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Fan L, Wang Y, Huang H, Wang Z, Liang C, Yang X, Ye P, Lin J, Shi W, Zhou Y, Yan H, Long Z, Wang Z, Liu L, Qian J. RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA. Emerg Microbes Infect 2024; 13:2300762. [PMID: 38164794 PMCID: PMC10773643 DOI: 10.1080/22221751.2023.2300762] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.
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Affiliation(s)
- Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhongyi Wang
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
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Villers J, Smith EM, DeLiberto AN, Arguello AE, Nyaanga J, Kleiner RE. Chemoproteomic Profiling of 8-Oxoguanosine-Sensitive RNA-Protein Interactions. Biochemistry 2023; 62:3411-3419. [PMID: 38010074 PMCID: PMC11031733 DOI: 10.1021/acs.biochem.3c00461] [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] [Indexed: 11/29/2023]
Abstract
Cellular nucleic acids are subject to assault by endogenous and exogenous agents that can perturb the flow of genetic information. Oxidative stress leads to the accumulation of 8-oxoguanine (8OG) in DNA and RNA. 8OG lesions on mRNA negatively impact translation, but their effect on global RNA-protein interactions is largely unknown. Here, we apply an RNA chemical proteomics approach to investigate the effect of 8OG on RNA-protein binding. We find proteins that bind preferentially to 8OG-modified RNA, including IGF2BP1-3 and hnRNPD, and proteins that are repelled by 8OG such as RBM4. We characterize these interactions using biochemical and biophysical assays to quantify the effect of 8OG on binding and show that a single 8OG abolishes the binding of RBM4 to its preferred CGG-containing substrate. Taken together, our work establishes the molecular consequences of 8OG on cellular RNA-protein binding and provides a framework for interrogating the role of RNA oxidation in biological systems.
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Affiliation(s)
- Jennifer Villers
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | | | | | - Joy Nyaanga
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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Xu M, Li B, Huang J, Jia R, Guo J. The N6-methyladenosine demethylase FTO is required for odontoblast differentiation in vitro and dentine formation in mice by promoting RUNX2 exon 5 inclusion through RBM4. Int Endod J 2023; 56:1534-1549. [PMID: 37698901 DOI: 10.1111/iej.13975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023]
Abstract
AIM Fat mass and obesity-associated (FTO) protein, the first discovered N6-methyladenine (m6A) demethylase, played positive roles in bone formation. In this study, the aim was to investigate the function and potential mechanism of Fto in dentine formation. METHODOLOGY In vivo model, postnatal 12-day (PN12), 4-week-old (4 wk), 6-week-old (6 wk) healthy male C57BL/6J were randomly divided into Fto knockout (Fto-/- ) mice and wild-type (WT) littermates according to their genotypes, with 3-5 mice in each group. The mandibles of Fto-/- mice and WT control littermates were isolated for analysis by micro-computed tomography (micro-CT), 3-dimensional reconstruction and Haematoxylin-eosin (HE) staining. In vitro, mouse dental papilla cells (mDPCs) and human dental stem pulp cells (hDPSCs) were cultured with odontogenetic medium to evaluate differentiation capacity; expression levels of odontoblastic related genes were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR). The inclusion levels of Runt-related transcription factor 2 (RUNX2) exon 5 in mDPCs and hDPSCs were detected by semiquantitative real-time polymerase chain reaction (RT-PCR). The RNA binding motif protein 4 (RBM4) m6A site was verified through m6A methylated RNA immunoprecipitation (MeRIP) and the stability of RBM4 mRNA influenced by FTO knockdown was measured by mRNA stability assay. Differences with p values < .05 were regarded as statistically significant. RESULTS We discovered that Fto-/- mice showed significant dentine formation defects characterized by widened pulp cavity, enlarged pulp-tooth volume ratio, thinned dentine and pre-dentine layer of root (p < .05). Fto-/- mDPCs and FTO-silencing hDPSCs not only exhibited insufficient mineralization ability and decreased expression levels of odontoblastic mineralization related genes (p < .05), but showed significantly reduced Runx2 exon 5 inclusion level (p < .05). FTO knockdown increased the m6A level of RBM4 and destabilized the mRNA of RBM4, thus contributing to the reduced RBM4 expression level. Moreover, Rbm4 overexpression in Fto-/- mDPCs can partly restore Runx2 exon 5 inclusion level and the differentiation ability disrupted by Fto knockout. CONCLUSION Thus, within the limitations of this study, the data suggest that FTO promotes odontoblastic differentiation during dentine formation by stabilizing RBM4 mRNA to promote RUNX2 exon 5 inclusion.
