1
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Jian W, Xue W, Wang T, Yu Y, Cai L, Meng Y, Xia Z, Zhang C. RBM4 inhibits the growth of clear cell renal cell carcinoma by enhancing the stability of p53 mRNA. Mol Carcinog 2023; 62:464-478. [PMID: 36585906 DOI: 10.1002/mc.23499] [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: 08/28/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 01/01/2023]
Abstract
RBM4 has been reported as a tumor suppressor gene in cancers, including lung cancer, colon cancer and gastric cancer. However, the role of RBM4 in clear cell renal cell carcinoma (ccRCC) remains unclear. Therefore, the present study investigated the expression and biological function of RBM4 in ccRCC. Analysis of the differential expression of RBM4 and its relationship with clinicopathological features using ccRCC samples data from TCGA database deminstrated that RBM4 expression in tumor samples of ccRCC was lower than that in normal samples, and RBM4 expression was closely related to the survival time of patients. RBM4 overexpression (RBM4-oe) cell lines were constructed to investigate the effect of RBM4 on biological function using CCK-8, EdU, flow cytometry and wound-healing assays. In addition, the regulatory effect of RBM4 on signaling pathways was investigated by GSEA and WB assays. RBM4-oe significantly reduced the proliferation of ccRCC cells by controlling the p53 signaling pathway, inhibited cell cycle progression and promoted apoptosis. In addition, RBM4-oe suppressed the migration and invasion of cells by EMT. Mechanistically, RBM4-oe facilitated the activity of the p53 signaling pathway by enhancing the stability of p53 mRNA. Finally, RBM4-oe markedly inhibited the growth of tumors formed with 786-O cells in vivo. In summary, there findings suggeated that RBM4 inhibits the progression of ccRCC by promoting p53 signaling pathway activity by enhancing the stability of p53 mRNA, suggesting that RBM4 may be a potential target for the treatment of patients.
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Affiliation(s)
- Wengang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wei Xue
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Tengda Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yongchun Yu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Licheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuyang Meng
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhinan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Department of Urology, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
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2
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Wang L, Zhang X, Sheng J, Chen L, Zhi L, Zheng Q, Qi Y, Wang L, Zhang J, Zhao J, Wang Y, Liu SX, Sun MZ, Zhang W. RBM4 regulates cellular senescence via miR1244/SERPINE1 axis. Cell Death Dis 2023; 14:27. [PMID: 36639375 PMCID: PMC9839707 DOI: 10.1038/s41419-023-05563-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Cellular senescence serves as a powerful tumor suppressing mechanism that inhibits the proliferation of cancer cells bearing oncogenic mutations at the initial stage of cancer development. RNA-binding proteins (RBPs) play important roles in cancer progression and treatment through distinct functions. However, functions and mechanisms of RNA binding proteins in regulating senescence remain elusive. Here we reported that the RNA binding protein RBM4 contributed to cellular senescence. Depletion of RBM4 induced senescence in different types of cells, including multiple cancer cells. Meanwhile, RBM4 ablation inhibited cancer cell progression both in vitro and in vivo. Specifically, knockdown of RBM4 significantly increased the level of SERPINE1, a known promoter of senescence, thereby inducing the senescence of lung cancer cells. Mechanistically, miR-1244 bound to the 3'-UTR of SERPINE1 to suppress its expression, whereas depletion of RBM4 reduced the level of miR-1244 by promoting the degradation of primary miR-1244 transcripts (pri-miR1244), thus increasing the expression of SERPINE1 and inducing subsequent senescence. Moreover, either SERPINE1 inhibitor or miR-1244 mimics attenuated the RBM4 depletion-induced senescence. Altogether, our study revealed a novel mechanism of RBM4 in the regulation of cancer progression through controlling senescence, providing a new avenue for targeting RBM4 in cancer therapeutics.
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Affiliation(s)
- Luning Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Xiaohong Zhang
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Junxiu Sheng
- Department of Radiation Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, 116044, China
| | - Lei Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Lili Zhi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Qianqian Zheng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Linlin Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Shu-Xin Liu
- Department of Nephrology, Dalian Municipal Central Hospital, Dalian Medical University, Dalian, 116033, China.
| | - Ming-Zhong Sun
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, 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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4
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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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5
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Li Z, Guo Q, Zhang J, Fu Z, Wang Y, Wang T, Tang J. The RNA-Binding Motif Protein Family in Cancer: Friend or Foe? Front Oncol 2021; 11:757135. [PMID: 34804951 PMCID: PMC8600070 DOI: 10.3389/fonc.2021.757135] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/19/2021] [Indexed: 01/22/2023] Open
Abstract
The RNA-binding motif (RBM) proteins are a class of RNA-binding proteins named, containing RNA-recognition motifs (RRMs), RNA-binding domains, and ribonucleoprotein motifs. RBM proteins are involved in RNA metabolism, including splicing, transport, translation, and stability. Many studies have found that aberrant expression and dysregulated function of RBM proteins family members are closely related to the occurrence and development of cancers. This review summarizes the role of RBM proteins family genes in cancers, including their roles in cancer occurrence and cell proliferation, migration, and apoptosis. It is essential to understand the mechanisms of these proteins in tumorigenesis and development, and to identify new therapeutic targets and prognostic markers.
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Affiliation(s)
- Zhigang Li
- Department of Orthopedics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Qingyu Guo
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Jiaxin Zhang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Zitong Fu
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Yifei Wang
- Department of Urology, Hainan General Hospital, Hainan, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Jing Tang
- Department of Pathology, Harbin Medical University, Harbin, China
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6
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Dai X, Li Y, Liu W, Pan X, Guo C, Zhao X, Lv J, Lei H, Zhang L. Application of RNA subcellular fraction estimation method to explore RNA localization regulation. G3-GENES GENOMES GENETICS 2021; 12:6427545. [PMID: 34791188 PMCID: PMC8727992 DOI: 10.1093/g3journal/jkab371] [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: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
RNA localization is involved in multiple biological processes. Recent advances in subcellular fractionation based sequencing approaches uncovered localization pattern on a global scale. Most of existing methods adopt relative localization ratios (such as ratios of separately normalized TPMs of different subcellular fractions without considering the difference in total RNA abundances in different fractions), however, absolute ratios may yield different results on the preference to different cellular compartment. Experimentally, adding external Spike-in RNAs to different fractionation can be used to obtain absolute ratios. In addition, a spike-in independent computational approach based on multiple linear regression model can also be used. However, currently no custom tool is available. To solve this problem, we developed a method called Subcellular Fraction Abundance Estimator (SFAE) to correctly estimate relative RNA abundances of different subcellular fractionations. The ratios estimated by our method were consistent with existing reports. By applying the estimated ratios for different fractions, we explored the RNA localization pattern in cell lines and also predicted RBP motifs that were associated with different localization patterns. In addition, we showed that different isoforms of same genes could exhibit distinct localization patterns. To conclude, we believed our tool will facilitate future subcellular fractionation related sequencing study to explore the function of RNA localization in various biological problems.
