1
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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2
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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3
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Yu Q, Wu T, Xu W, Wei J, Zhao A, Wang M, Li M, Chi G. PTBP1 as a potential regulator of disease. Mol Cell Biochem 2023:10.1007/s11010-023-04905-x. [PMID: 38129625 DOI: 10.1007/s11010-023-04905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which plays a key role in alternative splicing of precursor mRNA and RNA metabolism. PTBP1 is universally expressed in various tissues and binds to multiple downstream transcripts to interfere with physiological and pathological processes such as the tumor growth, body metabolism, cardiovascular homeostasis, and central nervous system damage, showing great prospects in many fields. The function of PTBP1 involves the regulation and interaction of various upstream molecules, including circular RNAs (circRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory systems are inseparable from the development and treatment of diseases. Here, we review the latest knowledge regarding the structure and molecular functions of PTBP1 and summarize its functions and mechanisms of PTBP1 in various diseases, including controversial studies. Furthermore, we recommend future studies on PTBP1 and discuss the prospects of targeting PTBP1 in new clinical therapeutic approaches.
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Affiliation(s)
- Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Tongtong Wu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
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4
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Kakumani PK, Ko Y, Ramakrishna S, Christopher G, Dodgson M, Shrinet J, Harvey LM, Shin C, Simard M. CSDE1 promotes miR-451 biogenesis. Nucleic Acids Res 2023; 51:9385-9396. [PMID: 37493604 PMCID: PMC10516617 DOI: 10.1093/nar/gkad619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
MicroRNAs are sequentially processed by RNase III enzymes Drosha and Dicer. miR-451 is a highly conserved miRNA in vertebrates which bypasses Dicer processing and instead relies on AGO2 for its maturation. miR-451 is highly expressed in erythrocytes and regulates the differentiation of erythroblasts into mature red blood cells. However, the mechanistic details underlying miR-451 biogenesis in erythrocytes remains obscure. Here, we report that the RNA binding protein CSDE1 which is required for the development of erythroblasts into erythrocytes, controls the expression of miR-451 in erythroleukemia cells. CSDE1 binds miR-451 and regulates AGO2 processing of pre-miR-451 through its N-terminal domains. CSDE1 further interacts with PARN and promotes the trimming of intermediate miR-451 to the mature length. Together, our results demonstrate that CSDE1 promotes biogenesis of miR-451 in erythroid progenitors.
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Affiliation(s)
- Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Yunkoo Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sushmitha Ramakrishna
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Grace Christopher
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Maria Dodgson
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Louis-Mathieu Harvey
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Martin J Simard
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
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5
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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6
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Chaudhary A, Chaurasia PK, Kushwaha S, Chauhan P, Chawade A, Mani A. Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions. Int J Biol Macromol 2022; 220:743-753. [PMID: 35987358 DOI: 10.1016/j.ijbiomac.2022.08.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 08/14/2022] [Indexed: 11/05/2022]
Abstract
Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.
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Affiliation(s)
- Amit Chaudhary
- Department of Metallurgical Engineering & Materials Science, Indian Institute of Technology Bombay
| | - Pankaj Kumar Chaurasia
- PG Department of Chemistry, L.S. College, Babasaheb Bhimrao Ambedkar Bihar University, Muzaffarpur, Bihar 842001, India
| | - Sandeep Kushwaha
- National Institute of Animal Biotechnology, Hyderabad 500032, India.
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden.
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
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7
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Upstream of N-Ras (Unr/CSDE1) Interacts with NCp7 and Gag, Modulating HIV-1 IRES-Mediated Translation Initiation. Viruses 2022; 14:v14081798. [PMID: 36016420 PMCID: PMC9413769 DOI: 10.3390/v14081798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) nucleocapsid protein (NC) as a mature protein or as a domain of the Gag precursor plays important roles in the early and late phases of the infection. To better understand its roles, we searched for new cellular partners and identified the RNA-binding protein Unr/CSDE1, Upstream of N-ras, whose interaction with Gag and NCp7 was confirmed by co-immunoprecipitation and FRET-FLIM. Unr interaction with Gag was found to be RNA-dependent and mediated by its NC domain. Using a dual luciferase assay, Unr was shown to act as an ITAF (IRES trans-acting factor), increasing the HIV-1 IRES-dependent translation. Point mutations of the HIV-1 IRES in a consensus Unr binding motif were found to alter both the IRES activity and its activation by Unr, suggesting a strong dependence of the IRES on Unr. Interestingly, Unr stimulatory effect is counteracted by NCp7, while Gag increases the Unr-promoted IRES activity, suggesting a differential Unr effect on the early and late phases of viral infection. Finally, knockdown of Unr in HeLa cells leads to a decrease in infection by a non-replicative lentivector, proving its functional implication in the early phase of viral infection.
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8
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Fan X, Zhao Z, Ma L, Huang X, Zhan Q, Song Y. PTBP1 promotes IRES-mediated translation of cyclin B1 in cancer. Acta Biochim Biophys Sin (Shanghai) 2022; 54:696-707. [PMID: 35643957 PMCID: PMC9828304 DOI: 10.3724/abbs.2022046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Cyclin B1 is an essential cyclin-dependent protein that involves in the G2/M transition. Multiple studies report that cyclin B1 is upregulated in cancers and promotes cancer progression. However, the mechanism of cyclin B1 upregulation remains unclear. Here we report that the 5'UTR of cyclin B1 mRNA contains an internal ribosome entry site (IRES) by using a bicistronic fluorescent reporter. We show that IRES can initiate the translation of cyclin B1, and the IRES-mediated translation is further activated under cell stress. Interacting trans-acting factors (ITAFs) are required by most IRES to initiate the translation. We find that PTBP1 promotes the IRES-mediated translation of cyclin B1 by binding to the 5'UTR of cyclin B1. On top of that, PTBP1 promotes the malignancy of ESCC cells. Our data suggest that the IRES-mediated translation of cyclin B1 plays an essential role in the cyclin B1 upregulation in cancers.
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Affiliation(s)
- Xinyi Fan
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
- Department of Radiation OncologyWeill Cornell Medical CollegeNew YorkNY10065USA
| | - Zitong Zhao
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
| | - Liying Ma
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
| | | | - Qimin Zhan
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Laboratory of Molecular OncologyPeking University Cancer Hospital & InstituteBeijing100142China
| | - Yongmei Song
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
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9
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Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X, He Y, Xia X, Chen B, Song W. PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol 2022; 237:2357-2373. [PMID: 35288937 DOI: 10.1002/jcp.30716] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.
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Affiliation(s)
- Shirui Dai
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Chao Wang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Cheng Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Lemeng Feng
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Wulong Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xuezhi Zhou
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Ye He
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xiaobo Xia
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
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10
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Wang Y, Lin S, Zhao Z, Xu P, Gao K, Qian H, Zhang Z, Guo X. Functional analysis of a putative Bombyx mori cypovirus miRNA BmCPV-miR-10 and its effect on virus replication. INSECT MOLECULAR BIOLOGY 2021; 30:552-565. [PMID: 34296485 DOI: 10.1111/imb.12725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Bombyx mori cypovirus (BmCPV) is an important pathogen of silkworm (B. mori), the economically beneficial insect. The mechanism of its interaction with host immune defence system in the process of infection is still not yet completely clear. Researches have demonstrated that virus-encoded microRNAs (miRNA) play a crucial role in regulating host-pathogen interaction, but few reports are available so far on miRNAs encoded by insect viruses, especially the RNA viruses. In this study, a putative miRNA encoded by the 10th segment of BmCPV genomic RNA, BmCPV-miR-10, was identified and functionally analysed. The expression of the putative BmCPV-miR-10 could be detected via stem-loop RT-PCR (reverse transcription-Polymerase Chain Reaction) in the midgut of silkworm larvae infected with BmCPV. BmCSDE1 (B. mori cold shock domain E1 protein) gene was predicted to be a candidate target gene for BmCPV-miR-10 with the miRNA binding site located in 3' untranslated region of its mRNA. The regulation effect of the putative BmCPV-miR-10 on BmCSDE1 was verified in HEK293 cells by lentiviral expression system, in BmN cells by transfecting BmCPV-miR-10 mimics. The qRT-PCR (quantitative real-time PCR) results showed that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1. By injection of BmCPV-miR-10 mimics into the silkworm larvae infected with BmCPV, it was further proved that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1 in vivo, then inhibit the expression of BmApaf-1 (B. mori apoptotic protease activating factor 1), while enhance the replication of BmCPV genomic RNAs to a certain extent. These results implied that the putative BmCPV-miR-10 could down-regulate the expression of BmCSDE1, then suppress the expression of BmApaf-1, thereby created a favourable intracellular environment for virus replication and proliferation.