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Affiliation(s)
- Mi Xu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Bingrong Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Junjun Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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Han H, Lin T, Wang Z, Song J, Fang Z, Zhang J, You X, Du Y, Ye J, Zhou G. RNA-binding motif 4 promotes angiogenesis in HCC by selectively activating VEGF-A expression. Pharmacol Res 2023; 187:106593. [PMID: 36496136 DOI: 10.1016/j.phrs.2022.106593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Increased angiogenesis in the liver plays a critical role in the progression of hepatocellular carcinoma (HCC). However, the molecular mechanism underlying increased angiogenesis in HCC is not well understood. Current study was designed to identify the potential angiogenic effect of RNA-binding motif 4 (RBM4)through a small-scale overexpression screening, followed by comparison of the expression level of RBM4 in cancer and adjacent tissues in multiple malignancies to explore the relationship between RBM4 and CD31 protein expression level and related clinical indicators, and understand the role of RBM4 in the hepatocellular carcinoma. To understand the specific mechanism of RBM4 in detail, transcriptome sequencing, mass spectrometry and multiple molecular cytological studies were performed. These cellular level results were verified by experiments in animal models of nude mice. The increased expression of RBM4 in cancer tissues, suggested its use as a prognostic biomarker. The RBM4 expression was found to be strongly correlated with tumor microvessel density. Mechanistically, RBM4 mediated its effects via interaction with HNRNP-M through the latter's WDR15 domain, which then stabilized RelA/p65 mRNA. Consequently, RBM4 induced the activation of the NF-kB signaling pathway, upregulating the expression of proangiogenic factor VEGF-A. The results confirmed the mechanism by which RBM4 promotes angiogenesis in hepatocellular carcinoma suggesting RBM4 as a crucial promoter of angiogenesis in HCC, helping understand regulation of NF-kB signaling in HCC.
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Affiliation(s)
- Hexu Han
- Department of Gastroenterology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu 225300, China
| | - Ting Lin
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhenyu Wang
- Department of pediatric surgery, Affiliated Hospital of Nantong University, Nantong University, Jiangsu 226001, China
| | - Jingjing Song
- Department of Pediatrics, the Second Affiliated Hospital &Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027 Zhejiang, China
| | - Ziyi Fang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong University, Jiangsu 226001, China
| | - Jing Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong University, Jiangsu 226001, China
| | - Xiaomin You
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong University, Jiangsu 226001, China
| | - Yanping Du
- Department of Gastroenterology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu 225300, China
| | - Jun Ye
- Center for Translational Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu 225300, China.
| | - Guoxiong Zhou
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong University, Jiangsu 226001, China.
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RNA-Binding Proteins in the Regulation of Adipogenesis and Adipose Function. Cells 2022; 11:cells11152357. [PMID: 35954201 PMCID: PMC9367552 DOI: 10.3390/cells11152357] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023] Open
Abstract
The obesity epidemic represents a critical public health issue worldwide, as it is a vital risk factor for many diseases, including type 2 diabetes (T2D) and cardiovascular disease. Obesity is a complex disease involving excessive fat accumulation. Proper adipose tissue accumulation and function are highly transcriptional and regulated by many genes. Recent studies have discovered that post-transcriptional regulation, mainly mediated by RNA-binding proteins (RBPs), also plays a crucial role. In the lifetime of RNA, it is bound by various RBPs that determine every step of RNA metabolism, from RNA processing to alternative splicing, nucleus export, rate of translation, and finally decay. In humans, it is predicted that RBPs account for more than 10% of proteins based on the presence of RNA-binding domains. However, only very few RBPs have been studied in adipose tissue. The primary aim of this paper is to provide an overview of RBPs in adipogenesis and adipose function. Specifically, the following best-characterized RBPs will be discussed, including HuR, PSPC1, Sam68, RBM4, Ybx1, Ybx2, IGF2BP2, and KSRP. Characterization of these proteins will increase our understanding of the regulatory mechanisms of RBPs in adipogenesis and provide clues for the etiology and pathology of adipose-tissue-related diseases.
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6
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Li S, Qi Y, Yu J, Hao Y, He B, Zhang M, Dai Z, Jiang T, Li S, Huang F, Chen N, Wang J, Yang M, Liang D, An F, Zhao J, Fan W, Pan Y, Deng Z, Luo Y, Guo T, Peng F, Hou Z, Wang C, Zheng F, Xu L, Xu J, Wen Q, Jin B, Wang Y, Liu Q. Nuclear Aurora kinase A switches m 6A reader YTHDC1 to enhance an oncogenic RNA splicing of tumor suppressor RBM4. Signal Transduct Target Ther 2022; 7:97. [PMID: 35361747 PMCID: PMC8971511 DOI: 10.1038/s41392-022-00905-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
Aberrant RNA splicing produces alternative isoforms of genes to facilitate tumor progression, yet how this process is regulated by oncogenic signal remains largely unknown. Here, we unveil that non-canonical activation of nuclear AURKA promotes an oncogenic RNA splicing of tumor suppressor RBM4 directed by m6A reader YTHDC1 in lung cancer. Nuclear translocation of AURKA is a prerequisite for RNA aberrant splicing, specifically triggering RBM4 splicing from the full isoform (RBM4-FL) to the short isoform (RBM4-S) in a kinase-independent manner. RBM4-S functions as a tumor promoter by abolishing RBM4-FL-mediated inhibition of the activity of the SRSF1-mTORC1 signaling pathway. Mechanistically, AURKA disrupts the binding of SRSF3 to YTHDC1, resulting in the inhibition of RBM4-FL production induced by the m6A-YTHDC1-SRSF3 complex. In turn, AURKA recruits hnRNP K to YTHDC1, leading to an m6A-YTHDC1-hnRNP K-dependent exon skipping to produce RBM4-S. Importantly, the small molecules that block AURKA nuclear translocation, reverse the oncogenic splicing of RBM4 and significantly suppress lung tumor progression. Together, our study unveils a previously unappreciated role of nuclear AURKA in m6A reader YTHDC1-dependent oncogenic RNA splicing switch, providing a novel therapeutic route to target nuclear oncogenic events.
