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Abstract
While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.
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Affiliation(s)
- Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Department of Medicine, University of Adelaide, Adelaide, SA, Australia.
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
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Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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Hauer C, Sieber J, Schwarzl T, Hollerer I, Curk T, Alleaume AM, Hentze MW, Kulozik AE. Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins. Cell Rep 2016; 16:1588-1603. [PMID: 27475226 PMCID: PMC4978704 DOI: 10.1016/j.celrep.2016.06.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/16/2016] [Accepted: 06/29/2016] [Indexed: 12/24/2022] Open
Abstract
The exon junction complex (EJC) connects spliced mRNAs to posttranscriptional processes including RNA localization, transport, and regulated degradation. Here, we provide a comprehensive analysis of bona fide EJC binding sites across the transcriptome including all four RNA binding EJC components eIF4A3, BTZ, UPF3B, and RNPS1. Integration of these data sets permits definition of high-confidence EJC deposition sites as well as assessment of whether EJC heterogeneity drives alternative nonsense-mediated mRNA decay pathways. Notably, BTZ (MLN51 or CASC3) emerges as the EJC subunit that is almost exclusively bound to sites 20–24 nucleotides upstream of exon-exon junctions, hence defining EJC positions. By contrast, eIF4A3, UPF3B, and RNPS1 display additional RNA binding sites suggesting accompanying non-EJC functions. Finally, our data show that EJCs are largely distributed across spliced RNAs in an orthodox fashion, with two notable exceptions: an EJC deposition bias in favor of alternatively spliced transcripts and against the mRNAs that encode ribosomal proteins. iCLIP analyses of EJC components provide a comprehensive map of bona fide EJCs EJC proteins, in particular BTZ, are largely restricted to canonical deposition sites EJCs are enriched on alternatively spliced mRNAs EJCs are underrepresented on mRNAs encoding ribosomal proteins
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Affiliation(s)
- Christian Hauer
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jana Sieber
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ina Hollerer
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tomaz Curk
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Faculty of Computer and Information Science, University of Ljubljana, Vecna Pot 113, 1000 Ljubljana, Slovenia
| | - Anne-Marie Alleaume
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.
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