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Affiliation(s)
- Y Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - S Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Z Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - P Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - K Gao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - H Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Z Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - X Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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11
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MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome. Noncoding RNA 2021; 7:ncrna7040061. [PMID: 34698276 PMCID: PMC8544657 DOI: 10.3390/ncrna7040061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs.
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12
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El Khouri E, Ghoumid J, Haye D, Giuliano F, Drevillon L, Briand-Suleau A, De La Grange P, Nau V, Gaillon T, Bienvenu T, Jacquemin-Sablon H, Goossens M, Amselem S, Giurgea I. Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders. Mol Psychiatry 2021; 26:3572-3585. [PMID: 33867523 DOI: 10.1038/s41380-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
Among the genetic factors playing a key role in the etiology of intellectual disabilities (IDs) and autism spectrum disorders (ASDs), several encode RNA-binding proteins (RBPs). In this study, we deciphered the molecular and cellular bases of ID-ASD in a patient followed from birth to the age of 21, in whom we identified a de novo CSDE1 (Cold Shock Domain-containing E1) nonsense variation. CSDE1 encodes an RBP that regulates multiple cellular pathways by monitoring the translation and abundance of target transcripts. Analyses performed on the patient's primary fibroblasts showed that the identified CSDE1 variation leads to haploinsufficiency. We identified through RNA-seq assays the Wnt/β-catenin signaling and cellular adhesion as two major deregulated pathways. These results were further confirmed by functional studies involving Wnt-specific luciferase and substrate adhesion assays. Additional data support a disease model involving APC Down-Regulated-1 (APCDD1) and cadherin-2 (CDH2), two components of the Wnt/β-catenin pathway, CDH2 being also pivotal for cellular adhesion. Our study, which relies on both the deep phenotyping and long-term follow-up of a patient with CSDE1 haploinsufficiency and on ex vivo studies, sheds new light on the CSDE1-dependent deregulated pathways in ID-ASD.
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Affiliation(s)
- E El Khouri
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - J Ghoumid
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - D Haye
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - F Giuliano
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - L Drevillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,CHU Caen Normandie, Caen, France
| | - A Briand-Suleau
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | | | - V Nau
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - T Gaillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - T Bienvenu
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | - H Jacquemin-Sablon
- INSERM UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - M Goossens
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - S Amselem
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - I Giurgea
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France. .,Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.
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13
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CSDE1 attenuates microRNA-mediated silencing of PMEPA1 in melanoma. Oncogene 2021; 40:3231-3244. [PMID: 33833398 DOI: 10.1038/s41388-021-01767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
MicroRNAs and RNA-binding proteins (RBPs) primarily target the 3' UTR of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in physiology and disease are yet to be fully explored. CSDE1 is an RBP that promotes metastasis in melanoma and mechanisms underlying its oncogenic activities need to be completely defined. Here we report that CSDE1 interacts with specific miRNA-induced silencing complexes (miRISC) in melanoma. We find an association of CSDE1 with AGO2, the essential component of miRISC, which is facilitated by target mRNAs and depends on the first cold shock domain of CSDE1. Both CSDE1 and AGO2 bind to 3' UTR of PMEPA1. CSDE1 counters AGO2 binding, leading to an increase of PMEPA1 expression. We also identify a miRNA, miR-129-5p, that represses PMEPA1 expression in melanoma. Collectively, our results show that PMEPA1 promotes tumorigenic traits and that CSDE1 along with miR-129-5p/AGO2 miRISC act antagonistically to fine-tune PMEPA1 expression toward the progression of melanoma.
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14
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Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions. Nat Genet 2021; 53:729-741. [PMID: 33821006 PMCID: PMC8825242 DOI: 10.1038/s41588-021-00830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023]
Abstract
The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5' untranslated regions (UTRs) in noncanonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5' UTRs decreased gene expression, and extremely conserved 5' UTRs possess cis-regulatory elements that promote cell-type-specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a new methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5' UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
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15
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Kim W, Shin JC, Lee KH, Kim KT. PTBP1 Positively Regulates the Translation of Circadian Clock Gene, Period1. Int J Mol Sci 2020; 21:ijms21186921. [PMID: 32967200 PMCID: PMC7555454 DOI: 10.3390/ijms21186921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Circadian oscillations of mRNAs and proteins are the main features of circadian clock genes. Among them, Period1 (Per1) is a key component in negative-feedback regulation, which shows a robust diurnal oscillation and the importance of circadian rhythm and translational regulation of circadian clock genes has been recognized. In the present study, we investigated the 5'-untranslated region (5'-UTR) of the mouse core clock gene, Per1, at the posttranscriptional level, particularly its translational regulation. The 5'-UTR of Per1 was found to promote its translation via an internal ribosomal entry site (IRES). We found that polypyrimidine tract-binding protein 1 (PTBP1) binds to the 5'-UTR of Per1 and positively regulates the IRES-mediated translation of Per1 without affecting the levels of Per1 mRNA. The reduction of PTBP1 level also decreased the endogenous levels of the PER1 protein but not of its mRNA. As for the oscillation of PER1 expression, the disruption of PTBP1 levels lowered the PER1 expression but not the phase of the oscillation. PTBP1 also changed the amplitudes of the mRNAs of other circadian clock genes, such as Cryptochrome 1 (Cry1) and Per3. Our results suggest that the PTBP1 is important for rhythmic translation of Per1 and it fine-tunes the overall circadian system.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | | | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
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16
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Handa K, Jindal R. Genotoxicity induced by hexavalent chromium leading to eryptosis in Ctenopharyngodon idellus. CHEMOSPHERE 2020; 247:125967. [PMID: 32069732 DOI: 10.1016/j.chemosphere.2020.125967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/02/2020] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
The initiation of eryptosis as a result of genotoxic action of Cr(VI), seen through micronucleus and comet assay in the peripheral erythrocytes of Ctenopharyngodon idellus was evaluated through RT-qPCR. For this, fish was exposed to sublethal concentration of hexavalent chromium (5.30 and 10.63 mg/L), and the blood was sampled on different endpoints (15, 30 and 45 days). Accumulation of chromium in the erythrocytes was also studied, which depicted a significant increase in toxicant concentration and time dependent manner. Both concentrations of hexavalent chromium induced DNA damage, visible in the form of comet tails. The presence of micronuclei in the erythrocytes was accompanied with occurrence of nuclear bud (NBu), lobed nucleus (Lb), notched nucleus (Nt), vacuolated nucleus (Vn), binucleated cell (Bn) as nuclear abnormalities; and acanthocytes (Ac), echinocytes (Ec), notched cells (Nc), microcytes (Mc) and vacuolated cytoplasm (Vc) as cytoplasmic abnormalities. The expression of genes related to intrinsic apoptotic pathway induced by Cr(VI) presented significant (p < 0.05) upregulation in the expression of p53, Bax, Apaf-1, caspase9 and caspase3, and downregulation of Bcl2; inferring the initiation of apoptotic pathway. The ration of Bax and Bcl2 also appended the apoptotic state of the erythrocytes. From the present investigation, it can be concluded that genotoxicity induced by hexavalent chromium lead to eryptosis in C. idellus.