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Affiliation(s)
- Xiaomin Dai
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangmengjie Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian, P.R. China 116044
| | - Weizhen Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiuqi Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chenyue Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jingwen Lv
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, 9 West Section, Lvshun South Rd, Dalian, P.R. China 116044
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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7
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Abstract
To infect nondividing cells, HIV-1 needs to cross the nuclear membrane. The importin transportin-SR2 (TRN-SR2 or transportin-3) has been proposed to mediate HIV-1 nuclear import, but the detailed mechanism remains unresolved. The direct interaction of TRN-SR2 with HIV-1 integrase (IN) has been proposed to drive HIV-1 nuclear import. Alternatively, TRN-SR2 may play an indirect role by mediating nuclear import of cleavage and polyadenylation specificity factor 6 (CPSF6). To unravel the role of TRN-SR2, we designed CRISPR/Cas9 guide RNAs targeting different exons of TNPO3. Although this approach failed to generate full knockouts, monoallelic knockout clones were generated with indel mutations. HIV-1 replication was hampered in those clones at the level of HIV-1 nuclear import without an effect on the cellular distribution of the TRN-SR2 cargoes CPSF6 or alternative splicing factor1/pre-mRNA splicing factor SF2 (ASF/SF2). Recombinant ΔV105 TRN-SR2 expressed in clone 15.15 was 2-fold impaired for interaction with HIV-1 IN and classified as an interaction mutant. Our data support a model whereby TRN-SR2 acts as a cofactor of HIV-1 nuclear import without compromising the nuclear import of cellular cargoes. CRISPR/Cas9-induced mutagenesis can be used as a method to generate interface mutants to characterize host factors of human pathogens. IMPORTANCE Combination antiretroviral therapy (cART) effectively controls HIV-1 by reducing viral loads, but it does not cure the infection. Lifelong treatment with cART is a prerequisite for sustained viral suppression. The rapid emergence of drug-resistant viral strains drives the necessity to discover new therapeutic targets. The nuclear import of HIV-1 is crucial in the HIV-1 replication cycle, but the detailed mechanism remains incompletely understood. This study provides evidence that TRN-SR2 directly mediates HIV-1 nuclear import via the interaction with HIV-1 integrase. The interaction between those proteins is therefore a promising target toward a rational drug design which could lead to new therapeutic strategies due to the bottleneck nature of HIV-1 nuclear import.
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8
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Ding B, Sepehrimanesh M. Nucleocytoplasmic Transport: Regulatory Mechanisms and the Implications in Neurodegeneration. Int J Mol Sci 2021; 22:4165. [PMID: 33920577 PMCID: PMC8072611 DOI: 10.3390/ijms22084165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) across the nuclear envelope is precisely regulated in eukaryotic cells, and it plays critical roles in maintenance of cellular homeostasis. Accumulating evidence has demonstrated that dysregulations of NCT are implicated in aging and age-related neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Huntington disease (HD). This is an emerging research field. The molecular mechanisms underlying impaired NCT and the pathogenesis leading to neurodegeneration are not clear. In this review, we comprehensively described the components of NCT machinery, including nuclear envelope (NE), nuclear pore complex (NPC), importins and exportins, RanGTPase and its regulators, and the regulatory mechanisms of nuclear transport of both protein and transcript cargos. Additionally, we discussed the possible molecular mechanisms of impaired NCT underlying aging and neurodegenerative diseases, such as ALS/FTD, HD, and AD.
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Affiliation(s)
- Baojin Ding
- Department of Biology, University of Louisiana at Lafayette, 410 East Saint Mary Boulevard, Lafayette, LA 70503, USA;
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9
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Kalita J, Kapinos LE, Lim RYH. On the asymmetric partitioning of nucleocytoplasmic transport - recent insights and open questions. J Cell Sci 2021; 134:239102. [PMID: 33912945 DOI: 10.1242/jcs.240382] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular cargoes are asymmetrically partitioned in the nucleus or cytoplasm by nucleocytoplasmic transport (NCT). At the center of this activity lies the nuclear pore complex (NPC), through which soluble factors circulate to orchestrate NCT. These include cargo-carrying importin and exportin receptors from the β-karyopherin (Kapβ) family and the small GTPase Ran, which switches between guanosine triphosphate (GTP)- and guanosine diphosphate (GDP)-bound forms to regulate cargo delivery and compartmentalization. Ongoing efforts have shed considerable light on how these soluble factors traverse the NPC permeability barrier to sustain NCT. However, this does not explain how importins and exportins are partitioned in the cytoplasm and nucleus, respectively, nor how a steep RanGTP-RanGDP gradient is maintained across the nuclear envelope. In this Review, we peel away the multiple layers of control that regulate NCT and juxtapose unresolved features against known aspects of NPC function. Finally, we discuss how NPCs might function synergistically with Kapβs, cargoes and Ran to establish the asymmetry of NCT.
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Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel CH4056, Switzerland
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10
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Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020; 117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.
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11
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TNPO3-Mediated Nuclear Entry of the Rous Sarcoma Virus Gag Protein Is Independent of the Cargo-Binding Domain. J Virol 2020; 94:JVI.00640-20. [PMID: 32581109 DOI: 10.1128/jvi.00640-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/16/2020] [Indexed: 11/20/2022] Open
Abstract
Retroviral Gag polyproteins orchestrate the assembly and release of nascent virus particles from the plasma membranes of infected cells. Although it was traditionally thought that Gag proteins trafficked directly from the cytosol to the plasma membrane, we discovered that the oncogenic avian alpharetrovirus Rous sarcoma virus (RSV) Gag protein undergoes transient nucleocytoplasmic transport as an intrinsic step in virus assembly. Using a genetic approach in yeast, we identified three karyopherins that engage the two independent nuclear localization signals (NLSs) in Gag. The primary NLS is in the nucleocapsid (NC) domain of Gag and binds directly to importin-α, which recruits importin-β to mediate nuclear entry. The second NLS (TNPO3), which resides in the matrix (MA) domain, is dependent on importin-11 and transportin-3 (TNPO3), which are known as MTR10p and Kap120p in yeast, although it is not clear whether these import factors are independent or additive. The functions of importin-α/importin-β and importin-11 have been verified in avian cells, whereas the role of TNPO3 has not been studied. In this report, we demonstrate that TNPO3 directly binds to Gag and mediates its nuclear entry. To our surprise, this interaction did not require the cargo-binding domain (CBD) of TNPO3, which typically mediates nuclear entry for other binding partners of TNPO3, including SR domain-containing splicing factors and tRNAs that reenter the nucleus. These results suggest that RSV hijacks this host nuclear import pathway using a unique mechanism, potentially allowing other cargo to simultaneously bind TNPO3.IMPORTANCE RSV Gag nuclear entry is facilitated using three distinct host import factors that interact with nuclear localization signals in the Gag MA and NC domains. Here, we show that the MA region is required for nuclear import of Gag through the TNPO3 pathway. Gag nuclear entry does not require the CBD of TNPO3. Understanding the molecular basis for TNPO3-mediated nuclear trafficking of the RSV Gag protein may lead to a deeper appreciation for whether different import factors play distinct roles in retrovirus replication.
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12
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RBM4 regulates M1 macrophages polarization through targeting STAT1-mediated glycolysis. Int Immunopharmacol 2020; 83:106432. [PMID: 32248017 DOI: 10.1016/j.intimp.2020.106432] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/11/2020] [Accepted: 03/19/2020] [Indexed: 12/20/2022]
Abstract
M1/M2 macrophages polarization play important roles in regulating tissue homeostasis. Recently, RNA-binding motif 4 (RBM4) has been reported to modulate the proliferation and expression of inflammatory factors in HeLa cells. However, whether RBM4 is involved in regulating macrophage polarization and inflammatory factor expression are still unknown. In this study, RAW264.7, a mouse macrophage cell line, were stimulated with interferon γ (IFN-γ) or interleukin-4 (IL-4) to induce M1/M2 macrophages polarization. We found that IFN-γ, but not IL-4, stimulation decreased RBM4 expression in macrophages, and RBM4 overexpression inhibits IFN-γ-induced M1 macrophage polarization. Furthermore, RNA-Sequencing, protein immunoprecipitation accompanied with mass spectrometry, and extracellular acidification rate analysis showed that RBM4 suppresses IFN-γ-induced M1 macrophage polarization though inhibiting glycolysis. Moreover, RBM4 knockdown promoted IFN-γ-induced signal transducer and activator of transcription 1 (STAT1) activation via increasing STAT1 mRNA stability, leading to the increase of glycolysis-related gene transcripts regulated by STAT1. Finally, we find that RBM4 interacts with YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) to degrade m6A modified STAT1 mRNA, thereby regulating glycolysis and M1 macrophage polarization. Collectively, the current study firstly reports that RBM4 regulates M1 macrophages polarization through targeting STAT1-mediated glycolysis and shows that RBM4 is a possible candidate for regulating macrophage M1 polarization and inflammatory responses.