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Affiliation(s)
- SiSi Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - YangFan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - JiaChuan Yu
- Department of Anesthesiology, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - YuChao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Bin He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - MengJuan Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - ZhenWei Dai
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - TongHui Jiang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - SuYi Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Fang Huang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Ning Chen
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jing Wang
- Department of Oncology, the First Affiliated Hospital of Gannan Medical College, Ganzhou, China
| | - MengYing Yang
- Department of Oncology, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - DaPeng Liang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Fan An
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - JinYao Zhao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - WenJun Fan
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - YuJia Pan
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - ZiQian Deng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - YuanYuan Luo
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Tao Guo
- Department of Thoracic surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fei Peng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - ZhiJie Hou
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - ChunLi Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - FeiMeng Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - LingZhi Xu
- Department of Oncology, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jie Xu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - QingPing Wen
- Department of Anesthesiology, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - BiLian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.
| | - Yang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China.
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Niu K, Zhang X, Song Q, Feng Q. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4. Int J Mol Sci 2022; 23:ijms23020743. [PMID: 35054929 PMCID: PMC8776124 DOI: 10.3390/ijms23020743] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
In eukaryotes, mRNAs translation is mainly mediated in a cap-dependent or cap-independent manner. The latter is primarily initiated at the internal ribosome entry site (IRES) in the 5'-UTR of mRNAs. It has been reported that the G-quadruplex structure (G4) in the IRES elements could regulate the IRES activity. We previously confirmed RBM4 (also known as LARK) as a G4-binding protein in human. In this study, to investigate whether RBM4 is involved in the regulation of the IRES activity by binding with the G4 structure within the IRES element, the IRES-A element in the 5'-UTR of vascular endothelial growth factor A (VEGFA) was constructed into a dicistronic reporter vector, psiCHECK2, and the effect of RBM4 on the IRES activity was tested in 293T cells. The results showed that the IRES insertion significantly increased the FLuc expression activity, indicating that this G4-containing IRES was active in 293T cells. When the G4 structure in the IRES was disrupted by base mutation, the IRES activity was significantly decreased. The IRES activity was notably increased when the cells were treated with G4 stabilizer PDS. EMSA results showed that RBM4 specifically bound the G4 structure in the IRES element. The knockdown of RBM4 substantially reduced the IRES activity, whereas over-expressing RBM4 increased the IRES activity. Taking all results together, we demonstrated that RBM4 promoted the mRNA translation of VEGFA gene by binding to the G4 structure in the IRES.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Correspondence:
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8
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Manet E, Polvèche H, Mure F, Mrozek-Gorska P, Roisné-Hamelin F, Hammerschmidt W, Auboeuf D, Gruffat H. Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein. Nucleic Acids Res 2021; 49:10657-10676. [PMID: 34530456 PMCID: PMC8501971 DOI: 10.1093/nar/gkab787] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Epstein-Barr virus (EBV) is a human herpesvirus associated with human cancers worldwide. Ex vivo, the virus efficiently infects resting human B lymphocytes and induces their continuous proliferation. This process is accompanied by a global reprogramming of cellular gene transcription. However, very little is known on the impact of EBV infection on the regulation of alternative splicing, a pivotal mechanism that plays an essential role in cell fate determination and is often deregulated in cancer. In this study, we have developed a systematic time-resolved analysis of cellular mRNA splice variant expression during EBV infection of resting B lymphocytes. Our results reveal that major modifications of alternative splice variant expression appear as early as day 1 post-infection and suggest that splicing regulation provides—besides transcription—an additional mechanism of gene expression regulation at the onset of B cell activation and proliferation. We also report a role for the viral proteins, EBNA2 and EBNA-LP, in the modulation of specific alternative splicing events and reveal a previously unknown function for EBNA-LP—together with the RBM4 splicing factor—in the alternative splicing regulation of two important modulators of cell proliferation and apoptosis respectively, NUMB and BCL-X.