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Affiliation(s)
- Kriti Handa
- Aquatic Biology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India.
| | - Rajinder Jindal
- Aquatic Biology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India.
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17
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Kakumani PK, Harvey LM, Houle F, Guitart T, Gebauer F, Simard MJ. CSDE1 controls gene expression through the miRNA-mediated decay machinery. Life Sci Alliance 2020; 3:3/4/e201900632. [PMID: 32161113 PMCID: PMC7067469 DOI: 10.26508/lsa.201900632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022] Open
Abstract
In animals, miRNAs are the most prevalent small non-coding RNA molecules controlling posttranscriptional gene regulation. The Argonaute proteins (AGO) mediate miRNA-guided gene silencing by recruiting multiple factors involved in translational repression, deadenylation, and decapping. Here, we report that CSDE1, an RNA-binding protein linked to stem cell maintenance and metastasis in cancer, interacts with AGO2 within miRNA-induced silencing complex and mediates gene silencing through its N-terminal domains. We show that CSDE1 interacts with LSM14A, a constituent of P-body assembly and further associates to the DCP1-DCP2 decapping complex, suggesting that CSDE1 could promote the decay of miRNA-induced silencing complex-targeted mRNAs. Together, our findings uncover a hitherto unknown mechanism used by CSDE1 in the control of gene expression mediated by the miRNA pathway.
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Affiliation(s)
- Pavan Kumar Kakumani
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada .,Laval University Cancer Research Centre, Québec City, Canada
| | - Louis-Mathieu Harvey
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada.,Laval University Cancer Research Centre, Québec City, Canada
| | - François Houle
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada.,Laval University Cancer Research Centre, Québec City, Canada
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada .,Laval University Cancer Research Centre, Québec City, Canada
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18
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Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal 2020; 18:14. [PMID: 31987048 PMCID: PMC6986143 DOI: 10.1186/s12964-019-0496-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases. Video Abstract
Graphical abstract ![]()
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, People's Republic of China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, People's Republic of China.
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19
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PTBP1-mediated regulation of AXL mRNA stability plays a role in lung tumorigenesis. Sci Rep 2019; 9:16922. [PMID: 31729427 PMCID: PMC6858377 DOI: 10.1038/s41598-019-53097-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/23/2019] [Indexed: 11/09/2022] Open
Abstract
AXL is expressed in many types of cancer and promotes cancer cell survival, metastasis and drug resistance. Here, we focus on identifying modulators that regulate AXL at the mRNA level. We have previously observed that the AXL promoter activity is inversely correlated with the AXL expression levels, suggesting that post-transcriptional mechanisms exist that down-regulate the expression of AXL mRNA. Here we show that the RNA binding protein PTBP1 (polypyrimidine tract-binding protein) directly targets the 5′-UTR of AXL mRNA in vitro and in vivo. Moreover, we also demonstrate that PTBP1, but not PTBP2, inhibits the expression of AXL mRNA and the RNA recognition motif 1 (RRM1) of PTBP1 is crucial for this interaction. To clarify how PTBP1 regulates AXL expression at the mRNA level, we found that, while the transcription rate of AXL was not significantly different, PTBP1 decreased the stability of AXL mRNA. In addition, over-expression of AXL may counteract the PTBP1-mediated apoptosis. Knock-down of PTBP1 expression could enhance tumor growth in animal models. Finally, PTBP1 was found to be negatively correlated with AXL expression in lung tumor tissues in Oncomine datasets and in tissue micro-array (TMA) analysis. In conclusion, we have identified a molecular mechanism of AXL expression regulation by PTBP1 through controlling the AXL mRNA stability. These findings may represent new thoughts alternative to current approaches that directly inhibit AXL signaling and may eventually help to develop novel therapeutics to avoid cancer metastasis and drug resistance.
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20
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Keiper BD. Cap-Independent mRNA Translation in Germ Cells. Int J Mol Sci 2019; 20:ijms20010173. [PMID: 30621249 PMCID: PMC6337596 DOI: 10.3390/ijms20010173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular mRNAs in plants and animals have a 5'-cap structure that is accepted as the recognition point to initiate translation by ribosomes. Consequently, it was long assumed that the translation initiation apparatus was built solely for a cap-dependent (CD) mechanism. Exceptions that emerged invoke structural damage (proteolytic cleavage) to eukaryotic initiation factor 4 (eIF4) factors that disable cap recognition. The residual eIF4 complex is thought to be crippled, but capable of cap-independent (CI) translation to recruit viral or death-associated mRNAs begrudgingly when cells are in great distress. However, situations where CI translation coexists with CD translation are now known. In such cases, CI translation is still a minor mechanism in the major background of CD synthesis. In this review, I propose that germ cells do not fit this mold. Using observations from various animal models of oogenesis and spermatogenesis, I suggest that CI translation is a robust partner to CD translation to carry out the translational control that is so prevalent in germ cell development. Evidence suggests that CI translation provides surveillance of germ cell homeostasis, while CD translation governs the regulated protein synthesis that ushers these meiotic cells through the remarkable steps in sperm/oocyte differentiation.
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Affiliation(s)
- Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA.
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21
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Lindquist JA, Mertens PR. Cold shock proteins: from cellular mechanisms to pathophysiology and disease. Cell Commun Signal 2018; 16:63. [PMID: 30257675 PMCID: PMC6158828 DOI: 10.1186/s12964-018-0274-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
Cold shock proteins are multifunctional RNA/DNA binding proteins, characterized by the presence of one or more cold shock domains. In humans, the best characterized members of this family are denoted Y-box binding proteins, such as Y-box binding protein-1 (YB-1). Biological activities range from the regulation of transcription, splicing and translation, to the orchestration of exosomal RNA content. Indeed, the secretion of YB-1 from cells via exosomes has opened the door to further potent activities. Evidence links a skewed cold shock protein expression pattern with cancer and inflammatory diseases. In this review the evidence for a causative involvement of cold shock proteins in disease development and progression is summarized. Furthermore, the potential application of cold shock proteins for diagnostics and as targets for therapy is elucidated.
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Affiliation(s)
- Jonathan A Lindquist
- Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
| | - Peter R Mertens
- Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany.