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13
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Park B, Han K. Discovering protein-binding RNA motifs with a generative model of RNA sequences. Comput Biol Chem 2020; 84:107171. [DOI: 10.1016/j.compbiolchem.2019.107171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/19/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023]
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14
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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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15
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The mutation of Transportin 3 gene that causes limb girdle muscular dystrophy 1F induces protection against HIV-1 infection. PLoS Pathog 2019; 15:e1007958. [PMID: 31465518 PMCID: PMC6715175 DOI: 10.1371/journal.ppat.1007958] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/03/2019] [Indexed: 01/10/2023] Open
Abstract
The causative mutation responsible for limb girdle muscular dystrophy 1F (LGMD1F) is one heterozygous single nucleotide deletion in the stop codon of the nuclear import factor Transportin 3 gene (TNPO3). This mutation causes a carboxy-terminal extension of 15 amino acids, producing a protein of unknown function (TNPO3_mut) that is co-expressed with wild-type TNPO3 (TNPO3_wt). TNPO3 has been involved in the nuclear transport of serine/arginine-rich proteins such as splicing factors and also in HIV-1 infection through interaction with the viral integrase and capsid. We analyzed the effect of TNPO3_mut on HIV-1 infection using PBMCs from patients with LGMD1F infected ex vivo. HIV-1 infection was drastically impaired in these cells and viral integration was reduced 16-fold. No significant effects on viral reverse transcription and episomal 2-LTR circles were observed suggesting that the integration of HIV-1 genome was restricted. This is the second genetic defect described after CCR5Δ32 that shows strong resistance against HIV-1 infection.
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16
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Mazloomian A, Araki S, Ohori M, El-Naggar AM, Yap D, Bashashati A, Nakao S, Sorensen PH, Nakanishi A, Shah S, Aparicio S. Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation. Commun Biol 2019; 2:165. [PMID: 31069274 PMCID: PMC6499833 DOI: 10.1038/s42003-019-0391-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
The RNA helicase EIF4A3 regulates the exon junction complex and nonsense-mediated mRNA decay functions in RNA transcript processing. However, a transcriptome-wide network definition of these functions has been lacking, in part due to the lack of suitable pharmacological inhibitors. Here we employ short-duration graded EIF4A3 inhibition using small molecule allosteric inhibitors to define the transcriptome-wide dependencies of EIF4A3. We thus define conserved cellular functions, such as cell cycle control, that are EIF4A3 dependent. We show that EIF4A3-dependent splicing reactions have a distinct genome-wide pattern of associated RNA-binding protein motifs. We also uncover an unanticipated role of EIF4A3 in the biology of RNA stress granules, which sequester and silence the translation of most mRNAs under stress conditions and are implicated in cell survival and tumour progression. We show that stress granule induction and maintenance is suppressed on the inhibition of EIF4A3, in part through EIF4A3-associated regulation of G3BP1 and TIA1 scaffold protein expression.
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Affiliation(s)
- Alborz Mazloomian
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shinsuke Araki
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Momoko Ohori
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shoichi Nakao
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Atsushi Nakanishi
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Sohrab Shah
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 417 E68th St, New York, NY 10065 USA
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
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Coltri PP, Dos Santos MGP, da Silva GHG. Splicing and cancer: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1527. [PMID: 30773852 DOI: 10.1002/wrna.1527] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators. While alterations in splice site preferences might generate alternative isoforms enabling different biological functions, these might also be responsible for nonfunctional isoforms that can eventually cause dysregulation in cellular processes. Molecular characteristics of regulatory sequences and proteins might also be important prognostic tools revealing a cancer-specific splicing pattern and linking splicing control to cancer development. The connection between cancer biology and splicing regulation is of primary importance to understand the mechanisms leading to disease and also to improve development of therapeutic approaches. Splicing modulation is being explored in new anti-cancer therapies and further investigation of targeted splicing factors is critical for the success of these strategies. This article is categorized under: RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria G P Dos Santos
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme H G da Silva
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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18
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Anvar SY, Allard G, Tseng E, Sheynkman GM, de Klerk E, Vermaat M, Yin RH, Johansson HE, Ariyurek Y, den Dunnen JT, Turner SW, 't Hoen PAC. Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing. Genome Biol 2018; 19:46. [PMID: 29598823 PMCID: PMC5877393 DOI: 10.1186/s13059-018-1418-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/08/2018] [Indexed: 01/30/2023] Open
Abstract
Background The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. Results In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Conclusions Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing. Electronic supplementary material The online version of this article (10.1186/s13059-018-1418-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands. .,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands. .,Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.
| | - Guy Allard
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA
| | - Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.,Department of Microbiology and Immunology, UCSF Diabetes Center, University of California San Francisco (UCSF), San Francisco, CA, 94143-0534, USA
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Raymund H Yin
- LGC Biosearch Technologies, Petaluma, CA, 94954-6904, USA
| | | | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Stephen W Turner
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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19
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Demeulemeester J, Blokken J, De Houwer S, Dirix L, Klaassen H, Marchand A, Chaltin P, Christ F, Debyser Z. Inhibitors of the integrase-transportin-SR2 interaction block HIV nuclear import. Retrovirology 2018; 15:5. [PMID: 29329553 PMCID: PMC5767004 DOI: 10.1186/s12977-018-0389-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
Background Combination antiretroviral therapy efficiently suppresses HIV replication in infected patients, transforming HIV/AIDS into a chronic disease. Viral resistance does develop however, especially under suboptimal treatment conditions such as poor adherence. As a consequence, continued exploration of novel targets is paramount to identify novel antivirals that do not suffer from cross-resistance with existing drugs. One new promising class of targets are HIV protein–cofactor interactions. Transportin-SR2 (TRN-SR2) is a β-karyopherin that was recently identified as an HIV-1 cofactor. It has been implicated in nuclear import of the viral pre-integration complex and was confirmed as a direct binding partner of HIV-1 integrase (IN). Nevertheless, consensus on its mechanism of action is yet to be reached. Results Here we describe the development and use of an AlphaScreen-based high-throughput screening cascade for small molecule inhibitors of the HIV-1 IN–TRN-SR2 interaction. False positives and nonspecific protein–protein interaction inhibitors were eliminated through different counterscreens. We identified and confirmed 2 active compound series from an initial screen of 25,608 small molecules. These compounds significantly reduced nuclear import of fluorescently labeled HIV particles. Conclusions Alphascreen-based high-throughput screening can allow the identification of compounds representing a novel class of HIV inhibitors. These results corroborate the role of the IN–TRN-SR2 interaction in nuclear import. These compounds represent the first in class small molecule inhibitors of HIV-1 nuclear import.
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Affiliation(s)
- Jonas Demeulemeester
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium.,The Francis Crick Institute, London, UK
| | - Jolien Blokken
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Stéphanie De Houwer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Lieve Dirix
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Hugo Klaassen
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium
| | - Arnaud Marchand
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium
| | - Patrick Chaltin
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium.,Center for Drug Design and Development (CD3), KU Leuven R&D, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium.
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20
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Serikawa T, Spanos C, von Hacht A, Budisa N, Rappsilber J, Kurreck J. Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs. Biochimie 2017; 144:169-184. [PMID: 29129743 DOI: 10.1016/j.biochi.2017.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
G-quadruplex structures in the 5' UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. The use of a control composed of samples from all G-quadruplex-forming sequences and their mutated controls ensured that the identified proteins are specific for RNA G-quadruplex structures and are not general RNA-binding proteins. Independent validation experiments based on pull-down assays and Western blotting confirmed the MS data. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). Several of the candidate proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. Interestingly, additional proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions are not only important for the fine-tuning of translation but are also relevant to the regulation of mRNA maturation and may play an important role in tumor biology. Proteomic data are available via ProteomeXchange with identifier PXD005761.