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Affiliation(s)
- Evelyne Manet
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Univ Lyon, Université Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, Lyon F-69007, France
| | | | - Fabrice Mure
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Univ Lyon, Université Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, Lyon F-69007, France
| | - Paulina Mrozek-Gorska
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research, D-81377 Munich, Germany
| | - Florian Roisné-Hamelin
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Univ Lyon, Université Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, Lyon F-69007, France
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research, D-81377 Munich, Germany
| | | | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Univ Lyon, Université Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, Lyon F-69007, France
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Wang Y, Yu Y, Pang Y, Yu H, Zhang W, Zhao X, Yu J. The distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism. RNA Biol 2021; 18:2107-2126. [PMID: 33787465 DOI: 10.1080/15476286.2021.1909320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The zinc finger CCHC-type (ZCCHC) superfamily proteins, characterized with the consensus sequence C-X2-C-X4-H-X4-C, are accepted to have high-affinity binding to single-stranded nucleic acids, especially single-stranded RNAs. In human beings 25 ZCCHC proteins have been annotated in the HGNC database. Of interest is that among the family, most members are involved in the multiple steps of RNA metabolism. In this review, we focus on the diverged roles of human ZCCHC proteins on RNA transcription, biogenesis, splicing, as well as translation and degradation.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Yu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yidan Pang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haojun Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqi Zhang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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10
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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11
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Lu LF, Zhang C, Zhou XY, Li ZC, Chen DD, Zhou Y, Zhou F, Zhang YA, Li S. Zebrafish RBM47 Promotes Lysosome-Dependent Degradation of MAVS to Inhibit IFN Induction. THE JOURNAL OF IMMUNOLOGY 2020; 205:1819-1829. [PMID: 32859727 DOI: 10.4049/jimmunol.1901387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 08/03/2020] [Indexed: 12/20/2022]
Abstract
IFN is essential for hosts to defend against viral invasion, whereas it must be tightly regulated to prevent hyperimmune responses. Fish mitochondrial antiviral signaling protein (MAVS) is a vital factor for IFN production, but until now, there have been few studies on the regulation mechanisms of fish MAVS enabling IFN to be properly controlled. In this study, we show that zebrafish RNA-binding motif protein 47 (RBM47) promotes MAVS degradation in a lysosome-dependent manner to suppress IFN production. First, the transcription of IFN activated by polyinosinic/polycytidylic acid (poly I:C), spring viremia of carp virus, or retinoic acid-inducible gene I (RIG-I)-like receptor pathway components were significantly suppressed by RBM47. Second, RBM47 interacted with MAVS and promoted lysosome-dependent degradation of MAVS, changing the cellular location of MAVS from the cytoplasm to the lysosome region. Finally, RBM47 inhibited downstream MITA and IRF3/7 activation, impairing the host antiviral response. Collectively, these data suggest that zebrafish RBM47 negatively regulates IFN production by promoting lysosome-dependent degradation of MAVS, providing insights into the role of RBM47 in the innate antiviral immune response in fish.
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Affiliation(s)
- Long-Feng Lu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Can Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Yu Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430070, China; and
| | - Zhuo-Cong Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan-Dan Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Yu Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shun Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; .,College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
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12
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Timaxian C, Raymond-Letron I, Bouclier C, Gulliver L, Le Corre L, Chébli K, Guillou A, Mollard P, Balabanian K, Lazennec G. The health status alters the pituitary function and reproduction of mice in a Cxcr2-dependent manner. Life Sci Alliance 2020; 3:3/3/e201900599. [PMID: 32041848 PMCID: PMC7010316 DOI: 10.26508/lsa.201900599] [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: 11/07/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
This study explores the effects of microbiota on reproductive function of Cxcr2 knockout animals. Cxcr2 is involved in the control of pituitary action and the subsequent development of mammary gland, uterus and ovary. Microbiota and chronic infections can affect not only immune status, but also the overall physiology of animals. Here, we report that chronic infections dramatically modify the phenotype of Cxcr2 KO mice, impairing in particular, their reproduction ability. We show that exposure of Cxcr2 KO females to multiple types of chronic infections prevents their ability to cycle, reduces the development of the mammary gland and alters the morphology of the uterus due to an impairment of ovary function. Mammary gland and ovary transplantation demonstrated that the hormonal contexture was playing a crucial role in this phenomenon. This was further evidenced by alterations to circulating levels of sex steroid and pituitary hormones. By analyzing at the molecular level the mechanisms of pituitary dysfunction, we showed that in the absence of Cxcr2, bystander infections affect leukocyte migration, adhesion, and function, as well as ion transport, synaptic function behavior, and reproduction pathways. Taken together, these data reveal that a chemokine receptor plays a direct role in pituitary function and reproduction in the context of chronic infections.