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22
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Moore KS, von Lindern M. RNA Binding Proteins and Regulation of mRNA Translation in Erythropoiesis. Front Physiol 2018; 9:910. [PMID: 30087616 PMCID: PMC6066521 DOI: 10.3389/fphys.2018.00910] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Control of gene expression in erythropoiesis has to respond to signals that may emerge from intracellular processes or environmental factors. Control of mRNA translation allows for relatively rapid modulation of protein synthesis from the existing transcriptome. For instance, the protein synthesis rate needs to be reduced when reactive oxygen species or unfolded proteins accumulate in the cells, but also when iron supply is low or when growth factors are lacking in the environment. In addition, regulation of mRNA translation can be important as an additional layer of control on top of gene transcription, in which RNA binding proteins (RBPs) can modify translation of a set of transcripts to the cell’s actual protein requirement. The 5′ and 3′ untranslated regions of mRNA (5′UTR, 3′UTR) contain binding sites for general and sequence specific translation factors. They also contain secondary structures that may hamper scanning of the 5′UTR by translation complexes or may help to recruit translation factors. In addition, the term 5′UTR is not fully correct because many transcripts contain small open reading frames in their 5′UTR that are translated and contribute to regulation of mRNA translation. It is becoming increasingly clear that the transcriptome only partly predicts the proteome. The aim of this review is (i) to summarize how the availability of general translation initiation factors can selectively regulate transcripts because the 5′UTR contains secondary structures or short translated sequences, (ii) to discuss mechanisms that control the length of the mRNA poly(A) tail in relation to mRNA translation, and (iii) to give examples of sequence specific RBPs and their targets. We focused on transcripts and RBPs required for erythropoiesis. Whereas differentiation of erythroblasts to erythrocytes is orchestrated by erythroid transcription factors, the production of erythrocytes needs to respond to the availability of growth factors and nutrients, particularly the availability of iron.
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Affiliation(s)
- Kat S Moore
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
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23
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A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nat Commun 2017; 8:1456. [PMID: 29129916 PMCID: PMC5682285 DOI: 10.1038/s41467-017-01744-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/11/2017] [Indexed: 12/29/2022] Open
Abstract
While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 (cold shock domain containing E1) is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs, as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis. Unlike transcriptional regulation of hESC identity, little is known post-transcriptionally. Here, the authors show that the RNA binding protein CSDE1 regulates core components of hESC identity, neurectoderm commitment and neurogenesis to maintain pluripotency and prevent neural differentiation.
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Kędzierska H, Piekiełko-Witkowska A. Splicing factors of SR and hnRNP families as regulators of apoptosis in cancer. Cancer Lett 2017; 396:53-65. [PMID: 28315432 DOI: 10.1016/j.canlet.2017.03.013] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022]
Abstract
SR and hnRNP proteins were initially discovered as regulators of alternative splicing: the process of controlled removal of introns and selective joining of exons through which multiple transcripts and, subsequently, proteins can be expressed from a single gene. Alternative splicing affects genes involved in all crucial cellular processes, including apoptosis. During cancerogenesis impaired apoptotic control facilitates survival of cells bearing molecular aberrations, contributing to their unrestricted proliferation and chemoresistance. Apparently, SR and hnRNP proteins regulate all levels of expression of apoptotic genes, including transcription initiation and elongation, alternative splicing, mRNA stability, translation, and protein degradation. The frequently disturbed expressions of SR/hnRNP proteins in cancers lead to impaired functioning of target apoptotic genes, including regulators of the extrinsic (Fas, caspase-8, caspase-2, c-FLIP) and the intrinsic pathway (Apaf-1, caspase-9, ICAD), genes encoding Bcl-2 proteins, IAPs, and p53 tumor suppressor. Prototypical members of SR/hnRNP families, SRSF1 and hnRNP A1, promote synthesis of anti-apoptotic splice variants of Bcl-x and Mcl-1, which results in attenuation of programmed cell death in breast cancer and chronic myeloid leukemia. SR/hnRNP proteins significantly affect responses to chemotherapy, acting as mediators or modulators of drug-induced apoptosis. Aberrant expression of SRSF1 and hnRNP K can interfere with tumor responses to chemotherapy in pancreatic and liver cancers. Currently, a number of splicing factor inhibitors is being tested in pre-clinical and clinical trials. In this review we discuss recent findings on the role of SR and hnRNP proteins in apoptotic control in cancer cells as well as their significance in anticancer treatments.
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Affiliation(s)
- Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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Shakeri R, Kheirollahi A, Davoodi J. Apaf-1: Regulation and function in cell death. Biochimie 2017; 135:111-125. [PMID: 28192157 DOI: 10.1016/j.biochi.2017.02.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 01/08/2023]
Abstract
Apoptosis, a form of programmed cell death, is responsible for eliminating damaged or unnecessary cells in multicellular organisms. Various types of intracellular stress trigger apoptosis by induction of cytochrome c release from mitochondria into the cytosol. Apoptotic protease activating factor-1 (Apaf-1) is a key molecule in the intrinsic or mitochondrial pathway of apoptosis, which oligomerizes in response to cytochrome c release and forms a large complex known as apoptosome. Procaspase-9, an initiator caspase in the mitochondrial pathway, is recruited and activated by the apoptosome leading to downstream caspase-3 processing. Various cellular proteins and small molecules can modulate apoptosome formation and function directly or indirectly. Despite recent progress in understanding the mitochondrial pathway of apoptosis, numerous questions such as the molecular mechanism of Apaf-1 oligomerization and caspase-9 activation remain poorly understood. In addition, reports have emerged showing non-apoptotic functions for Apaf-1. The current review summarizes the latest findings regarding structure-function relationship of Apaf-1 as well as its modifiers.
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Affiliation(s)
- Raheleh Shakeri
- Department of Biological Science and Biotechnology, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Asma Kheirollahi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Science, Tehran, Iran
| | - Jamshid Davoodi
- Institute of Biochemistry and Biophysics, Department of Biochemistry, University of Tehran, Tehran, Iran.
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Taniguchi K, Sakai M, Sugito N, Kumazaki M, Shinohara H, Yamada N, Nakayama T, Ueda H, Nakagawa Y, Ito Y, Futamura M, Uno B, Otsuki Y, Yoshida K, Uchiyama K, Akao Y. PTBP1-associated microRNA-1 and -133b suppress the Warburg effect in colorectal tumors. Oncotarget 2017; 7:18940-52. [PMID: 26980745 PMCID: PMC4951342 DOI: 10.18632/oncotarget.8005] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/05/2016] [Indexed: 01/24/2023] Open
Abstract
It is known that pyruvate kinase in muscle (PKM), which is a rate-limiting glycolytic enzyme, has essential roles in the Warburg effect and that expression of cancer-dominant PKM2 is increased by polypyrimidine tract-binding protein 1 (PTBP1), which is a splicer of the PKM gene. In other words, PKM2 acts as a promoter of the Warburg effect. Previously, we demonstrated that the Warburg effect was partially established by down-regulation of several microRNAs (miRs) that bind to PTBP1 and that ectopic expression of these miRs suppressed the Warburg effect. In this study, we investigated the functions of miR-1 and -133b, which are well known as muscle-specific miRs, from the viewpoint of the Warburg effect in colorectal tumors. The expression levels of miR-1 and -133b were relatively high in colon tissue except muscle and very frequently down-regulated in 75 clinical colorectal tumors samples, even in adenomas, compared with those of the adjacent normal tissue samples. The ectopic expression of these miRs induced growth suppression and autophagic cell death through the switching of PKM isoform expression from PKM2 to PKM1 by silencing PTBP1 expression both in vitro and in vivo. Also, we showed that the resultant increase in the intracellular level of reactive oxygen species (ROS) was involved in this mechanism. Furthermore, PTBP1 was highly expressed in most of the 30 clinical colorectal tumor samples examined, even in adenomas. Our results suggested that PTBP1 and PTBP1-associated miR-1 and -133b are crucial molecules for the maintenance of the Warburg effect in colorectal tumors.
