- and PFBTZ-VIGS flowers. Intron-retention in the transcripts of P. floridana dysfunctional tapetum1 (PFDYT1) occurred in these mutated flowers. Additionally, the expression level of WRKY genes in defense-related pathways in the shoot apex of PFMAGO- or PFY14-VIGS plants and in the root collar of PFeIF4AIII-VIGS plants was significantly downregulated. Taken together, the Physalis EJC core genes play multiple roles including a conserved role in male fertility and newly discovered roles in Chinese lantern development, carpel functionality and defense-related processes. These data increase our understanding of the evolution and functions of EJC core genes in plants.
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Affiliation(s)
- Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Simabuco FM, Pavan ICB, Pestana NF, Carvalho PC, Basei FL, Campos Granato D, Paes Leme AF, Zanchin NIT. Interactome analysis of the human Cap‐specific mRNA (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1) protein. J Cell Biochem 2018; 120:5597-5611. [DOI: 10.1002/jcb.27843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/14/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Fernando Moreira Simabuco
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas Limeira SP Brazil
| | | | - Nathalie Fortes Pestana
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas Limeira SP Brazil
- Centro Universitário da Fundação Hermínio Ometto‐FHO Araras SP Brazil
| | | | | | - Daniela Campos Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
| | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais Campinas SP Brazil
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Ryu I, Park Y, Seo JW, Park OH, Ha H, Nam JW, Kim YK. HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions. FASEB J 2018; 33:2680-2693. [PMID: 30303743 DOI: 10.1096/fj.201800431r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
All metazoan mRNAs have a poly(A) tail at the 3' end with the exception of replication-dependent histone (RDH) mRNAs, which end in a highly conserved stem-loop (SL) structure. However, a subset of RDH mRNAs are reported to be polyadenylated under physiologic conditions. The molecular details of the biogenesis of polyadenylated RDH [poly(A)+ RDH] mRNAs remain unknown. In this study, our genome-wide analyses reveal that puromycin treatment or UVC irradiation stabilizes poly(A)+ RDH mRNAs, relative to canonical RDH mRNAs, which end in an SL structure. We demonstrate that the stabilization of poly(A)+ RDH mRNAs occurs in a translation-independent manner and is regulated via human antigen R (HuR) binding to the extended 3' UTR under stress conditions. Our data suggest that HuR regulates the expression of poly(A)+ RDH mRNAs.-Ryu, I., Park, Y., Seo, J.-W., Park, O. H., Ha, H., Nam, J.-W., Kim, Y. K. HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions.
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Affiliation(s)
- Incheol Ryu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.,Division of Life Sciences, Korea University, Seoul, South Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.,Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jwa-Won Seo
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea; and
| | - Ok Hyun Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.,Division of Life Sciences, Korea University, Seoul, South Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.,Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea; and.,Research Institute for Natural Sciences, Hanyang University, Seoul, South Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.,Division of Life Sciences, Korea University, Seoul, South Korea
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Chen HH, Yu HI, Yang MH, Tarn WY. DDX3 Activates CBC-eIF3-Mediated Translation of uORF-Containing Oncogenic mRNAs to Promote Metastasis in HNSCC. Cancer Res 2018; 78:4512-4523. [PMID: 29921696 DOI: 10.1158/0008-5472.can-18-0282] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/26/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022]
Abstract
Mutated or dysregulated DDX3 participates in the progression and metastasis of cancer via its multiple roles in regulating gene expression and cellular signaling. Here, we show that the high expression levels of DDX3 in head and neck squamous cell carcinoma (HNSCC) correlate with lymph node metastasis and poor prognosis and demonstrate that DDX3 is essential for the proliferation, invasion, and metastasis of oral squamous cell carcinoma (OSCC) cells. Microarray analyses revealed that DDX3 is required for the expression of a set of pro-metastatic genes, including ATF4-modulated genes in an aggressive OSCC cell line. DDX3 activated translation of ATF4 and a set of its downstream targets, all of which contain upstream open reading frames (uORF). DDX3 promoted translation of these targets, likely by skipping the inhibitory uORF. DDX3 specifically enhanced the association of the cap-binding complex (CBC) with uORF-containing mRNAs and facilitated recruitment of the eukaryotic initiation factor 3 (eIF3). CBC and certain eIF3 subunits contributed to the expression of metastatic-related gene expression. Taken together, our results indicate a role for the novel DDX3-CBC-eIF3 translational complex in promoting metastasis.Significance: The discovery of DDX3-mediated expression of oncogenic uORF-containing genes expands knowledge on translational control mechanisms and provides potential targets for cancer therapy.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/16/4512/F1.large.jpg Cancer Res; 78(16); 4512-23. ©2018 AACR.