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Affiliation(s)
- Colin Timaxian
- Centre National de la Recherche Scientifique (CNRS), SYS2DIAG-ALCEDIAG, Cap Delta, Montpellier, France.,CNRS, Groupement de Recherche 3697 "Microenvironment of Tumor Niches," Micronit, France
| | - Isabelle Raymond-Letron
- Department of Histopathology, National Veterinary School of Toulouse, France and Platform of Experimental and Compared Histopathology, STROMALab, Unité de recherche mixte (UMR) Université Paul Sabatier/CNRS 5223, Etablissement français du sang, Institut national de la santé et de la recherche médicale (Inserm) U1031, Toulouse, France
| | - Céline Bouclier
- Centre National de la Recherche Scientifique (CNRS), SYS2DIAG-ALCEDIAG, Cap Delta, Montpellier, France
| | | | - Ludovic Le Corre
- Nutrition et Toxicologie Alimentaire (NUTOX) Laboratory - INSERM Lipides, Nutrition, Cancer UMR 1231 - AgrosupDijon, Dijon, France
| | - Karim Chébli
- Equipe Metazoan Messenger RNAs Metabolism, Montpellier, France
| | - Anne Guillou
- Institut de Génomique Fonctionnelle, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Patrice Mollard
- Institut de Génomique Fonctionnelle, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Karl Balabanian
- CNRS, Groupement de Recherche 3697 "Microenvironment of Tumor Niches," Micronit, France.,Université de Paris, Institut de Recherche Saint-Louis, EMiLy, INSERM U1160, Paris, France
| | - Gwendal Lazennec
- Centre National de la Recherche Scientifique (CNRS), SYS2DIAG-ALCEDIAG, Cap Delta, Montpellier, France .,CNRS, Groupement de Recherche 3697 "Microenvironment of Tumor Niches," Micronit, France
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13
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Wang WY, Quan W, Yang F, Wei YX, Chen JJ, Yu H, Xie J, Zhang Y, Li ZF. RBM4 modulates the proliferation and expression of inflammatory factors via the alternative splicing of regulatory factors in HeLa cells. Mol Genet Genomics 2019; 295:95-106. [DOI: 10.1007/s00438-019-01606-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022]
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14
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Signaling pathways involved in the expression of SZNF and the target genes binding with SZNF related to cyadox. Biomed Pharmacother 2018; 108:1879-1893. [DOI: 10.1016/j.biopha.2018.09.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/11/2018] [Accepted: 09/26/2018] [Indexed: 11/22/2022] Open
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15
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Hsu JCC, Reid DW, Hoffman AM, Sarkar D, Nicchitta CV. Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs. RNA (NEW YORK, N.Y.) 2018; 24:688-703. [PMID: 29438049 PMCID: PMC5900566 DOI: 10.1261/rna.063313.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/30/2018] [Indexed: 05/04/2023]
Abstract
Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence >5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream from encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA-binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA-binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease.
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Affiliation(s)
- Jack C-C Hsu
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University Institute of Molecular Medicine, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, USA
| | - Christopher V Nicchitta
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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16
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Kumar A, Karthikeyan S. Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2018; 74:166-173. [PMID: 29497021 PMCID: PMC5947703 DOI: 10.1107/s2053230x18002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.
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Affiliation(s)
- Adarsh Kumar
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
| | - Subramanian Karthikeyan
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
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17
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Rambout X, Dequiedt F, Maquat LE. Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing. Chem Rev 2017; 118:4339-4364. [PMID: 29251915 DOI: 10.1021/acs.chemrev.7b00470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whereas individual steps of protein-coding gene expression in eukaryotes can be studied in isolation in vitro, it has become clear that these steps are intimately connected within cells. Connections not only ensure quality control but also fine-tune the gene expression process, which must adapt to environmental changes while remaining robust. In this review, we systematically present proven and potential mechanisms by which sequence-specific DNA-binding transcription factors can alter gene expression beyond transcription initiation and regulate pre-mRNA splicing, and thereby mRNA isoform production, by (i) influencing transcription elongation rates, (ii) binding to pre-mRNA to recruit splicing factors, and/or (iii) blocking the association of splicing factors with pre-mRNA. We propose various mechanistic models throughout the review, in some cases without explicit supportive evidence, in hopes of providing fertile ground for future studies.
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18
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Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants. Oncotarget 2016; 7:7497-533. [PMID: 26848775 PMCID: PMC4884935 DOI: 10.18632/oncotarget.7120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue--obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT)--and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the "canonical" way of thymus functioning. Conversely, DS networks represent a "non-canonical" way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes.
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19
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Prognostic value of decreased expression of RBM4 in human gastric cancer. Sci Rep 2016; 6:28222. [PMID: 27324405 PMCID: PMC4915006 DOI: 10.1038/srep28222] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/01/2016] [Indexed: 12/21/2022] Open
Abstract
RNA-binding motif 4 (RBM4) is a multifunctional protein that participates in regulating alternative splicing and mRNA translation. Its reduced expression has been associated with poor overall survival in lung cancer, breast cancer and ovarian cancer. We assessed RBM4 protein expression levels with immunohistochemistry in tissue microarrays containing malignant gastric cancer tissues and benign tissues from 813 patients. We also examined the expression levels of RBM4 mRNA in twenty-five paired gastric cancer samples and adjacent noncancerous tissues. Both RBM4 protein and mRNA expression levels were significantly lower in gastric cancer tissues compared with the adjacent noncancerous tissues. There was a significant association between reduced RBM4 protein expression and differentiation (P < 0.001), lymph node metastasis (P = 0.026), TNM state (P = 0.014) and distant metastasis (P = 0.036). Patients with reduced RBM4 expression (P < 0.001, CI = 0.315–0.710) and TNM stage III and IV (P < 0.001, CI = 4.757–11.166) had a poor overall survival. These findings suggest that RBM4 is a new biomarker in gastric cancer, as the reduced expression of this protein is correlated with poor differentiation, lymph node status and distant metastasis. Further, lower RBM4 expression is an independent prognostic marker for gastric cancer.