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Affiliation(s)
- Kohei Taniguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.,Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Miku Sakai
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Nobuhiko Sugito
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Minami Kumazaki
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Haruka Shinohara
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Nami Yamada
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Tatsushi Nakayama
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hiroshi Ueda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University, School of Medicine, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yuko Ito
- Department of Anatomy and Cell Biology, Division of Life Sciences, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Manabu Futamura
- Department of Oncological Surgery, Gifu University School of Medicine, Gifu 501-1193, Japan
| | - Bunji Uno
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yoshinori Otsuki
- Department of Anatomy and Cell Biology, Division of Life Sciences, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Kazuhiro Yoshida
- Department of Oncological Surgery, Gifu University School of Medicine, Gifu 501-1193, Japan
| | - Kazuhisa Uchiyama
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
| | - Yukihiro Akao
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
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Cellular Stress and p53-Associated Apoptosis by Juniperus communis L. Berry Extract Treatment in the Human SH-SY5Y Neuroblastoma Cells. Int J Mol Sci 2016; 17:ijms17071113. [PMID: 27420050 PMCID: PMC4964488 DOI: 10.3390/ijms17071113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/19/2022] Open
Abstract
Plant phenolics have shown to activate apoptotic cell death in different tumourigenic cell lines. In this study, we evaluated the effects of juniper berry extract (Juniperus communis L.) on p53 protein, gene expression and DNA fragmentation in human neuroblastoma SH-SY5Y cells. In addition, we analyzed the phenolic composition of the extract. We found that juniper berry extract activated cellular relocalization of p53 and DNA fragmentation-dependent cell death. Differentially expressed genes between treated and non-treated cells were evaluated with the cDNA-RDA (representational difference analysis) method at the early time point of apoptotic process when p53 started to be activated and no caspase activity was detected. Twenty one overexpressed genes related to cellular stress, protein synthesis, cell survival and death were detected. Interestingly, they included endoplasmic reticulum (ER) stress inducer and sensor HSPA5 and other ER stress-related genes CALM2 and YKT6 indicating that ER stress response was involved in juniper berry extract mediated cell death. In composition analysis, we identified and quantified low concentrations of fifteen phenolic compounds. The main groups of them were flavones, flavonols, phenolic acids, flavanol and biflavonoid including glycosides of quercetin, apigenin, isoscutellarein and hypolaetin. It is suggested that juniper berry extract induced the p53-associated apoptosis through the potentiation and synergism by several phenolic compounds.
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Walters B, Thompson SR. Cap-Independent Translational Control of Carcinogenesis. Front Oncol 2016; 6:128. [PMID: 27252909 PMCID: PMC4879784 DOI: 10.3389/fonc.2016.00128] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 01/04/2023] Open
Abstract
Translational regulation has been shown to play an important role in cancer and tumor progression. Despite this fact, the role of translational control in cancer is an understudied and under appreciated field, most likely due to the technological hurdles and paucity of methods available to establish that changes in protein levels are due to translational regulation. Tumors are subjected to many adverse stress conditions such as hypoxia or starvation. Under stress conditions, translation is globally downregulated through several different pathways in order to conserve energy and nutrients. Many of the proteins that are synthesized during stress in order to cope with the stress use a non-canonical or cap-independent mechanism of initiation. Tumor cells have utilized these alternative mechanisms of translation initiation to promote survival during tumor progression. This review will specifically discuss the role of cap-independent translation initiation, which relies on an internal ribosome entry site (IRES) to recruit the ribosomal subunits internally to the messenger RNA. We will provide an overview of the role of IRES-mediated translation in cancer by discussing the types of genes that use IRESs and the conditions under which these mechanisms of initiation are used. We will specifically focus on three well-studied examples: Apaf-1, p53, and c-Jun, where IRES-mediated translation has been demonstrated to play an important role in tumorigenesis or tumor progression.
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Affiliation(s)
- Beth Walters
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
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Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction. Sci Rep 2016; 6:22461. [PMID: 26936655 PMCID: PMC4776140 DOI: 10.1038/srep22461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/11/2016] [Indexed: 11/09/2022] Open
Abstract
The RNA binding protein Unr, which contains five cold shock domains, has several specific roles in post-transcriptional control of gene expression. It can act as an activator or inhibitor of translation initiation, promote mRNA turnover, or stabilise mRNA. Its role depends on the mRNA and other proteins to which it binds, which includes cytoplasmic poly(A) binding protein 1 (PABP1). Since PABP1 binds to all polyadenylated mRNAs, and is involved in translation initiation by interaction with eukaryotic translation initiation factor 4G (eIF4G), we investigated whether Unr has a general role in translational control. We found that Unr strongly stimulates translation in vitro, and mutation of cold shock domains 2 or 4 inhibited its translation activity. The ability of Unr and its mutants to stimulate translation correlated with its ability to bind RNA, and to interact with PABP1. We found that Unr stimulated the binding of PABP1 to mRNA, and that Unr was required for the stable interaction of PABP1 and eIF4G in cells. siRNA-mediated knockdown of Unr reduced the overall level of cellular translation in cells, as well as that of cap-dependent and IRES-dependent reporters. These data describe a novel role for Unr in regulating cellular gene expression.
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Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res 2016; 44:e32. [PMID: 26467480 PMCID: PMC4770198 DOI: 10.1093/nar/gkv1025] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/11/2015] [Accepted: 09/28/2015] [Indexed: 12/21/2022] Open
Abstract
RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time. Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp.
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Affiliation(s)
- Sai Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Jingtian Zhou
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hailin Hu
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Ligong Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chao Cheng
- Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
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Identification of Proteins Bound to Dengue Viral RNA In Vivo Reveals New Host Proteins Important for Virus Replication. mBio 2016; 7:e01865-15. [PMID: 26733069 PMCID: PMC4725007 DOI: 10.1128/mbio.01865-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Due to the limited coding capacity of the viral genome and the complexity of the viral life cycle, host cell proteins play essential roles throughout the course of viral infection. Host RNA-binding proteins mediate various aspects of virus replication through their physical interactions with viral RNA. Here we describe a technique designed to identify such interactions in the context of infected cells using UV cross-linking followed by antisense-mediated affinity purification and mass spectrometry. Using this approach, we identified interactions, several of them novel, between host proteins and dengue viral RNA in infected Huh7 cells. Most of these interactions were subsequently validated using RNA immunoprecipitation. Using small interfering RNA (siRNA)-mediated gene silencing, we showed that more than half of these host proteins are likely involved in regulating virus replication, demonstrating the utility of this method in identifying biologically relevant interactions that may not be identified using traditional in vitro approaches. Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Viral RNA molecules physically interact with cellular RNA-binding proteins (RBPs) throughout the course of infection; the identification of such interactions will lead to the elucidation of the molecular mechanisms of virus replication. Until now, the identification of host proteins bound to dengue viral RNA has been accomplished using in vitro strategies. Here, we used a method for the specific purification of dengue viral ribonucleoprotein (RNP) complexes from infected cells and subsequently identified the associated proteins by mass spectrometry. We then validated a functional role for the majority of these proteins in mediating efficient virus replication. This approach has broad relevance to virology and RNA biology, as it could theoretically be used to purify any viral RNP complex of interest.
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Abstract
Unr (upstream of N-ras) is a post-transcriptional regulator of gene expression, essential for mammalian development and mutated in many human cancers. The expression of unr is itself regulated at many levels; transcription of unr, which also affects expression of the downstream N-ras gene, is tissue and developmental stage-dependent and is repressed by c-Myc and Max (Myc associated factor X). Alternative splicing gives rise to six transcript variants, which include three different 5′-UTRs. The transcripts are further diversified by the use of three alternative polyadenylation signals, which governs whether AU-rich instability elements are present in the 3′-UTR or not. Translation of at least some unr transcripts can occur by internal initiation and is regulated in a cell-cycle-dependent manner; binding of PTB (polypyrimidine tract-binding protein) and Unr to the 5′-UTR inhibits translation, but these are displaced by heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNPC1/C2) during mitosis to stimulate translation. Finally, Unr is post-translationally modified by phosphorylation and lysine acetylation, although it is not yet known how these modifications affect Unr activity.