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Affiliation(s)
- Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsin-I Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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40
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Sloan KE, Bohnsack MT. Unravelling the Mechanisms of RNA Helicase Regulation. Trends Biochem Sci 2018; 43:237-250. [PMID: 29486979 DOI: 10.1016/j.tibs.2018.02.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/28/2018] [Accepted: 02/01/2018] [Indexed: 12/22/2022]
Abstract
RNA helicases are critical regulators at the nexus of multiple pathways of RNA metabolism, and in the complex cellular environment, tight spatial and temporal regulation of their activity is essential. Dedicated protein cofactors play key roles in recruiting helicases to specific substrates and modulating their catalytic activity. Alongside individual RNA helicase cofactors, networks of cofactors containing evolutionarily conserved domains such as the G-patch and MIF4G domains highlight the potential for cross-regulation of different aspects of gene expression. Structural analyses of RNA helicase-cofactor complexes now provide insight into the diverse mechanisms by which cofactors can elicit specific and coordinated regulation of RNA helicase action. Furthermore, post-translational modifications (PTMs) and long non-coding RNA (lncRNA) regulators have recently emerged as novel modes of RNA helicase regulation.
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Affiliation(s)
- Katherine E Sloan
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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Abstract
In mammals, cap-dependent translation of mRNAs is initiated by two distinct mechanisms: cap-binding complex (CBC; a heterodimer of CBP80 and 20)-dependent translation (CT) and eIF4E-dependent translation (ET). Both translation initiation mechanisms share common features in driving cap-dependent translation; nevertheless, they can be distinguished from each other based on their molecular features and biological roles. CT is largely associated with mRNA surveillance such as nonsense-mediated mRNA decay (NMD), whereas ET is predominantly involved in the bulk of protein synthesis. However, several recent studies have demonstrated that CT and ET have similar roles in protein synthesis and mRNA surveillance. In a subset of mRNAs, CT preferentially drives the cap-dependent translation, as ET does, and ET is responsible for mRNA surveillance, as CT does. In this review, we summarize and compare the molecular features of CT and ET with a focus on the emerging roles of CT in translation.
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Affiliation(s)
- Incheol Ryu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841,
Korea
- School of Life Sciences, Korea University, Seoul 02841,
Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841,
Korea
- School of Life Sciences, Korea University, Seoul 02841,
Korea
- Corresponding author. Tel: +82-2-3290-3410; Fax: +82-2-923-9923; E-mail:
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42
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Vaklavas C, Blume SW, Grizzle WE. Translational Dysregulation in Cancer: Molecular Insights and Potential Clinical Applications in Biomarker Development. Front Oncol 2017; 7:158. [PMID: 28798901 PMCID: PMC5526920 DOI: 10.3389/fonc.2017.00158] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 01/04/2023] Open
Abstract
Although transcript levels have been traditionally used as a surrogate measure of gene expression, it is increasingly recognized that the latter is extensively and dynamically modulated at the level of translation (messenger RNA to protein). Over the recent years, significant progress has been made in dissecting the complex posttranscriptional mechanisms that regulate gene expression. This advancement in knowledge came hand in hand with the progress made in the methodologies to study translation both at gene-specific as well as global genomic level. The majority of translational control is exerted at the level of initiation; nonetheless, protein synthesis can be modulated at the level of translation elongation, termination, and recycling. Sequence and structural elements and epitranscriptomic modifications of individual transcripts allow for dynamic gene-specific modulation of translation. Cancer cells usurp the regulatory mechanisms that govern translation to carry out translational programs that lead to the phenotypic hallmarks of cancer. Translation is a critical nexus in neoplastic transformation. Multiple oncogenes and signaling pathways that are activated, upregulated, or mutated in cancer converge on translation and their transformative impact "bottlenecks" at the level of translation. Moreover, this translational dysregulation allows cancer cells to adapt to a diverse array of stresses associated with a hostile microenviroment and antitumor therapies. All elements involved in the process of translation, from the transcriptional template, the components of the translational machinery, to the proteins that interact with the transcriptome, have been found to be qualitatively and/or quantitatively perturbed in cancer. This review discusses the regulatory mechanisms that govern translation in normal cells and how translation becomes dysregulated in cancer leading to the phenotypic hallmarks of malignancy. We also discuss how dysregulated mediators or components of translation can be utilized as biomarkers with potential diagnostic, prognostic, or predictive significance. Such biomarkers have the potential advantage of uniform applicability in the face of inherent tumor heterogeneity and deoxyribonucleic acid instability. As translation becomes increasingly recognized as a process gone awry in cancer and agents are developed to target it, the utility and significance of these potential biomarkers is expected to increase.