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Affiliation(s)
- Tatsuo Serikawa
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Annekathrin von Hacht
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry, L 1, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, TIB 4/4-3, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jens Kurreck
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany.
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21
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Sánchez-Hernández N, Prieto-Sánchez S, Moreno-Castro C, Muñoz-Cobo JP, El Yousfi Y, Boyero-Corral S, Suñé-Pou M, Hernández-Munain C, Suñé C. Targeting proteins to RNA transcription and processing sites within the nucleus. Int J Biochem Cell Biol 2017; 91:194-202. [DOI: 10.1016/j.biocel.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
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22
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Tsirkone VG, Blokken J, De Wit F, Breemans J, De Houwer S, Debyser Z, Christ F, Strelkov SV. N-terminal half of transportin SR2 interacts with HIV integrase. J Biol Chem 2017; 292:9699-9710. [PMID: 28356354 PMCID: PMC5465493 DOI: 10.1074/jbc.m117.777029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/14/2017] [Indexed: 11/06/2022] Open
Abstract
The karyopherin transportin SR2 (TRN-SR2, TNPO3) is responsible for shuttling specific cargoes such as serine/arginine-rich splicing factors from the cytoplasm to the nucleus. This protein plays a key role in HIV infection by facilitating the nuclear import of the pre-integration complex (PIC) that contains the viral DNA as well as several cellular and HIV proteins, including the integrase. The process of nuclear import is considered to be the bottleneck of the viral replication cycle and therefore represents a promising target for anti-HIV drug design. Previous studies have demonstrated that the direct interaction between TRN-SR2 and HIV integrase predominantly involves the catalytic core domain (CCD) and the C-terminal domain (CTD) of the integrase. We aimed at providing a detailed molecular view of this interaction through a biochemical characterization of the respective protein complex. Size-exclusion chromatography was used to characterize the interaction of TRN-SR2 with a truncated variant of the HIV-1 integrase, including both the CCD and CTD. These experiments indicate that one TRN-SR2 molecule can specifically bind one CCD-CTD dimer. Next, the regions of the solenoid-like TRN-SR2 molecule that are involved in the interaction with integrase were identified using AlphaScreen binding assays, revealing that the integrase interacts with the N-terminal half of TRN-SR2 principally through the HEAT repeats 4, 10, and 11. Combining these results with small-angle X-ray scattering data for the complex of TRN-SR2 with truncated integrase, we propose a molecular model of the complex. We speculate that nuclear import of the PIC may proceed concurrently with the normal nuclear transport.
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Affiliation(s)
| | - Jolien Blokken
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Flore De Wit
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | | | - Stéphanie De Houwer
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Zeger Debyser
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
| | - Frauke Christ
- the Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000 Leuven, Belgium
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RBM4 Regulates Neuronal Differentiation of Mesenchymal Stem Cells by Modulating Alternative Splicing of Pyruvate Kinase M. Mol Cell Biol 2017; 37:MCB.00466-16. [PMID: 27821480 DOI: 10.1128/mcb.00466-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/01/2016] [Indexed: 12/31/2022] Open
Abstract
RBM4 promotes differentiation of neuronal progenitor cells and neurite outgrowth of cultured neurons via its role in splicing regulation. In this study, we further explored the role of RBM4 in neuronal differentiation. During neuronal differentiation, energy production shifts from glycolysis to oxidative phosphorylation. We found that the splice isoform change of the metabolic enzyme pyruvate kinase M (PKM) from PKM2 to PKM1 occurs during brain development and is impaired in RBM4-deficient brains. The PKM isoform change could be recapitulated in human mesenchymal stem cells (MSCs) during neuronal induction. Using a PKM minigene, we demonstrated that RBM4 plays a direct role in regulating alternative splicing of PKM. Moreover, RBM4 antagonized the function of the splicing factor PTB and induced the expression of a PTB isoform with attenuated splicing activity in MSCs. Overexpression of RBM4 or PKM1 induced the expression of neuronal genes, increased the mitochondrial respiration capacity in MSCs, and, accordingly, promoted neuronal differentiation. Finally, we demonstrated that RBM4 is induced and is involved in the PKM splicing switch and neuronal gene expression during hypoxia-induced neuronal differentiation. Hence, RBM4 plays an important role in the PKM isoform switch and the change in mitochondrial energy production during neuronal differentiation.
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24
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Yamaguchi A, Takanashi K. FUS interacts with nuclear matrix-associated protein SAFB1 as well as Matrin3 to regulate splicing and ligand-mediated transcription. Sci Rep 2016; 6:35195. [PMID: 27731383 PMCID: PMC5059712 DOI: 10.1038/srep35195] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/26/2016] [Indexed: 11/23/2022] Open
Abstract
FUS (Fused-in-Sarcoma) is a multifunctional DNA/RNA binding protein linked to familial amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Since FUS is localized mainly in the nucleus with nucleo-cytoplasmic shuttling, it is critical to understand physiological functions in the nucleus to clarify pathogenesis. Here we report a yeast two-hybrid screening identified FUS interaction with nuclear matrix-associated protein SAFB1 (scaffold attachment factor B1). FUS and SAFB1, abundant in chromatin-bound fraction, interact in a DNA-dependent manner. N-terminal SAP domain of SAFB1, a DNA-binding motif, was required for its localization to chromatin-bound fraction and splicing regulation. In addition, depletion of SAFB1 reduced FUS’s localization to chromatin-bound fraction and splicing activity, suggesting SAFB1 could tether FUS to chromatin compartment thorough N-terminal DNA-binding motif. FUS and SAFB1 also interact with Androgen Receptor (AR) regulating ligand-dependent transcription. Moreover, FUS interacts with another nuclear matrix-associated protein Matrin3, which is muted in a subset of familial ALS cases and reportedly interacts with TDP-43. Interestingly, ectopic ALS-linked FUS mutant sequestered endogenous Matrin3 and SAFB1 in the cytoplasmic aggregates. These findings indicate SAFB1 could be a FUS’s functional platform in chromatin compartment to regulate RNA splicing and ligand-dependent transcription and shed light on the etiological significance of nuclear matrix-associated proteins in ALS pathogenesis.
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Affiliation(s)
- Atsushi Yamaguchi
- Department of Neurobiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Takanashi
- Department of Neurobiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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25
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Swain A, Misulovin Z, Pherson M, Gause M, Mihindukulasuriya K, Rickels RA, Shilatifard A, Dorsett D. Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements. PLoS Genet 2016; 12:e1006331. [PMID: 27662615 PMCID: PMC5035082 DOI: 10.1371/journal.pgen.1006331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022] Open
Abstract
The cohesin protein complex mediates sister chromatid cohesion and participates in transcriptional control of genes that regulate growth and development. Substantial reduction of cohesin activity alters transcription of many genes without disrupting chromosome segregation. Drosophila Nipped-B protein loads cohesin onto chromosomes, and together Nipped-B and cohesin occupy essentially all active transcriptional enhancers and a large fraction of active genes. It is unknown why some active genes bind high levels of cohesin and some do not. Here we show that the TBPH and Lark RNA-binding proteins influence association of Nipped-B and cohesin with genes and gene regulatory sequences. In vitro, TBPH and Lark proteins specifically bind RNAs produced by genes occupied by Nipped-B and cohesin. By genomic chromatin immunoprecipitation these RNA-binding proteins also bind to chromosomes at cohesin-binding genes, enhancers, and Polycomb response elements (PREs). RNAi depletion reveals that TBPH facilitates association of Nipped-B and cohesin with genes and regulatory sequences. Lark reduces binding of Nipped-B and cohesin at many promoters and aids their association with several large enhancers. Conversely, Nipped-B facilitates TBPH and Lark association with genes and regulatory sequences, and interacts with TBPH and Lark in affinity chromatography and immunoprecipitation experiments. Blocking transcription does not ablate binding of Nipped-B and the RNA-binding proteins to chromosomes, indicating transcription is not required to maintain binding once established. These findings demonstrate that RNA-binding proteins help govern association of sister chromatid cohesion proteins with genes and enhancers.