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Abstract
Unr (upstream of N-ras) is a eukaryotic RNA-binding protein that has a number of roles in the post-transcriptional regulation of gene expression. Originally identified as an activator of internal initiation of picornavirus translation, it has since been shown to act as an activator and inhibitor of cellular translation and as a positive and negative regulator of mRNA stability, regulating cellular processes such as mitosis and apoptosis. The different post-transcriptional functions of Unr depend on the identity of its mRNA and protein partners and can vary with cell type and changing cellular conditions. Recent high-throughput analyses of RNA–protein interactions indicate that Unr binds to a large subset of cellular mRNAs, suggesting that Unr may play a wider role in translational responses to cellular signals than previously thought.
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Souii A, Ben M'hadheb-Gharbi M, Gharbi J. Role of RNA structure motifs in IRES-dependent translation initiation of the coxsackievirus B3: new insights for developing live-attenuated strains for vaccines and gene therapy. Mol Biotechnol 2014; 55:179-202. [PMID: 23881360 DOI: 10.1007/s12033-013-9674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5' untranslated region (5'UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA-protein and RNA-RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5' and 3'UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.
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Affiliation(s)
- Amira Souii
- Institut Supérieur de Biotechnologie de Monastir-Université de Monastir, Avenue Tahar Hadded, BP 74, 5000, Monastir, Tunisia
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Juan WC, Roca X, Ong ST. Identification of cis-acting elements and splicing factors involved in the regulation of BIM Pre-mRNA splicing. PLoS One 2014; 9:e95210. [PMID: 24743263 PMCID: PMC3990581 DOI: 10.1371/journal.pone.0095210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/25/2014] [Indexed: 11/25/2022] Open
Abstract
Aberrant changes in the expression of the pro-apoptotic protein, BCL-2-like 11 (BIM), can result in either impaired or excessive apoptosis, which can contribute to tumorigenesis and degenerative disorders, respectively. Altering BIM pre-mRNA splicing is an attractive approach to modulate apoptosis because BIM activity is partly determined by the alternative splicing of exons 3 or 4, whereby exon 3-containing transcripts are not apoptotic. Here we identified several cis-acting elements and splicing factors involved in BIM alternative splicing, as a step to better understand the regulation of BIM expression. We analyzed a recently discovered 2,903-bp deletion polymorphism within BIM intron 2 that biased splicing towards exon 3, and which also impaired BIM-dependent apoptosis. We found that this region harbors multiple redundant cis-acting elements that repress exon 3 inclusion. Furthermore, we have isolated a 23-nt intronic splicing silencer at the 3′ end of the deletion that is important for excluding exon 3. We also show that PTBP1 and hnRNP C repress exon 3 inclusion, and that downregulation of PTBP1 inhibited BIM-mediated apoptosis. Collectively, these findings start building our understanding of the cis-acting elements and splicing factors that regulate BIM alternative splicing, and also suggest potential approaches to alter BIM splicing for therapeutic purposes.
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Affiliation(s)
- Wen Chun Juan
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (XR); (STO)
| | - S. Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Chapel Hill, North Carolina, United States of America
- * E-mail: (XR); (STO)
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Giudice J, Cooper TA. RNA-binding proteins in heart development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:389-429. [PMID: 25201112 DOI: 10.1007/978-1-4939-1221-6_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA-binding proteins (RBPs) are key players of posttranscriptional regulation occurring during normal tissue development. All tissues examined thus far have revealed the importance of RBPs in the regulation of complex networks involved in organ morphogenesis, maturation, and function. They are responsible for controlling tissue-specific gene expression by regulating alternative splicing, mRNA stability, translation, and poly-adenylation. The heart is the first organ form during embryonic development and is also the first to acquire functionality. Numerous remodeling processes take place during late cardiac development since fetal heart first adapts to birth and then undergoes a transition to adult functionality. This physiological remodeling involves transcriptional and posttranscriptional networks that are regulated by RBPs. Disruption of the normal regulatory networks has been shown to cause cardiomyopathy in humans and animal models. Here we review the complexity of late heart development and the current information regarding how RBPs control aspects of postnatal heart development. We also review how activities of RBPs are modulated adding complexity to the regulation of developmental networks.
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Affiliation(s)
- Jimena Giudice
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA,
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Ye J, Llorian M, Cardona M, Rongvaux A, Moubarak RS, Comella JX, Bassel-Duby R, Flavell RA, Olson EN, Smith CWJ, Sanchis D. A pathway involving HDAC5, cFLIP and caspases regulates expression of the splicing regulator polypyrimidine tract binding protein in the heart. J Cell Sci 2013; 126:1682-91. [PMID: 23424201 PMCID: PMC3647441 DOI: 10.1242/jcs.121384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2013] [Indexed: 01/07/2023] Open
Abstract
Polypyrimidine tract binding protein (PTB) regulates pre-mRNA splicing, having special relevance for determining gene expression in the differentiating muscle. We have previously shown that PTB protein abundance is progressively reduced during heart development without reduction of its own transcript. Simultaneous reduction of histone deacetylase (HDAC) expression prompted us to investigate the potential link between these events. HDAC5-deficient mice have reduced cardiac PTB protein abundance, and HDAC inhibition in myocytes causes a reduction in endogenous expression of cellular FLICE-like inhibitory protein (cFLIP) and caspase-dependent cleavage of PTB. In agreement with this, cardiac PTB expression is abnormally high in mice with cardiac-specific executioner caspase deficiency, and cFLIP overexpression prevents PTB cleavage in vitro. Caspase-dependent cleavage triggers further fragmentation of PTB, and these fragments accumulate in the presence of proteasome inhibitors. Experimental modification of the above processes in vivo and in vitro results in coherent changes in the alternative splicing of genes encoding tropomyosin-1 (TPM1), tropomyosin-2 (TPM2) and myocyte enhancer factor-2 (MEF2). Thus, we report a pathway connecting HDAC, cFLIP and caspases regulating the progressive disappearance of PTB, which enables the expression of the adult variants of proteins involved in the regulation of contraction and transcription during cardiac muscle development.
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Affiliation(s)
- Junmei Ye
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK
| | - Maria Cardona
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
| | - Anthony Rongvaux
- Department of Immunobiology, and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana S. Moubarak
- Ciberned, Institut de Recerca Hospital, Universitari Vall d'Hebró-UAB, Barcelona, 08035, Spain
| | - Joan X. Comella
- Ciberned, Institut de Recerca Hospital, Universitari Vall d'Hebró-UAB, Barcelona, 08035, Spain
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Richard A. Flavell
- Department of Immunobiology, and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Christopher W. J. Smith
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK
| | - Daniel Sanchis
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
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Ye J, Cardona M, Llovera M, Comella JX, Sanchis D. Translation of Myocyte Enhancer Factor-2 is induced by hypertrophic stimuli in cardiomyocytes through a Calcineurin-dependent pathway. J Mol Cell Cardiol 2012; 53:578-87. [DOI: 10.1016/j.yjmcc.2012.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 10/28/2022]
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Veo BL, Krushel LA. Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5' leader. RNA Biol 2012; 9:1344-60. [PMID: 22995835 DOI: 10.4161/rna.22181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mechanisms by which eukaryotic internal ribosomal entry sites (IRESs) initiate translation have not been well described. Viral IRESs utilize a combination of secondary/tertiary structure concomitant with sequence specific elements to initiate translation. Eukaryotic IRESs are proposed to utilize the same components, although it appears that short sequence specific elements are more common. In this report we perform an extensive analysis of the IRES in the human tau mRNA. We demonstrate that the tau IRES exhibits characteristics similar to viral IRESs. It contains two main structural domains that exhibit secondary interactions, which are essential for internal initiation. Moreover, the tau IRES is extremely sensitive to small nucleotide substitutions. Our data also indicates that the 40S ribosome is recruited to the middle of the IRES, but whether it scans to the initiation codon in a linear fashion is questioned. Overall, these results identify structural and sequence elements critical for tau IRES activity and consequently, provide a novel target to regulate tau protein expression in disease states including Alzheimer disease and other tauopathies.