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20
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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21
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Gowen BG, Chim B, Marceau CD, Greene TT, Burr P, Gonzalez JR, Hesser CR, Dietzen PA, Russell T, Iannello A, Coscoy L, Sentman CL, Carette JE, Muljo SA, Raulet DH. A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells. eLife 2015; 4. [PMID: 26565589 PMCID: PMC4629278 DOI: 10.7554/elife.08474] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023] Open
Abstract
Recognition and elimination of tumor cells by the immune system is crucial for limiting tumor growth. Natural killer (NK) cells become activated when the receptor NKG2D is engaged by ligands that are frequently upregulated in primary tumors and on cancer cell lines. However, the molecular mechanisms driving NKG2D ligand expression on tumor cells are not well defined. Using a forward genetic screen in a tumor-derived human cell line, we identified several novel factors supporting expression of the NKG2D ligand ULBP1. Our results show stepwise contributions of independent pathways working at multiple stages of ULBP1 biogenesis. Deeper investigation of selected hits from the screen showed that the transcription factor ATF4 drives ULBP1 gene expression in cancer cell lines, while the RNA-binding protein RBM4 supports ULBP1 expression by suppressing a novel alternatively spliced isoform of ULBP1 mRNA. These findings offer insight into the stress pathways that alert the immune system to danger. DOI:http://dx.doi.org/10.7554/eLife.08474.001 Cancer is caused by a series of mutations that result in uncontrolled cell growth and division. Yet, the body's immune system can often detect and destroy abnormal cells before they cause tumors and disease. Natural killer cells are part of the immune system and have receptors on their surface that allow them to tell the difference between healthy host cells and host cells that are stressed or abnormal. Some of these receptors activate the natural killer cells when they bind to their target molecules. Other receptors have the opposite effect and inhibit the natural killer cells. Activation occurs when the signaling from the activating receptors is stronger than the signals from the inhibitory receptors. One of the well-studied activating receptors recognizes a number of proteins and molecules that are produced by abnormal or tumor cells, including a protein called ULBP1. This protein is absent from the surface of healthy cells but is found in abundance on tumor cells. However, it is still not clear what drives tumor cells to produce ULBP1 (or other molecules) that are recognized by natural killer cell receptors. Now, Gowen et al. report on a genetic screen that has revealed numerous genes that regulate the levels of ULBP1 in human cells. Many of these genes had independent effects that when added together accounted for most of the ULBP1 present on the cell surface. Gowen et al. then explored some of the ‘regulators’ encoded by these genes in more detail. One called ATF4, which had previously been linked to stress responses, was shown to increase the expression of the gene for ULBP1 in cancer cells. Another regulator called RBM4 instead acted in a different way and at a later stage in ULBP1 production. All together, these findings offer insight into the stress pathways that alert the immune system to abnormal cells. The next challenge will be investigating how these pathways might be exploited for cancer immunotherapy. DOI:http://dx.doi.org/10.7554/eLife.08474.002
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Affiliation(s)
- Benjamin G Gowen
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Bryan Chim
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Caleb D Marceau
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Trever T Greene
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Patrick Burr
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Jeanmarie R Gonzalez
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Charles R Hesser
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Peter A Dietzen
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Teal Russell
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Alexandre Iannello
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Laurent Coscoy
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
| | - Charles L Sentman
- Center for Synthetic Immunity, Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Lebanon, United States
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Stefan A Muljo
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - David H Raulet
- Department of Molecular and Cell Biology, Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States
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22
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Yamada E, Demachi-Okamura A, Kondo S, Akatsuka Y, Suzuki S, Shibata K, Kikkawa F, Kuzushima K. Identification of a naturally processed HLA-Cw7-binding peptide that cross-reacts with HLA-A24-restricted ovarian cancer-specific CTLs. ACTA ACUST UNITED AC 2015. [PMID: 26216489 DOI: 10.1111/tan.12607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Here, we describe an human leukocyte antigen (HLA)-A*24:02-restricted cytotoxic T-lymphocyte (CTL) clone, 1G3, established from naïve CD8(+) T-lymphocytes obtained from a healthy donor stimulated with HLA-modified TOV21G, an ovarian cancer cell line. The 1G3 clone responds not only to ovarian cancer cells in the context of HLA-A*24:02 but also to allogeneic HLA-Cw*07:02 molecules through cross-reactive T-cell receptor recognition. Expression screening using a complementary DNA library constructed from TOV21G messenger RNA revealed that this alloreactivity was mediated through the nine-mer peptide VRTPYTMSY, derived from RNA-binding motif protein 4. To our knowledge, this study presents the first example of the allorecognition of an HLA-Cw molecule by HLA-A-restricted T-cells, thereby revealing a naturally processed epitope peptide. These findings provide the structural bases for the allorecognition of human T-cells. In addition, this study suggests that unexpected alloresponses occur in certain HLA combinations, and further study is needed to understand the mechanisms of alloreactivity for better prediction of alloresponses in clinical settings.