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Affiliation(s)
- Amanda Swain
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Michelle Pherson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Kathie Mihindukulasuriya
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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26
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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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27
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Markus MA, Yang YHJ, Morris BJ. Transcriptome-wide targets of alternative splicing by RBM4 and possible role in cancer. Genomics 2016; 107:138-44. [PMID: 26898347 DOI: 10.1016/j.ygeno.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/22/2016] [Accepted: 02/16/2016] [Indexed: 10/25/2022]
Abstract
This study determined transcriptome-wide targets of the splicing factor RBM4 using Affymetrix GeneChip(®) Human Exon 1.0 ST Arrays and HeLa cells treated with RBM4-specific siRNA. This revealed 238 transcripts that were targeted for alternative splicing. Cross-linking and immunoprecipitation experiments identified 945 RBM4 targets in mouse HEK293 cells, 39% of which were ascribed to "alternative splicing" by in silico pathway analysis. Mouse embryonic stem cells transfected with Rbm4 siRNA hairpins exhibited reduced colony numbers and size consistent with involvement of RBM4 in cell proliferation. RBM4 cDNA probing of a cancer cDNA array involving 18 different tumor types from 13 different tissues and matching normal tissue found overexpression of RBM4 mRNA (p<0.01) in cervical, breast, lung, colon, ovarian and rectal cancers. Many RBM4 targets we identified have been implicated in these cancers. In conclusion, our findings reveal transcriptome-wide targets of RBM4 and point to potential cancer-related targets and mechanisms that may involve RBM4.
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Affiliation(s)
- M Andrea Markus
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, New South Wales, Australia.
| | - Yee Hwa J Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
| | - Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, New South Wales, Australia.
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28
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Abstract
The Karyopherin-β family of proteins mediates nuclear transport of macromolecules. Nuclear versus cytoplasmic localization of proteins is often suggested by the presence of NLSs (nuclear localization signals) or NESs (nuclear export signals). Import-Karyopherin-βs or Importins bind to NLSs in their protein cargos to transport them through nuclear pore complexes into the nucleus. Until recently, only two classes of NLS had been biochemically and structurally characterized: the classical NLS, which is recognized by the Importin-α/β heterodimer and the PY-NLS (proline-tyrosine NLS), which is recognized by Karyopherin-β2 or Transportin-1. Structures of two other Karyopherin-βs, Kap121 and Transportin-SR2, in complex with their respective cargos were reported for the first time recently, revealing two new distinct classes of NLSs. The present paper briefly describes the classical NLS, reviews recent literature on the PY-NLS and provides in-depth reviews of the two newly discovered classes of NLSs that bind Kap121p and Transportin-SR respectively.
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29
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Ali MK, Kim J, Hamid FB, Shin CG. Knockdown of the host cellular protein transportin 3 attenuates prototype foamy virus infection. Biosci Biotechnol Biochem 2015; 79:943-51. [PMID: 25660973 DOI: 10.1080/09168451.2015.1008973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Transportin 3 (TNPO3) is a member of the importin-ß superfamily proteins. Despite numerous studies, the exact molecular mechanism of TNPO3 in retroviral infection is still controversial. Here, we provide evidence for the role and mechanism of TNPO3 in the replication of prototype foamy virus (PFV). Our findings revealed that PFV infection was reduced 2-fold by knockdown (KD) of TNPO3. However, late stage of viral replication including transcription, translation, viral assembly, and release was not influenced. The differential cellular localization of PFV integrase (IN) in KD cells pinpointed a remarkable reduction of viral replication at the nuclear import step. We also found that TNPO3 interacted with PFV IN but not with Gag, suggesting that IN-TNPO3 interaction is important for nuclear import of PFV pre-integration complex. Our report enlightens the mechanism of PFV interaction with TNPO3 and support ongoing research on PFV as a promising safe vector for gene therapy.
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Affiliation(s)
- Md Khadem Ali
- a Department of Systems Biotechnology , Chung Ang University , Ansung , Republic of Korea
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30
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Chang SH, Chang WL, Lu CC, Tarn WY. Alanine repeats influence protein localization in splicing speckles and paraspeckles. Nucleic Acids Res 2014; 42:13788-98. [PMID: 25414336 PMCID: PMC4267627 DOI: 10.1093/nar/gku1159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ.
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Affiliation(s)
- Shuo-Hsiu Chang
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Lun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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31
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Wang Y, Chen D, Qian H, Tsai YS, Shao S, Liu Q, Dominguez D, Wang Z. The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Cancer Cell 2014; 26:374-389. [PMID: 25203323 PMCID: PMC4159621 DOI: 10.1016/j.ccr.2014.07.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/29/2014] [Accepted: 07/15/2014] [Indexed: 11/26/2022]
Abstract
Splicing dysregulation is one of the molecular hallmarks of cancer. However, the underlying molecular mechanisms remain poorly defined. Here we report that the splicing factor RBM4 suppresses proliferation and migration of various cancer cells by specifically controlling cancer-related splicing. Particularly, RBM4 regulates Bcl-x splicing to induce apoptosis, and coexpression of Bcl-xL partially reverses the RBM4-mediated tumor suppression. Moreover, RBM4 antagonizes an oncogenic splicing factor, SRSF1, to inhibit mTOR activation. Strikingly, RBM4 expression is decreased dramatically in cancer patients, and the RBM4 level correlates positively with improved survival. In addition to providing mechanistic insights of cancer-related splicing dysregulation, this study establishes RBM4 as a tumor suppressor with therapeutic potential and clinical values as a prognostic factor.
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Affiliation(s)
- Yang Wang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University, Dalian 116044, China; Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Dan Chen
- Department of Pathology, First Affiliated Hospital. Dalian Medical University, Dalian 116001, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Yihsuan S Tsai
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shujuan Shao
- Key Laboratory of Proteomics of Liaoning Province, Dalian Medical University, Dalian 116044, China
| | - Quentin Liu
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University, Dalian 116044, China
| | - Daniel Dominguez
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Zefeng Wang
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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32
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De Houwer S, Demeulemeester J, Thys W, Rocha S, Dirix L, Gijsbers R, Christ F, Debyser Z. The HIV-1 integrase mutant R263A/K264A is 2-fold defective for TRN-SR2 binding and viral nuclear import. J Biol Chem 2014; 289:25351-61. [PMID: 25063804 DOI: 10.1074/jbc.m113.533281] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Transportin-SR2 (Tnpo3, TRN-SR2), a human karyopherin encoded by the TNPO3 gene, has been identified as a cellular cofactor of HIV-1 replication, specifically interacting with HIV-1 integrase (IN). Whether this interaction mediates the nuclear import of HIV remains controversial. We previously characterized the TRN-SR2 binding interface in IN and introduced mutations at these positions to corroborate the biological relevance of the interaction. The pleiotropic nature of IN mutations complicated the interpretation. Indeed, all previously tested IN interaction mutants also affected RT. Here we report on a virus with a pair of IN mutations, IN(R263A/K264A), that significantly reduce interaction with TRN-SR2. The virus retains wild-type reverse transcription activity but displays a block in nuclear import and integration, as measured by quantitative PCR. The defect in integration of this mutant resulted in a smaller increase in the number of two-long terminal repeat circles than for virus specifically blocked at integration by raltegravir or catalytic site mutations (IN(D64N/D116N/E152Q)). Finally, using an eGFP-IN-labeled HIV fluorescence-based import assay, the defect in nuclear import was corroborated. These data altogether underscore the importance of the HIV-IN TRN-SR2 protein-protein interaction for HIV nuclear import and validate the IN/TRN-SR2 interaction interface as a promising target for future antiviral therapy.
