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Balbinot C, Vanier M, Armant O, Nair A, Penichon J, Soret C, Martin E, Saandi T, Reimund JM, Deschamps J, Beck F, Domon-Dell C, Gross I, Duluc I, Freund JN. Fine-tuning and autoregulation of the intestinal determinant and tumor suppressor homeobox gene CDX2 by alternative splicing. Cell Death Differ 2017; 24:2173-2186. [PMID: 28862703 DOI: 10.1038/cdd.2017.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
On the basis of phylogenetic analyses, we uncovered a variant of the CDX2 homeobox gene, a major regulator of the development and homeostasis of the gut epithelium, also involved in cancer. This variant, miniCDX2, is generated by alternative splicing coupled to alternative translation initiation, and contains the DNA-binding homeodomain but is devoid of transactivation domain. It is predominantly expressed in crypt cells, whereas the CDX2 protein is present in crypt cells but also in differentiated villous cells. Functional studies revealed a dominant-negative effect exerted by miniCDX2 on the transcriptional activity of CDX2, and conversely similar effects regarding several transcription-independent functions of CDX2. In addition, a regulatory role played by the CDX2 and miniCDX2 homeoproteins on their pre-mRNA splicing is displayed, through interactions with splicing factors. Overexpression of miniCDX2 in the duodenal Brunner glands leads to the expansion of the territory of these glands and ultimately to brunneroma. As a whole, this study characterized a new and original variant of the CDX2 homeobox gene. The production of this variant represents not only a novel level of regulation of this gene, but also a novel way to fine-tune its biological activity through the versatile functions exerted by the truncated variant compared to the full-length homeoprotein. This study highlights the relevance of generating protein diversity through alternative splicing in the gut and its diseases.
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Affiliation(s)
- Camille Balbinot
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Marie Vanier
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Olivier Armant
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Postfach 3640, Karlsruhe 76021, Germany
| | - Asmaa Nair
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Julien Penichon
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Christine Soret
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Thoueiba Saandi
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Marie Reimund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jacqueline Deschamps
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Felix Beck
- Barts and The London School of Medicine and Dentistry, London E1 2ES, UK
| | - Claire Domon-Dell
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Gross
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Isabelle Duluc
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
| | - Jean-Noël Freund
- Université de Strasbourg, Inserm, UMR_S1113, FMTS, Strasbourg 67000, France
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PTBP1 is required for glucose-stimulated cap-independent translation of insulin granule proteins and Coxsackieviruses in beta cells. Mol Metab 2014; 3:518-30. [PMID: 25061557 PMCID: PMC4099505 DOI: 10.1016/j.molmet.2014.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 12/15/2022] Open
Abstract
Glucose and GLP-1 stimulate not only insulin secretion, but also the post-transcriptional induction of insulin granule biogenesis. This process involves the nucleocytoplasmic translocation of the RNA binding protein PTBP1. Binding of PTBP1 to the 3'-UTRs of mRNAs for insulin and other cargoes of beta cell granules increases their stability. Here we show that glucose enhances also the binding of PTBP1 to the 5'-UTRs of these transcripts, which display IRES activity, and their translation exclusively in a cap-independent fashion. Accordingly, glucose-induced biosynthesis of granule cargoes was unaffected by pharmacological, genetic or Coxsackievirus-mediated inhibition of cap-dependent translation. Infection with Coxsackieviruses, which also depend on PTBP1 for their own cap-independent translation, reduced instead granule stores and insulin release. These findings provide insight into the mechanism for glucose-induction of insulin granule production and on how Coxsackieviruses, which have been implicated in the pathogenesis of type 1 diabetes, can foster beta cell failure.
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Key Words
- Beta cells
- CV, Coxsackievirus
- Diabetes
- ER, endoplasmic reticulum
- EV, Enterovirus
- F, Faulkner
- FL, firefly luciferase
- IRES, internal ribosomal entry site
- ITAF, IRES-trans-acting factor
- Insulin
- MCA, MIN6 cell adapted
- PABP, poly(A)-binding protein
- PC, prohormone convertase
- PTBP1, polypyrimidine tract-binding protein 1
- Polypyrimidine tract-binding protein
- S6K1, p70S6 Kinase 1
- Secretory granules
- T1D, type 1 diabetes
- Translation
- UTR, untranslated region
- Virus
- eIF4E-V5, eIF4E tagged at its C-terminus with a V5-epitope
- mTORC1, mammalian Target Of Rapamycin Complex 1
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Pichon X, Wilson LA, Stoneley M, Bastide A, King HA, Somers J, Willis AEE. RNA binding protein/RNA element interactions and the control of translation. Curr Protein Pept Sci 2013; 13:294-304. [PMID: 22708490 PMCID: PMC3431537 DOI: 10.2174/138920312801619475] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 01/18/2023]
Abstract
A growing body of work demonstrates the importance of post-transcriptional control, in particular translation
initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the
5’ and 3’ untranslated regions of mRNA to gene expression in eukaryotic cells including terminal oligopyrimidine tracts,
internal ribosome entry segments, upstream open reading frames and cytoplasmic polyadenylation elements. These
mRNA regulatory elements may adopt complex secondary structures and/or contain sequence motifs that allow their interaction
with a variety of regulatory proteins, RNAs and RNA binding proteins, particularly hnRNPs. The resulting interactions
are context-sensitive, and provide cells with a sensitive and fast response to cellular signals such as hormone exposure
or cytotoxic stress. Importantly, an increasing number of diseases have been identified, particularly cancers and
those associated with neurodegeneration, which originate either from mutation of these regulatory motifs, or from deregulation
of their cognate binding partners.