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Affiliation(s)
- Christos Vaklavas
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Scott W Blume
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - William E Grizzle
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
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Iwatani-Yoshihara M, Ito M, Ishibashi Y, Oki H, Tanaka T, Morishita D, Ito T, Kimura H, Imaeda Y, Aparicio S, Nakanishi A, Kawamoto T. Discovery and Characterization of a Eukaryotic Initiation Factor 4A-3-Selective Inhibitor That Suppresses Nonsense-Mediated mRNA Decay. ACS Chem Biol 2017; 12:1760-1768. [PMID: 28440616 DOI: 10.1021/acschembio.7b00041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic initiation factor 4A-3 (eIF4A3) is an Asp-Glu-Ala-Asp (DEAD) box-family adenosine triphosphate (ATP)-dependent RNA helicase. Subtypes eIF4A1 and eIF4A2 are required for translation initiation, but eIF4A3 participates in the exon junction complex (EJC) and functions in RNA metabolism including nonsense-mediated RNA decay (NMD). No small molecules for NMD inhibition via selective inhibition of eIF4A3 have been discovered. Here, we identified allosteric eIF4A3 inhibitors from a high-throughput screening campaign. Chemical optimization of the lead compounds based on ATPase activity yielded compound 2, which exhibited noncompetitive inhibition with ATP or RNA and high selectivity for eIF4A3 over other helicases. The optimized compounds suppressed the helicase activity of eIF4A3 in an ATPase-dependent manner. Hydrogen/deuterium exchange mass spectrometry demonstrated that the deuterium-incorporation pattern of compound 2 overlapped with that of an allosteric pan-eIF4A inhibitor, hippuristanol, suggesting that compound 2 binds to an allosteric region on eIF4A3. We examined NMD activity using a luciferase-based cellular reporter system and a quantitative real-time polymerase chain-reaction-based cellular system to monitor levels of endogenous NMD substrates. NMD suppression by the compounds correlated positively with their ATPase-inhibitory activity. In conclusion, we developed a novel eIF4A3 inhibitor that targets the EJC. The optimized chemical probes represent useful tools for understanding the functions of eIF4A3 in RNA homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Samuel Aparicio
- BC Cancer Agency, Department of Molecular Oncology, Vancouver, British Columbia V5Z 1L3, Canada
- University of British Columbia, Department of Pathology
and Laboratory Medicine, Vancouver, British Columbia V6T 2B5, Canada
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Salton GD, Laurino CCFC, Mega NO, Delgado-Cañedo A, Setterblad N, Carmagnat M, Xavier RM, Cirne-Lima E, Lenz G, Henriques JAP, Laurino JP. Deletion of eIF2β lysine stretches creates a dominant negative that affects the translation and proliferation in human cell line: A tool for arresting the cell growth. Cancer Biol Ther 2017; 18:560-570. [PMID: 28692326 DOI: 10.1080/15384047.2017.1345383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Eukaryote initiation factor 2 subunit β (eIF2β) plays a crucial role in regulation protein synthesis, which mediates the interaction of eIF2 with mRNA. eIF2β contains evolutionarily conserved polylysine stretches in amino-terminal region and a zinc finger motif in the carboxy-terminus. METHODS The gene eIF2β was cloned under tetracycline transcription control and the polylysine stretches were deleted by site-directed mutagenesis (eIF2βΔ3K). The plasmid was transfected into HEK 293 TetR cells. These cells were analyzed for their proliferative and translation capacities as well as cell death rate. Experiments were performed using gene reporter assays, western blotting, flow cytometry, cell sorting, cell proliferation assays and confocal immunofluorescence. RESULTS eIF2βΔ3K affected negatively the protein synthesis, cell proliferation and cell survival causing G2 cell cycle arrest and increased cell death, acting in a negative dominant manner against the native protein. Polylysine stretches are also essential for eIF2β translocated from the cytoplasm to the nucleus, accumulating in the nucleolus and eIF2βΔ3K did not make this translocation. DISCUSSION eIF2β is involved in the protein synthesis process and should act in nuclear processes as well. eIF2βΔ3K reduces cell proliferation and causes cell death. Since translation control is essential for normal cell function and survival, the development of drugs or molecules that inhibit translation has become of great interest in the scenario of proliferative disorders. In conclusion, our results suggest the dominant negative eIF2βΔ3K as a therapeutic strategy for the treatment of proliferative disorders and that eIF2β polylysine stretch domains are promising targets for this.