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Affiliation(s)
- Stéphanie De Houwer
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jonas Demeulemeester
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Wannes Thys
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Susana Rocha
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Lieve Dirix
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Rik Gijsbers
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Frauke Christ
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Zeger Debyser
- From the Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
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33
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Lin JC, Tarn WY, Hsieh WK. Emerging role for RNA binding motif protein 4 in the development of brown adipocytes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:769-79. [PMID: 24389249 DOI: 10.1016/j.bbamcr.2013.12.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 12/21/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
Abstract
RNA-binding motif protein 4 (RBM4) reportedly reprograms the tissue-specific splicing network which modulates the development of muscles and pancreatic β-islets. Herein, we report that Rbm4a(-/-) mice exhibited hyperlipidemia accompanied with reduced mass of interscapular brown adipose tissue (iBAT). Elevated RBM4a led to the isoform shift of IR, Ppar-γ, and Pref-1 genes which play pivotal roles in the different stages of adipogenesis. Overexpression of RBM4a enhanced the mitochondrial activity of brown adipocyte-like lineage in the presence of uncoupling agent. RBM4a-ablated adipocytes inversely exhibited impaired development and inefficient energy expenditure. Intriguingly, overexpressed RBM4a induced the expression of brown adipocyte-specific factors (Prdm16 and Bmp7) in white adipocyte-like lineage, which suggested the potential action of RBM4a on the white-to-brown trans-differentiation of adipocytes. In differentiating adipocytes, RBM4a constituted a feed-forward circuit through autoregulating the splicing pattern of its own transcript. Based on these results, we propose the emerging role of RBM4 in regulating the adipocyte-specific splicing events and transcription cascade, which subsequently facilitate the development and function of brown adipocyte-like cells.
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Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Kou Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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34
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Abstract
Classic nuclear shuttling is mediated by an importin-α∙β heterodimer that binds to cargoes containing a nuclear localization signal, and shuttles most nuclear proteins immediately after their translation. Aside from this canonical mechanism, kariopheryn-βs or β-like importins operate by binding to non-canonical nuclear localization signals to mediate translocation without the assistance of importin-α. The mechanism by which these components operate is much less understood and is currently under investigation. Recently, several β-like importins have been implicated in the stimulated nuclear translocation of signaling proteins. Here, we propose that this group of importins might be responsible for the swift nuclear shuttling of many proteins following various stimuli.
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Paraquat modulates alternative pre-mRNA splicing by modifying the intracellular distribution of SRPK2. PLoS One 2013; 8:e61980. [PMID: 23613995 PMCID: PMC3628584 DOI: 10.1371/journal.pone.0061980] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/16/2013] [Indexed: 11/24/2022] Open
Abstract
Paraquat (PQ) is a neurotoxic herbicide that induces superoxide formation. Although it is known that its toxic properties are linked to ROS production, the cellular response to PQ is still poorly understood. We reported previously that treatment with PQ induced genome-wide changes in pre-mRNA splicing. Here, we investigated the molecular mechanism underlying PQ-induced pre-mRNA splicing alterations. We show that PQ treatment leads to the phosphorylation and nuclear accumulation of SRPK2, a member of the family of serine/arginine (SR) protein-specific kinases. Concomitantly, we observed increased phosphorylation of SR proteins. Site-specific mutagenesis identified a single serine residue that is necessary and sufficient for nuclear localization of SRPK2. Transfection of a phosphomimetic mutant modified splice site selection of the E1A minigene splicing reporter similar to PQ-treatment. Finally, we found that PQ induces DNA damage and vice versa that genotoxic treatments are also able to promote SRPK2 phosphorylation and nuclear localization. Consistent with these observations, treatment with PQ, cisplatin or γ-radiation promote changes in the splicing pattern of genes involved in DNA repair, cell cycle control, and apoptosis. Altogether, our findings reveal a novel regulatory mechanism that connects PQ to the DNA damage response and to the modulation of alternative splicing via SRPK2 phosphorylation.
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36
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Liu Y, Conaway L, Rutherford Bethard J, Al-Ayoubi AM, Thompson Bradley A, Zheng H, Weed SA, Eblen ST. Phosphorylation of the alternative mRNA splicing factor 45 (SPF45) by Clk1 regulates its splice site utilization, cell migration and invasion. Nucleic Acids Res 2013; 41:4949-62. [PMID: 23519612 PMCID: PMC3643583 DOI: 10.1093/nar/gkt170] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative mRNA splicing is a mechanism to regulate protein isoform expression and is regulated by alternative splicing factors. The alternative splicing factor 45 (SPF45) is overexpressed in cancer, although few biological effects of SPF45 are known, and few splicing targets have been identified. We previously showed that Extracellular Regulated Kinase 2 (ERK2) phosphorylation of SPF45 regulates cell proliferation and adhesion to fibronectin. In this work, we show that Cdc2-like kinase 1 (Clk1) phosphorylates SPF45 on eight serine residues. Clk1 expression enhanced, whereas Clk1 inhibition reduced, SPF45-induced exon 6 exclusion from Fas mRNA. Mutational analysis of the Clk1 phosphorylation sites on SPF45 showed both positive and negative regulation of splicing, with a net effect of inhibiting SPF45-induced exon 6 exclusion, correlating with reduced Fas mRNA binding. However, Clk1 enhanced SPF45 protein expression, but not mRNA expression, whereas inhibition of Clk1 increased SPF45 degradation through a proteasome-dependent pathway. Overexpression of SPF45 or a phospho-mimetic mutant, but not a phospho-inhibitory mutant, stimulated ovarian cancer cell migration and invasion, correlating with increased fibronectin expression, ERK activation and enhanced splicing and phosphorylation of full-length cortactin. Our results demonstrate for the first time that SPF45 overexpression enhances cell migration and invasion, dependent on biochemical regulation by Clk1.
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Affiliation(s)
- Yuying Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
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37
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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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38
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Khadem Ali M, Alamgir Hossain M, Shin CG. Comparative sequence and expression analyses of African green monkey (Cercopithecus aethiops) TNPO3 from CV-1 cells. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0102-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Chen PH, Lee CI, Weng YT, Tarn WY, Tsao YP, Kuo PC, Hsu PH, Huang CW, Huang CS, Lee HH, Wu JT, Chen SL. BCAS2 is essential for Drosophila viability and functions in pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2013; 19:208-218. [PMID: 23249746 PMCID: PMC3543084 DOI: 10.1261/rna.034835.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 11/14/2012] [Indexed: 06/01/2023]
Abstract
Here, we show that dBCAS2 (CG4980, human Breast Carcinoma Amplified Sequence 2 ortholog) is essential for the viability of Drosophila melanogaster. We find that ubiquitous or tissue-specific depletion of dBCAS2 leads to larval lethality, wing deformities, impaired splicing, and apoptosis. More importantly, overexpression of hBCAS2 rescues these defects. Furthermore, the C-terminal coiled-coil domain of hBCAS2 binds directly to CDC5L and recruits hPrp19/PLRG1 to form a core complex for splicing in mammalian cells and can partially restore wing damage induced by knocking down dBCAS2 in flies. In summary, Drosophila and human BCAS2 share a similar function in RNA splicing, which affects cell viability.