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Affiliation(s)
- Bethany L Veo
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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Licursi M, Komatsu Y, Pongnopparat T, Hirasawa K. Promotion of viral internal ribosomal entry site-mediated translation under amino acid starvation. J Gen Virol 2012; 93:951-962. [DOI: 10.1099/vir.0.040386-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cap-dependent and internal ribosomal entry site (IRES)-mediated translation are regulated differently within cells. Viral IRES-mediated translation often remains active when cellular cap-dependent translation is severely impaired under cellular stresses induced by virus infection. To investigate how cellular stresses influence the efficiency of viral IRES-mediated translation, we used a bicistronic luciferase reporter construct harbouring IRES elements from the following viruses: encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV), hepatitis C virus (HCV) or human rhinovirus (HRV). NIH3T3 cells transfected with these bicistronic reporter constructs were subjected to different cellular stresses. Increased translation initiation was only observed under amino acid starvation when EMCV or FMDV IRES elements were present. To identify cellular mechanisms that promoted viral IRES-mediated translation, we tested the involvement of eukaryotic initiation factor 4E-binding protein (4E-BP), general control non-depressed 2 (GCN2) and eukaryotic initiation factor 2B (eIF2B), as these are known to be modulated under amino acid starvation. Knockdown of 4E-BP1 impaired the promotion of EMCV and FMDV IRES-mediated translation under amino acid starvation, whereas GCN2 and eIF2B were not involved. To further investigate how 4E-BP1 regulates translation initiated by EMCV and FMDV IRES elements, we used a phosphoinositide kinase-3 inhibitor (LY294002), an mTOR inhibitor (Torin1) or leucine starvation to mimic 4E-BP1 dephosphorylation induced by amino acid starvation. 4E-BP1 dephosphorylation induced by the treatments was not sufficient to promote viral IRES-mediated translation. These results suggest that 4E-BP1 regulates EMCV and FMDV IRES-mediated translation under amino acid starvation, but not via its dephosphorylation.
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Affiliation(s)
- Maria Licursi
- Division of Biomedical Science, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St John’s, NL A1B 3V6, Canada
| | - Yumiko Komatsu
- Division of Biomedical Science, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St John’s, NL A1B 3V6, Canada
| | - Theerawat Pongnopparat
- Division of Biomedical Science, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St John’s, NL A1B 3V6, Canada
| | - Kensuke Hirasawa
- Division of Biomedical Science, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St John’s, NL A1B 3V6, Canada
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Plank TDM, Kieft JS. The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2012; 3:195-212. [PMID: 22215521 PMCID: PMC3973487 DOI: 10.1002/wrna.1105] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Internal ribosome entry sites (IRESs) are RNA sequences that can recruit the translation machinery independent of the 5' end of the messenger RNA. IRESs are found in both viral and cellular RNAs and are important for regulating gene expression. There is great diversity in the mechanisms used by IRESs to recruit the ribosome and this is reflected in a variety of RNA sequences that function as IRESs. The ability of an RNA sequence to function as an IRES is conferred by structures operating at multiple levels from primary sequence through higher-order three-dimensional structures within dynamic ribonucleoproteins (RNPs). When these diverse structures are compared, some trends are apparent, but overall it is not possible to find universal rules to describe IRES structure and mechanism. Clearly, many different sequences and structures have evolved to perform the function of recruiting, positioning, and activating a ribosome without using the canonical cap-dependent mechanism. However, as our understanding of the specific sequences, structures, and mechanisms behind IRES function improves, more common features may emerge to link these diverse RNAs.
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Affiliation(s)
- Terra-Dawn M. Plank
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Jeffrey S. Kieft
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
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42
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Elatmani H, Dormoy-Raclet V, Dubus P, Dautry F, Chazaud C, Jacquemin-Sablon H. The RNA-binding protein Unr prevents mouse embryonic stem cells differentiation toward the primitive endoderm lineage. Stem Cells 2012; 29:1504-16. [PMID: 21954113 DOI: 10.1002/stem.712] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The maintenance of embryonic stem cells (ESCs) pluripotency depends on key transcription factors, chromatin remodeling proteins, and microRNAs. The roles of RNA-binding proteins are however poorly understood. We report that the cytoplasmic RNA-binding protein Unr prevents the differentiation of ESCs into primitive endoderm (PrE). We show that unr knockout (unr(-/-) ) ESCs spontaneously differentiate into PrE, and that Unr re-expression in unr(-/-) ESCs reverses this phenotype. Nevertheless, unr(-/-) ESCs retain pluripotency, producing differentiated teratomas, and the differentiated unr(-/-) ESCs coexpress the PrE inducer Gata6 and the pluripotency factors Oct4, Nanog, and Sox2. Interestingly, in the differentiated unr(-/-) ESCs, Nanog and Sox2 exhibit a dual nuclear and cytoplasmic localization. This situation, that has never been reported, likely reflects an early differentiation state toward PrE. Finally, we show that Unr destabilizes Gata6 mRNAs and we propose that the post-transcriptional repression of Gata6 expression by Unr contributes to the stabilization of the ESCs pluripotent state.
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Affiliation(s)
- Habiba Elatmani
- Physiopathologie du Cancer du Foie, Université de Bordeaux, Physiopathologie du cancer du foie, U1053, Bordeaux, France
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Abstract
The majority of mRNAs in eukaryotic cells are translated via a method that is dependent upon the recognition of, and binding to, the methylguanosine cap at the 5' end of the mRNA, by a set of protein factors termed eIFs (eukaryotic initiation factors). However, many of the eIFs involved in this process are modified and become less active under a number of pathophysiological stress conditions, including amino acid starvation, heat shock, hypoxia and apoptosis. During these conditions, the continued synthesis of proteins essential to recovery from stress or maintenance of a cellular programme is mediated via an alternative form of translation initiation termed IRES (internal ribosome entry site)-mediated translation. This relies on the mRNA containing a complex cis-acting structural element in its 5'-UTR (untranslated region) that is able to recruit the ribosome independently of the cap, and is often dependent upon additional factors termed ITAFs (IRES trans-acting factors). A limited number of ITAFs have been identified to date, particularly for cellular IRESs, and it is not yet fully understood how they exert their control and which cellular pathways are involved in their regulation.
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44
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Mittal S, Mir RA, Chauhan SS. Post-transcriptional regulation of human cathepsin L expression. Biol Chem 2011; 392:405-13. [PMID: 21395501 DOI: 10.1515/bc.2011.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The expression of cathepsin L, a lysosomal protease, is known to be elevated in cancer and other pathologies. Multiple splice variants of human cathepsin L with variable 5'UTRs exist, which encode for the same protein. Previously we have observed that variant hCATL A (bearing the longest 5'UTR) was translated in vitro with significantly lower efficiency than variant hCATL AIII (bearing the shortest 5'UTR). Contrary to these findings, results of the present study reveal that in cancer cells, hCATL A mRNA exhibits higher translatability in spite of having lower stability than AIII. This is the first report demonstrating a highly contrasting trend in translation efficiencies of hCATL variants in rabbit reticulocytes and live cells. Expression from chimeric mRNAs containing 5'UTRs of A or AIII upstream to luciferase reporter cDNA established the A UTR to be the sole determinant for this effect. Transient transfections of bicistronic plasmids and mRNAs confirmed the presence of a functional Internal Ribosome Entry Site in this UTR. Our data suggest that differential stability and translation initiation modes mediated by the 5'UTRs of human cathepsin L variants are involved in regulating its expression.