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Affiliation(s)
- Gabrielle Dias Salton
- a Post-Graduation Program in Cellular and Molecular Biology, Molecular Radiobiology Laboratory, Biotechnology Center , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil , Cryobiology Unit and Umbilical Cord Blood Bank, Hemotherapy Service , Hospital de Clínicas de Porto Alegre , Porto Alegre (RS) , Brazil
| | - Claudia Cilene Fernandes Correia Laurino
- b Molecular Biology for Auto-immune and Infectious Diseases Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil . Embriology and Cellular Differentiation Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre; Faculdade de Veterinária , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil . Faculdade Nossa Senhora de Fátima , Caxias do Sul (RS) , Brazil . Instituto Brasileiro de Saúde , Porto Alegre (RS) , Brazil
| | - Nicolás Oliveira Mega
- c Animal Biology Post-Graduation Program , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil
| | - Andrés Delgado-Cañedo
- d Biotechnology Research Center for Interdisciplinary Research , Universidade Federal do Pampa , São Gabriel (RS) , Brazil
| | - Niclas Setterblad
- e Imaging, Cell Selection and Genomics Platform , Institut Universitaire d'Hématologie, Hôpital Saint-Louis , Paris , France
| | - Maryvonnick Carmagnat
- f Immunology and Histocompatibility Laboratory AP-HP , INSERM UMRS 940, Institut Universitaire d'Hématologie , Paris , France
| | - Ricardo Machado Xavier
- g Molecular Biology for Auto-immune and Infectious Diseases Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil
| | - Elizabeth Cirne-Lima
- h Embriology and Cellular Differentiation Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre; Faculdade de Veterinária , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil
| | - Guido Lenz
- i Cell Signaling Laboratory, Biophysics Department, Biotechnology Center and Post-Graduation Program in Cellular and Molecular Biology , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) , Brazil
| | - João Antonio Pêgas Henriques
- j Molecular Radiobiology Laboratory, Biotechnology Center and Post-Graduation Program in Cellular and Molecular Biology , Universidade Federal do Rio Grande do Sul , Porto Alegre (RS) ; Biotechnology Institute , Universidade de Caxias do Sul , Caxias do Sul (RS) , Brazil
| | - Jomar Pereira Laurino
- k Biotechnology Institute , Universidade de Caxias do Sul, Caxias do Sul (RS) and Instituto Brasileiro de Saúde , Porto Alegre (RS) , Brazil
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Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol 2017; 91:145-155. [PMID: 28673892 DOI: 10.1016/j.biocel.2017.06.016] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 01/18/2023]
Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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Park OH, Park J, Yu M, An HT, Ko J, Kim YK. Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay. Genes Dev 2017; 30:2093-2105. [PMID: 27798850 PMCID: PMC5066615 DOI: 10.1101/gad.286484.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
In this study, Park et al. investigated the molecular mechanisms regulating glucocorticoid receptor-mediated mRNA decay (GMD). The authors characterize the molecular details of GMD, identify specific factors required for efficient GMD, and perform RNA sequencing, identifying many endogenous GMD substrates. Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.