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Affiliation(s)
- Po-Han Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chia-I Lee
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Tzu Weng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei 104, Taiwan
| | - Ping-Chang Kuo
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, College of Life Sciences, National Taiwan Ocean University, Keelung 202, Taiwan
- Institute of Bioscience and Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Chu-Wei Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, College of Medicine, National Taiwan University and Hospital, Taipei 100, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - June-Tai Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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40
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Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat Struct Mol Biol 2012; 19:1044-52. [PMID: 22983564 PMCID: PMC3753194 DOI: 10.1038/nsmb.2377] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 08/07/2012] [Indexed: 12/16/2022]
Abstract
Most human genes produce multiple splicing isoforms with distinct functions. To systematically understand splicing regulation, we conducted an unbiased screen and identified >100 intronic splicing enhancers (ISEs) that were clustered by sequence similarity into six groups. All ISEs functioned in another cell type and heterologous introns, and their distribution and conservation patterns in different pre-mRNA regions are similar to exonic splicing silencers. Consistently all ISEs inhibited use of splice sites from exonic locations. The putative trans-factors of each ISE group were identified and validated. Five distinct ISE motifs were recognized by hnRNP H and F whose C-terminal domains were sufficient to render context-dependent activities of ISEs. The sixth group was controlled by factors that either activate or suppress splicing. This work provided a comprehensive picture of general ISE activities and provided new models of how a single element can function oppositely depending on its locations and binding factors.
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Cellular cofactors of lentiviral integrase: from target validation to drug discovery. Mol Biol Int 2012; 2012:863405. [PMID: 22928108 PMCID: PMC3420096 DOI: 10.1155/2012/863405] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/03/2012] [Accepted: 06/27/2012] [Indexed: 01/30/2023] Open
Abstract
To accomplish their life cycle, lentiviruses make use of host proteins, the so-called cellular cofactors. Interactions between host cell and viral proteins during early stages of lentiviral infection provide attractive new antiviral targets. The insertion of lentiviral cDNA in a host cell chromosome is a step of no return in the replication cycle, after which the host cell becomes a permanent carrier of the viral genome and a producer of lentiviral progeny. Integration is carried out by integrase (IN), an enzyme playing also an important role during nuclear import. Plenty of cellular cofactors of HIV-1 IN have been proposed. To date, the lens epithelium-derived growth factor (LEDGF/p75) is the best studied cofactor of HIV-1 IN. Moreover, small molecules that block the LEDGF/p75-IN interaction have recently been developed for the treatment of HIV infection. The nuclear import factor transportin-SR2 (TRN-SR2) has been proposed as another interactor of HIV IN-mediating nuclear import of the virus. Using both proteins as examples, we will describe approaches to be taken to identify and validate novel cofactors as new antiviral targets. Finally, we will highlight recent advances in the design and the development of small-molecule inhibitors binding to the LEDGF/p75-binding pocket in IN (LEDGINs).
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De Houwer S, Demeulemeester J, Thys W, Taltynov O, Zmajkovicova K, Christ F, Debyser Z. Identification of residues in the C-terminal domain of HIV-1 integrase that mediate binding to the transportin-SR2 protein. J Biol Chem 2012; 287:34059-68. [PMID: 22872638 DOI: 10.1074/jbc.m112.387944] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transportin-SR2 (TRN-SR2 and TNPO3) is a cellular cofactor of HIV replication that has been implicated in the nuclear import of HIV. TRN-SR2 was originally identified in a yeast two-hybrid screen as an interaction partner of HIV integrase (IN) and in two independent siRNA screens as a cofactor of viral replication. We have now studied the interaction of TRN-SR2 and HIV IN in molecular detail and identified the TRN-SR2 interacting regions of IN. A weak interaction with the catalytic core domain (CCD) and a strong interaction with the C-terminal domain (CTD) of IN were detected. By dissecting the catalytic core domain (CCD) of IN into short structural fragments, we identified a peptide (INIP(1), amino acids (170)EHLKTAVQMAVFIHNFKRKGGI(191)) retaining the ability to interact with TRN-SR2. By dissecting the C-terminal domain (CTD) of IN, we could identify two interacting peptides (amino acids (214)QKQITKIQNFRVYYR(228) and (262)RRKVKIIRDYGK(273)) that come together in the CTD tertiary structure to form an exposed antiparallel β-sheet. Through site-specific mutagenesis, we defined the following sets of amino acids in IN as important for the interaction with TRN-SR2: Phe-185/Lys-186/Arg-187/Lys-188 in the CCD and Arg-262/Arg-263/Lys-264 and Lys-266/Arg-269 in the CTD. An HIV-1 strain carrying K266A/R269A in IN was replication-defective due to a block in reverse transcription, confounding the study of nuclear import. Insight into the IN/TRN-SR2 interaction interface is necessary to guide drug discovery efforts targeting the nuclear entry step of replication.
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Affiliation(s)
- Stephanie De Houwer
- Laboratory for Molecular Virology and Gene Therapy, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
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43
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The Role of TNPO3 in HIV-1 Replication. Mol Biol Int 2012; 2012:868597. [PMID: 22888429 PMCID: PMC3409535 DOI: 10.1155/2012/868597] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 12/12/2022] Open
Abstract
TNPO3, transportin-SR2 or Tnp3, a member of the karyopherin β superfamily of proteins, is important for the ability of human immunodeficiency virus (HIV-1) to achieve productive infection, as TNPO3 depletion in human cells leads to a dramatic reduction of infection. Here we describe and discuss recent findings suggesting that TNPO3 assists HIV-1 replication in the nucleus and in fact that TNPO3 may assist PIC maturation in the nucleus. In addition, the viral determinant for the requirement of TNPO3 in HIV-1 infection is discussed. This paper summarizes the most significant recent discoveries about this important host factor and its role in HIV-1 replication.
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Chen CH, Chu PC, Lee L, Lien HW, Lin TL, Fan CC, Chi P, Huang CJ, Chang MS. Disruption of murine mp29/Syf2/Ntc31 gene results in embryonic lethality with aberrant checkpoint response. PLoS One 2012; 7:e33538. [PMID: 22448250 PMCID: PMC3308990 DOI: 10.1371/journal.pone.0033538] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 02/10/2012] [Indexed: 11/19/2022] Open
Abstract
Human p29 is a putative component of spliceosomes, but its role in pre-mRNA is elusive. By siRNA knockdown and stable overexpression, we demonstrated that human p29 is involved in DNA damage response and Fanconi anemia pathway in cultured cells. In this study, we generated p29 knockout mice (mp29(GT/GT)) using the mp29 gene trap embryonic stem cells to study the role of mp29 in DNA damage response in vivo. Interruption of mp29 at both alleles resulted in embryonic lethality. Embryonic abnormality occurred as early as E6.5 in mp29(GT/GT) mice accompanied with decreased mRNA levels of α-tubulin and Chk1. The reduction of α-tubulin and Chk1 mRNAs is likely due to an impaired post-transcriptional event. An aberrant G2/M checkpoint was found in mp29 gene trap embryos when exposed to aphidicolin and UV light. This embryonic lethality was rescued by crossing with mp29 transgenic mice. Additionally, the knockdown of zfp29 in zebrafish resulted in embryonic death at 72 hours of development postfertilization (hpf). A lower level of acetylated α-tubulin was also observed in zfp29 morphants. Together, these results illustrate an indispensable role of mp29 in DNA checkpoint response during embryonic development.