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Affiliation(s)
- Shivani Mittal
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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Polypyrimidine tract-binding protein stimulates the poliovirus IRES by modulating eIF4G binding. EMBO J 2010; 29:3710-22. [PMID: 20859255 DOI: 10.1038/emboj.2010.231] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 08/19/2010] [Indexed: 11/08/2022] Open
Abstract
Tethered hydroxyl-radical probing has been used to determine the orientation of binding of polypyrimidine tract-binding protein (PTB) to the poliovirus type 1 (Mahoney) (PV-1(M)) internal ribosome entry site/segment (IRES)-the question of which RNA-binding domain (RBD) binds to which sites on the IRES. The results show that under conditions in which PTB strongly stimulates IRES activity, a single PTB is binding to the IRES, a finding which was confirmed by mass spectrometry of PTB/IRES complexes. RBDs1 and 2 interact with the basal part of the Domain V irregular stem loop, very close to the binding site of eIF4G, and RBDs3 and 4 interact with the single-stranded regions flanking Domain V. The binding of PTB is subtly altered in the presence of the central domain (p50) of eIF4G, and p50 binding is likewise modified if PTB is present. This suggests that PTB stimulates PV-1(M) IRES activity by inducing eIF4G to bind in the optimal position and orientation to promote internal ribosome entry, which, in PV-1(M), is at an AUG triplet 30 nt downstream of the base of Domain V.
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46
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He X, Arslan AD, Pool MD, Ho TT, Darcy KM, Coon JS, Beck WT. Knockdown of splicing factor SRp20 causes apoptosis in ovarian cancer cells and its expression is associated with malignancy of epithelial ovarian cancer. Oncogene 2010; 30:356-65. [PMID: 20856201 PMCID: PMC3010329 DOI: 10.1038/onc.2010.426] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our previous study revealed that two splicing factors, polypyrimidine tract-binding protein (PTB) and SRp20, were up-regulated in epithelial ovarian cancer (EOC) and knockdown of PTB expression inhibited ovarian tumor cell growth and transformation properties. In this report, we show that knockdown of SRp20 expression in ovarian cancer cells also causes substantial inhibition of tumor cell growth and colony formation in soft agar and the extent of such inhibition appeared to correlate with the extent of suppression of SRp20. Massive knockdown of SRp20 expression triggered remarkable apoptosis in these cells. These results suggest that overexpression of SRp20 is required for ovarian tumor cell growth and survival. Immunohistochemical staining for PTB and SRp20 of two specialized tissue microarrays (TMAs), one containing benign ovarian tumors, borderline/low malignant potential (LMP) ovarian tumors as well as invasive EOC and the other containing invasive EOC ranging from stage I to stage IV disease, reveals that PTB and SRp20 are both expressed differentially between benign tumors and invasive EOC, and between borderline/LMP tumors and invasive EOC. There were more all-negative or mixed staining cases (at least two evaluable section cores per case) in benign tumors than in invasive EOC while there were more all positive staining cases in invasive EOC than in the other two disease classifications. Among invasive EOC, the great majority of cases were stained all-positive for both PTB and SRp20 and there were no significant differences in average staining or frequency of positive cancer cells between any of the tumor stages. Therefore, the expression of PTB and SRp20 is associated with malignancy of ovarian tumors but not with stage of invasive EOC.
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Affiliation(s)
- X He
- Department of Biopharmaceutical Sciences, College of Pharmacy and Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.
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47
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Mihailovich M, Militti C, Gabaldón T, Gebauer F. Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays 2010; 32:109-18. [PMID: 20091748 DOI: 10.1002/bies.200900122] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cold shock domain (CSD)-containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post-transcriptional gene regulation. The CSD is an ancient beta-barrel fold that serves to bind nucleic acids. The CSD is structurally and functionally similar to the S1 domain, a fold with otherwise unrelated primary sequence. The flexibility of the CSD/S1 domain for RNA recognition confers an enormous functional versatility to the proteins that contain them. This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD.
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Affiliation(s)
- Marija Mihailovich
- Gene Regulation Programme, Centre de Regulació Genòmica (CRG-UPF), Barcelona, Spain
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48
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Mishra PJ, Menon LG, Mishra PJ, Mayer-Kuckuk P, Bertino JR, Banerjee D. Translational modulation of proteins expressed from bicistronic vectors. Mol Imaging 2009; 8:305-18. [PMID: 20003889 PMCID: PMC2864087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Bicistronic vectors are useful tools for exogenous expression of two gene products from a single promoter element; however, reduced expression of protein from the second cistron compared with the first cistron is a common limitation to this approach. To overcome this limitation, we explored use of dihydrofolate reductase (DHFR) complementary DNA encoded in bicistronic vectors to induce a second protein of interest by methotrexate (MTX) treatment. Previous studies have demonstrated that levels of DHFR protein and DHFR fusion protein can be induced translationally following MTX treatment of cells. We demonstrated that in response to MTX treatment, DHFR partner protein in a bicistronic construct is induced for longer periods of time when compared with endogenous DHFR and DHFR fusion protein, in vitro and in vivo. Using rapamycin pretreatment followed by MTX treatment, we also devised a strategy to modulate levels of two proteins expressed from a bicistronic construct in a cap-independent manner. To our knowledge, this is the first report demonstrating that levels of proteins in DHFR-based bicistronic constructs can be induced and modulated using MTX and rapamycin treatment.
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Affiliation(s)
- Prasun J Mishra
- Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, USA
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49
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Mishra PJ, Menon LG, Mishra PJ, Mayer-Kuckuk P, Bertino JR, Banerjee D. Translational Modulation of Proteins Expressed from Bicistronic Vectors. Mol Imaging 2009. [DOI: 10.2310/7290.2009.00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Prasun J. Mishra
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
| | - Lata G. Menon
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
| | - Pravin J. Mishra
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
| | - Philipp Mayer-Kuckuk
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
| | - Joseph R. Bertino
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
| | - Debabrata Banerjee
- From the Department of Pharmacology, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Medicine, Robert Wood Johnson Medical School, Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ; Department of Neurosurgery, Brigham and Women's
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50
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Shibayama M, Ohno S, Osaka T, Sakamoto R, Tokunaga A, Nakatake Y, Sato M, Yoshida N. Polypyrimidine tract-binding protein is essential for early mouse development and embryonic stem cell proliferation. FEBS J 2009; 276:6658-68. [PMID: 19843185 DOI: 10.1111/j.1742-4658.2009.07380.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polypyrimidine tract-binding protein (PTB) is a widely expressed RNA-binding protein with multiple roles in RNA processing, including the splicing of alternative exons, mRNA stability, mRNA localization, and internal ribosome entry site-dependent translation. Although it has been reported that increased expression of PTB is correlated with cancer cell growth, the role of PTB in mammalian development is still unclear. Here, we report that a homozygous mutation in the mouse Ptb gene causes embryonic lethality shortly after implantation. We also established Ptb(-/-) embryonic stem (ES) cell lines and found that these mutant cells exhibited severe defects in cell proliferation without aberrant differentiation in vitro or in vivo. Furthermore, cell cycle analysis and a cell synchronization assay revealed that Ptb(-/-) ES cells have a prolonged G(2)/M phase. Thus, our data indicate that PTB is essential for early mouse development and ES cell proliferation.
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Affiliation(s)
- Masaki Shibayama
- Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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