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Affiliation(s)
- E Yamada
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - A Demachi-Okamura
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - S Kondo
- Department of Gynecologic Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Y Akatsuka
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Hematology & Oncology, Fujita Health University, Toyoake, Japan
| | - S Suzuki
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - K Shibata
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - F Kikkawa
- Department of Gynecology, Graduate School of Medicine, Nagoya, Japan
| | - K Kuzushima
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Abstract
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
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24
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Pereira LE, Tsang J, Mrázek J, Hoover TR. The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria. MICROBIAL INFORMATICS AND EXPERIMENTATION 2014; 1:1-10. [PMID: 22408721 PMCID: PMC3372290 DOI: 10.1186/2042-5783-1-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Helicobacter pylori HP0958 protein (FlgZ) prevents the rapid turnover of RpoN (σ54), a transcription factor required for expression of several flagellar genes in H. pylori. FlgZ possesses a zinc-ribbon domain (DUF164) that contains two conserved CXXC motifs which coordinate a zinc ion and is thought to interact with nucleic acids or proteins. Two conserved cysteine residues in FlgZ (Cys-202 and Cys-223) were replaced with serine to assess their significance in FlgZ function. After confirming the importance of the CXXC motifs in the DUF164 domain of FlgZ, the distribution of DUF164 proteins and RpoN homologs in other bacteria was examined to determine if a correlation existed for the concurrence of the two proteins. Results Levels of RpoN were greatly reduced in H. pylori strains that expressed the FlgZC202S or FlgZC223S variants. The FlgZC202S variant, but not the FlgZC223S variant, accumulated at levels similar to the wild-type protein. DUF164 proteins are not universally distributed and appear to be absent in several major bacterial taxa, including Cyanobacteria as well as Alpha-, Beta- and Gammaproteobacteria. With the exception of the Actinobacteria, members of which generally lack RpoN, genes encoding DUF164 proteins and RpoN are frequently found in the same genome. Interestingly, many of the DUF164 proteins in Actinobacteria and Bacteroidetes lack most or even all of the conserved cysteine residues. Conclusions These findings suggest the importance of the zinc-ribbon domain of FlgZ in protecting RpoN from turnover. Since many bacteria that possess a DUF164 protein also contain RpoN, DUF164 proteins may have roles in RpoN protection or function in other bacteria.
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Affiliation(s)
- Lara E Pereira
- Emory Vaccine Center, 954 Gatewood Road, Emory University, Atlanta, GA 30329, USA
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25
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Guan R, El-Rass S, Spillane D, Lam S, Wang Y, Wu J, Chen Z, Wang A, Jia Z, Keating A, Hu J, Wen XY. rbm47, a novel RNA binding protein, regulates zebrafish head development. Dev Dyn 2013; 242:1395-404. [PMID: 24038582 DOI: 10.1002/dvdy.24039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 08/02/2013] [Accepted: 08/14/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Vertebrate trunk induction requires inhibition of bone morphogenetic protein (BMP) signaling, whereas vertebrate head induction requires concerted inhibition of both Wnt and BMP signaling. RNA binding proteins play diverse roles in embryonic development and their roles in vertebrate head development remain to be elucidated. RESULTS We first characterized the human RBM47 as an RNA binding protein that specifically binds RNA but not single-stranded DNA. Next, we knocked down rbm47 gene function in zebrafish using morpholinos targeting the start codon and exon-1/intron-1 splice junction. Down-regulation of rbm47 resulted in headless and small head phenotypes, which can be rescued by a wnt8a blocking morpholino. To further reveal the mechanism of rbm47's role in head development, microarrays were performed to screen genes differentially expressed in normal and knockdown embryos. epcam and a2ml were identified as the most significantly up- and down-regulated genes, respectively. The microarrays also confirmed up-regulation of several genes involved in head development, including gsk3a, otx2, and chordin, which are important regulators of Wnt signaling. CONCLUSIONS Altogether, our findings reveal that Rbm47 is a novel RNA-binding protein critical for head formation and embryonic patterning during zebrafish embryogenesis which may act through a Wnt8a signaling pathway.
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Affiliation(s)
- Rui Guan
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medicine, Physiology and Institute of Medical Science, University of Toronto, Canada; Department of Laboratory Medicine and Pathology, University of Toronto & Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Canada; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital and Cancer Research Institute, Central South, Hunan Province, China
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26
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A compendium of RNA-binding motifs for decoding gene regulation. Nature 2013; 499:172-7. [PMID: 23846655 DOI: 10.1038/nature12311] [Citation(s) in RCA: 1025] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 05/17/2013] [Indexed: 01/03/2023]
Abstract
RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes. The sequence specificities of RNA-binding proteins display deep evolutionary conservation, and the recognition preferences for a large fraction of metazoan RNA-binding proteins can thus be inferred from their RNA-binding domain sequence. The motifs that we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA-binding proteins both in normal physiology and in human disease. These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes.
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27
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Lu CC, Chen TH, Wu JR, Chen HH, Yu HY, Tarn WY. Phylogenetic and molecular characterization of the splicing factor RBM4. PLoS One 2013; 8:e59092. [PMID: 23527094 PMCID: PMC3602429 DOI: 10.1371/journal.pone.0059092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/11/2013] [Indexed: 12/13/2022] Open
Abstract
The mammalian multi-functional RNA-binding motif 4 (RBM4) protein regulates alterative splicing of precursor mRNAs and thereby affects pancreas and muscle cell differentiation. RBM4 homologs exist in all metazoan lineages. The C-terminal unstructured domain of RBM4 is evolutionarily divergent and contains stretches of low-complexity sequences, including single amino acid and/or dipeptide repeats. Here we examined the splicing activity, phosphorylation potential, and subcellular localization of RBM4 homologs from a wide range of species. The results show that these RBM4 homologs exert different effects on 5′ splice site utilization and exon selection, and exhibit different subnuclear localization patterns. Therefore, the C-terminal domain of RBM4 may contribute to functional divergence between homologs. On the other hand, analysis of chimeric human RBM4 proteins containing heterologous sequences at the C-terminus revealed that the N-terminal RNA binding domain of RBM4 could have a dominant role in determining splicing outcome. Finally, all RBM4 homologs examined could be phosphorylated by an SR protein kinase, suggesting that they are regulated by a conserved mechanism in different species. This study offers a first clue to functional evolution of a splicing factor.