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Affiliation(s)
- Chia-Hsin Chen
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Po-Chen Chu
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Liekyeow Lee
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Huang-Wei Lien
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Tse-Ling Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Chen Fan
- Department of Physiology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chang-Jen Huang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Mau-Sun Chang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail:
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45
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Xia Y, Tang L, Yao L, Wan B, Yang X, Yu L. Literature and patent analysis of the cloning and identification of human functional genes in China. SCIENCE CHINA. LIFE SCIENCES 2012; 55:268-282. [PMID: 22527523 DOI: 10.1007/s11427-012-4299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 10/13/2011] [Indexed: 05/31/2023]
Abstract
The Human Genome Project was launched at the end of the 1980s. Since then, the cloning and identification of functional genes has been a major focus of research across the world. In China too, the potentially profound impact of such studies on the life sciences and on human health was realized, and relevant studies were initiated in the 1990s. To advance China's involvement in the Human Genome Project, in the mid-1990s, Committee of Experts in Biology from National High Technology Research and Development Program of China (863 Program) proposed the "two 1%" goal. This goal envisaged China contributing 1% of the total sequencing work, and cloning and identifying 1% of the total human functional genes. Over the past 20 years, tremendous achievement has been accomplished by Chinese scientists. It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project, whereas, there is no comprehensive report about "whether China had finished cloning and identifying 1% of human functional genes". In the present study, the GenBank database at the National Center of Biotechnology Information, the PubMed search tool, and the patent database of the State Intellectual Property Office, China, were used to retrieve entries based on two screening standards: (i) Were the newly cloned and identified genes first reported by Chinese scientists? (ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further. The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented (http://gene.fudan.sh.cn/introduction/database/chinagene/chinagene.html). This study systematically summarizes China's contributions to human functional genomics research and answers the question "has China finished cloning and identifying 1% of human functional genes?" in the affirmative.
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Affiliation(s)
- Yan Xia
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
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46
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Eblen ST. Regulation of chemoresistance via alternative messenger RNA splicing. Biochem Pharmacol 2012; 83:1063-72. [PMID: 22248731 DOI: 10.1016/j.bcp.2011.12.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 12/17/2022]
Abstract
The acquisition of resistance to chemotherapy is a significant problem in the treatment of cancer, greatly increasing patient morbidity and mortality. Tumors are often sensitive to chemotherapy upon initial treatment, but repeated treatments can select for those cells that were able to survive initial therapy and have acquired cellular mechanisms to enhance their resistance to subsequent chemotherapy treatment. Many cellular mechanisms of drug resistance have been identified, most of which result from changes in gene and protein expression. While changes at the transcriptional level have been duly noted, it is primarily the post-transcriptional processing of pre-mRNA into mature mRNA that regulates the composition of the proteome and it is the proteome that actually regulates the cell's response to chemotherapeutic insult, inducing cell survival or death. During pre-mRNA processing, intronic non-protein-coding sequences are removed and protein-coding exons are spliced to form a continuous template for protein translation. Alternative splicing involves the differential inclusion or exclusion of exonic sequences into the mature transcript, generating different mRNA templates for protein production. This regulatory mechanism enables the potential to produce many different protein isoforms from the same gene. In this review I will explain the mechanism of alternative pre-mRNA splicing and look at some specific examples of how splicing factors, splicing factor kinases and alternative splicing of specific pre-mRNAs from genes have been shown to contribute to acquisition of the drug resistant phenotype.
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Affiliation(s)
- Scott T Eblen
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, 29425, USA.
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Anguissola S, McCormack WJ, Morrin MA, Higgins WJ, Fox DM, Worrall DM. Pigment epithelium-derived factor (PEDF) interacts with transportin SR2, and active nuclear import is facilitated by a novel nuclear localization motif. PLoS One 2011; 6:e26234. [PMID: 22028839 PMCID: PMC3196545 DOI: 10.1371/journal.pone.0026234] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/22/2011] [Indexed: 02/04/2023] Open
Abstract
PEDF (Pigment epithelium-derived factor) is a non-inhibitory member of the serpin gene family (serpinF1) that displays neurotrophic and anti-angiogenic properties. PEDF contains a secretion signal sequence, but although originally regarded as a secreted extracellular protein, endogenous PEDF is found in the cytoplasm and nucleus of several mammalian cell types. In this study we employed a yeast two-hybrid interaction trap screen to identify transportin-SR2, a member of the importin-β family of nuclear transport karyopherins, as a putative PEDF binding partner. The interaction was supported in vitro by GST-pulldown and co-immunoprecipitation. Following transfection of HEK293 cells with GFP-tagged PEDF the protein was predominantly localised to the nucleus, suggesting that active import of PEDF occurs. A motif (YxxYRVRS) shared by PEDF and the unrelated transportin-SR2 substrate, RNA binding motif protein 4b, was identified and we investigated its potential as a nuclear localization signal (NLS) sequence. Site-directed mutagenesis of this helix A motif in PEDF resulted in a GFP-tagged mutant protein being excluded from the nucleus, and mutation of two arginine residues (R67, R69) was sufficient to abolish nuclear import and PEDF interaction with transportin-SR2. These results suggest a novel NLS and mechanism for serpinF1 nuclear import, which may be critical for anti-angiogenic and neurotrophic function.
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Affiliation(s)
- Sergio Anguissola
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - William J. McCormack
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Michelle A. Morrin
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Wayne J. Higgins
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Denise M. Fox
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - D. Margaret Worrall
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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48
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Kojima S, Shingle DL, Green CB. Post-transcriptional control of circadian rhythms. J Cell Sci 2011; 124:311-20. [PMID: 21242310 DOI: 10.1242/jcs.065771] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian rhythms exist in most living organisms. The general molecular mechanisms that are used to generate 24-hour rhythms are conserved among organisms, although the details vary. These core clocks consist of multiple regulatory feedback loops, and must be coordinated and orchestrated appropriately for the fine-tuning of the 24-hour period. Many levels of regulation are important for the proper functioning of the circadian clock, including transcriptional, post-transcriptional and post-translational mechanisms. In recent years, new information about post-transcriptional regulation in the circadian system has been discovered. Such regulation has been shown to alter the phase and amplitude of rhythmic mRNA and protein expression in many organisms. Therefore, this Commentary will provide an overview of current knowledge of post-transcriptional regulation of the clock genes and clock-controlled genes in dinoflagellates, plants, fungi and animals. This article will also highlight how circadian gene expression is modulated by post-transcriptional mechanisms and how this is crucial for robust circadian rhythmicity.
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Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, NB4.204G, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Lin JC, Tarn WY. RBM4 down-regulates PTB and antagonizes its activity in muscle cell-specific alternative splicing. ACTA ACUST UNITED AC 2011; 193:509-20. [PMID: 21518792 PMCID: PMC3087008 DOI: 10.1083/jcb.201007131] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RBM4 activates exon skipping of PTB transcripts to suppress PTB expression and counteracts PTB-mediated inhibition of alternative splicing during myogenesis. Alternative splicing contributes largely to cell differentiation and functional specification. We previously reported that the RNA-binding protein RBM4 antagonizes the activity of splicing factor PTB to modulate muscle cell–specific exon selection of α-tropomyosin. Here we show that down-regulation of PTB and its neuronal analogue nPTB during muscle cell differentiation may involve alternative splicing-coupled nonsense-mediated mRNA decay. RBM4 regulates PTB/nPTB expression by activating exon skipping of their transcripts during myogenesis. Moreover, RBM4 and PTB target a common set of transcripts that undergo muscle cell–specific alternative splicing. Overexpression of RBM4 invariably promoted expression of muscle cell–specific isoforms, which recapitulated in vivo alternative splicing changes during muscle differentiation, whereas PTB acted oppositely to RBM4 in expression of mRNA isoforms specific for late-stage differentiation. Therefore, RBM4 may synergize its effect on muscle cell–specific alternative splicing by down-regulating PTB expression and antagonizing the activity of PTB in exon selection, which highlights a hierarchical role for RBM4 in a splicing cascade that regulates myogenesis.
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Affiliation(s)
- Jung-Chun Lin
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
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50
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Sun Y, Dierssen M, Toran N, Pollak DD, Chen WQ, Lubec G. A gel-based proteomic method reveals several protein pathway abnormalities in fetal Down syndrome brain. J Proteomics 2011; 74:547-57. [DOI: 10.1016/j.jprot.2011.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/05/2011] [Accepted: 01/15/2011] [Indexed: 11/25/2022]
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