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Affiliation(s)
- Ok Hyun Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Mira Yu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyoung-Tae An
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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47
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Park J, Park Y, Ryu I, Choi MH, Lee HJ, Oh N, Kim K, Kim KM, Choe J, Lee C, Baik JH, Kim YK. Misfolded polypeptides are selectively recognized and transported toward aggresomes by a CED complex. Nat Commun 2017; 8:15730. [PMID: 28589942 PMCID: PMC5467238 DOI: 10.1038/ncomms15730] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Misfolded polypeptides are rapidly cleared from cells via the ubiquitin–proteasome system (UPS). However, when the UPS is impaired, misfolded polypeptides form small cytoplasmic aggregates, which are sequestered into an aggresome and ultimately degraded by aggrephagy. Despite the relevance of the aggresome to neurodegenerative proteinopathies, the molecular mechanisms underlying aggresome formation remain unclear. Here we show that the CTIF–eEF1A1–DCTN1 (CED) complex functions in the surveillance of either pre-existing or newly synthesized polypeptides by linking two molecular events: selective recognition and aggresomal targeting of misfolded polypeptides. These events are accompanied by CTIF sequestration into the aggresome, preventing the additional synthesis of misfolded polypeptides from mRNAs bound by nuclear cap-binding complex. These events render cells more resistant to apoptosis induced by proteotoxic stresses. Collectively, our data provide compelling evidence for a previously unappreciated protein surveillance pathway and a regulatory gene expression network for coping with misfolded polypeptides. Misfolded polypeptide aggregates are actively transported to aggresomes, where they are degraded through aggrephagy. Here the authors show that these aggregates are selectively recognized by the CTIF–eEF1A1–DCTN1 (CED) complex and transported to aggresomes through the interactions of DCTN1 with dynein motors.
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Affiliation(s)
- Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Incheol Ryu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Mi-Hyun Choi
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyo Jin Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Nara Oh
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kyutae Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.,BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Kyoung Mi Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Junho Choe
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Cheolju Lee
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Ja-Hyun Baik
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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48
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Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA (NEW YORK, N.Y.) 2017; 23:270-283. [PMID: 27994090 PMCID: PMC5311483 DOI: 10.1261/rna.059105.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/14/2016] [Indexed: 06/01/2023]
Abstract
Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5' proximal-intron-minus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC.
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Affiliation(s)
- Can Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Hon Nian Chua
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- DataRobot, Inc., Boston, Massachusetts 02109, USA
| | - Guramrit Singh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston 02215, Massachusetts, USA
- The Canadian Institute for Advanced Research, Toronto M5G 1Z8, Ontario, Canada
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49
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Choudhury SR, Singh AK, McLeod T, Blanchette M, Jang B, Badenhorst P, Kanhere A, Brogna S. Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster. eLife 2016; 5:e19881. [PMID: 27879206 PMCID: PMC5158136 DOI: 10.7554/elife.19881] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022] Open
Abstract
Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells. The association of the EJC proteins with nascent transcripts does not require CWC22 and that of Y14 and MAGO is independent of eIF4AIII. We also show that eIF4AIII associates with both polysomal and monosomal RNA in S2 cell extracts, whereas Y14 and MAGO fractionate separately. Cumulatively, our data indicate a global role of eIF4AIII in gene expression, which would be independent of Y14 and MAGO, splicing, and of the EJC, as currently understood.
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Affiliation(s)
| | - Anand K Singh
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Tina McLeod
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas city, United States
| | - Boyun Jang
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Paul Badenhorst
- Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Saverio Brogna
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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50
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Boehm V, Gehring NH. Exon Junction Complexes: Supervising the Gene Expression Assembly Line. Trends Genet 2016; 32:724-735. [PMID: 27667727 DOI: 10.1016/j.tig.2016.09.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/23/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
The exon junction complex (EJC) is an RNA-binding protein complex that is assembled and deposited onto mRNAs during splicing. The EJC comprises four core components that bind to not only canonical sites upstream of exon-exon junctions, but also to noncanonical sites at other positions in exons. EJC-associated proteins are recruited by the EJC at different steps of gene expression to execute the multiple functions of the EJC. Recently, new insights have been obtained into how EJCs stimulate pre-mRNA splicing, and mRNA export, translation, and degradation. Furthermore, mutations in EJC core components were shown to result in severe disorders in humans, demonstrating the critical physiological role of the EJC. Hence, the EJC has been identified as an important player in post-transcriptional gene regulation in metazoans.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
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