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Affiliation(s)
- Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tz-Hao Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jhe-Rong Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- * E-mail:
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28
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El Gazzar M, Church A, Liu T, McCall CE. MicroRNA-146a regulates both transcription silencing and translation disruption of TNF-α during TLR4-induced gene reprogramming. J Leukoc Biol 2011; 90:509-19. [PMID: 21562054 DOI: 10.1189/jlb.0211074] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Following the TLR-dependent initiation phase of acute systemic proinflammatory responses such as sepsis, an adaptive phase represses or activates a specific pattern of gene expression until the inflammation resolves. Here, we used the THP-1 sepsis cell model of bacterial LPS/endotoxin tolerance to show that TLR4-induced miR-146a supports the feed-forward adaptive processes that silence transcription and disrupt translation of acute proinflammatory genes. First, we found that miR-146a regulates a pathway that promotes the binding of transcription repressor RelB to the TNF-α promoter, a step known to precede histone and DNA modifications, which generate facultative heterochromatin to silence acute proinflammatory genes. However, once RelB binding occurred, miR-146a inhibition could not reverse compacted chromatin, and endotoxin tolerance persisted. Second, we observed that miR-146a regulates a pathway that supports assembly of the translation repressor complex of TNF-α by preventing the interaction of the RNA-binding protein effector Ago2 and RBM4. We also determined that once endotoxin tolerance is established, and specific genes have been reprogrammed, transcription and translation disruption can be reversed only by simultaneously depleting RelB and inhibiting miR-146a. Thus, miR-146a induction supports the TLR4-dependent shift from initiation to gene-specific repression at two levels. Our results also imply that therapies designed to reverse endotoxin tolerance as potential therapies for sepsis should be directed at the transcription and translation pathways of reprogramming.
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Affiliation(s)
- Mohamed El Gazzar
- Department of Internal Medicine, East Tennessee State University College of Medicine, Johnson City, TN 37614, USA.
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29
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Affiliation(s)
- Brian J. Morris
- From the Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
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30
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RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5' splice site. Mol Cell Biol 2011; 31:1812-21. [PMID: 21343338 DOI: 10.1128/mcb.01149-10] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Regulation of tau exon 10 splicing plays an important role in tauopathy. One of the cis elements regulating tau alternative splicing is a stem-loop structure at the 5' splice site of tau exon 10. The RNA helicase(s) modulating this stem-loop structure was unknown. We searched for splicing regulators interacting with this stem-loop region using an RNA affinity pulldown-coupled mass spectrometry approach and identified DDX5/RNA helicase p68 as an activator of tau exon 10 splicing. The activity of p68 in stimulating tau exon 10 inclusion is dependent on RBM4, an intronic splicing activator. RNase H cleavage and U1 protection assays suggest that p68 promotes conformational change of the stem-loop structure, thereby increasing the access of U1snRNP to the 5' splice site of tau exon 10. This study reports the first RNA helicase interacting with a stem-loop structure at the splice site and regulating alternative splicing in a helicase-dependent manner. Our work uncovers a previously unknown function of p68 in regulating tau exon 10 splicing. Furthermore, our experiments reveal functional interaction between two splicing activators for tau exon 10, p68 binding at the stem-loop region and RBM4 interacting with the intronic splicing enhancer region.
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31
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Lam YW, Evans VC, Heesom KJ, Lamond AI, Matthews DA. Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol Cell Proteomics 2009; 9:117-30. [PMID: 19812395 PMCID: PMC2808258 DOI: 10.1074/mcp.m900338-mcp200] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Adenoviruses replicate primarily in the host cell nucleus, and it is well
established that adenovirus infection affects the structure and function of host
cell nucleoli in addition to coding for a number of nucleolar targeted viral
proteins. Here we used unbiased proteomics methods, including high throughput
mass spectrometry coupled with stable isotope labeling by amino acids in cell
culture (SILAC) and traditional two-dimensional gel electrophoresis, to identify
quantitative changes in the protein composition of the nucleolus during
adenovirus infection. Two-dimensional gel analysis revealed changes in six
proteins. By contrast, SILAC-based approaches identified 351 proteins with 24
proteins showing at least a 2-fold change after infection. Of those, four were
previously reported to have aberrant localization and/or functional relevance
during adenovirus infection. In total, 15 proteins identified as changing in
amount by proteomics methods were examined in infected cells using confocal
microscopy. Eleven of these proteins showed altered patterns of localization in
adenovirus-infected cells. Comparing our data with the effects of actinomycin D
on the nucleolar proteome revealed that adenovirus infection apparently
specifically targets a relatively small subset of nucleolar antigens at the time
point examined.
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Affiliation(s)
- Yun W Lam
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China
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