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Affiliation(s)
- Xavier Pichon
- Medical Research Council Toxicology Unit, Leicester, UK
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Evdokimova V, Tognon C, Ng T, Ruzanov P, Melnyk N, Fink D, Sorokin A, Ovchinnikov LP, Davicioni E, Triche TJ, Sorensen PHB. Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition. Cancer Cell 2009; 15:402-15. [PMID: 19411069 DOI: 10.1016/j.ccr.2009.03.017] [Citation(s) in RCA: 366] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2007] [Revised: 10/30/2008] [Accepted: 03/06/2009] [Indexed: 12/30/2022]
Abstract
Increased expression of the transcription/translation regulatory protein Y-box binding protein-1 (YB-1) is associated with cancer aggressiveness, particularly in breast carcinoma. Here we establish that YB-1 levels are elevated in invasive breast cancer cells and correlate with reduced expression of E-cadherin and poor patient survival. Enforced expression of YB-1 in noninvasive breast epithelial cells induced an epithelial-mesenchymal transition (EMT) accompanied by enhanced metastatic potential and reduced proliferation rates. YB-1 directly activates cap-independent translation of messenger RNAs encoding Snail1 and other transcription factors implicated in downregulation of epithelial and growth-related genes and activation of mesenchymal genes. Hence, translational regulation by YB-1 is a restriction point enabling coordinated expression of a network of EMT-inducing transcription factors, likely acting together to promote metastatic spread.
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Affiliation(s)
- Valentina Evdokimova
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
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5
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Abstract
The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5'-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5'-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.
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Affiliation(s)
- Stephen D Baird
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
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Mitchell SA, Spriggs KA, Bushell M, Evans JR, Stoneley M, Le Quesne JPC, Spriggs RV, Willis AE. Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Genes Dev 2005; 19:1556-71. [PMID: 15998809 PMCID: PMC1172062 DOI: 10.1101/gad.339105] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 05/19/2005] [Indexed: 02/05/2023]
Abstract
We have identified a novel motif which consists of the sequence (CCU)(n) as part of a polypyrimidine-rich tract and permits internal ribosome entry. A number of constructs containing variations of this motif were generated and these were found to function as artificial internal ribosome entry segments (AIRESs) in vivo and in vitro in the presence of polypyrimidine tract-binding protein (PTB). The data show that for these sequences to function as IRESs the RNA must be present as a double-stranded stem and, in agreement with this, rather surprisingly, we show that PTB binds strongly to double-stranded RNA. All the cellular 5' untranslated regions (UTRs) tested that harbor this sequence were shown to contain internal ribosome entry segments that are dependent upon PTB for function in vivo and in vitro. This therefore raises the possibility that PTB or its interacting protein partners could provide a bridge between the IRES-RNA and the ribosome. Given the number of putative cellular IRESs that could be dependent on PTB for function, these data strongly suggest that PTB-1 is a universal IRES-trans-acting factor.
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Affiliation(s)
- Sally A Mitchell
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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7
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Larsen LK, Amri EZ, Mandrup S, Pacot C, Kristiansen K. Genomic organization of the mouse peroxisome proliferator-activated receptor beta/delta gene: alternative promoter usage and splicing yield transcripts exhibiting differential translational efficiency. Biochem J 2002; 366:767-75. [PMID: 12059785 PMCID: PMC1222822 DOI: 10.1042/bj20011821] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2001] [Revised: 05/07/2002] [Accepted: 06/12/2002] [Indexed: 11/17/2022]
Abstract
Peroxisome proliferator-activated receptor (PPAR) beta/delta is ubiquitously expressed, but the level of expression differs markedly between different cell types. In order to determine the molecular mechanisms governing PPARbeta/delta gene expression, we have isolated and characterized the mouse gene encoding PPARbeta/delta. The gene spans approx. 41 kb and comprises 11 exons of which the six exons located in the 3'-end of the gene are included in all transcripts. Primer-extension and 5'-rapid amplification of cDNA ends experiments revealed the presence of multiple transcription start points and splice variants, originating from the use of at least four different promoters. One of these transcription start points was found to be used predominantly in all tissues examined. Initiation from this major transcription start point gives rise to a transcript with a 548 nt 5'-untranslated leader containing eight upstream AUG codons. We show that the presence of the 548 nt leader resulted in a low translational efficiency of the corresponding PPARbeta/delta mRNA and propose, based on structural features of the 5'-untranslated region, that translational initiation may be mediated via an internal ribosome entry site-dependent mechanism.
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MESH Headings
- 3T3 Cells
- 5' Untranslated Regions
- Animals
- Blotting, Northern
- Blotting, Southern
- Blotting, Western
- Cloning, Molecular
- Codon
- DNA, Complementary/metabolism
- Exons
- Mice
- Models, Genetic
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
- Receptors, Cytoplasmic and Nuclear/biosynthesis
- Receptors, Cytoplasmic and Nuclear/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Tissue Distribution
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Transcription, Genetic
- Transfection
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Affiliation(s)
- Leif K Larsen
- Rheoscience A/S, Glerupvej 2, DK-2610 Rødovre, Denmark.
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8
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Schneider R, Agol VI, Andino R, Bayard F, Cavener DR, Chappell SA, Chen JJ, Darlix JL, Dasgupta A, Donzé O, Duncan R, Elroy-Stein O, Farabaugh PJ, Filipowicz W, Gale M, Gehrke L, Goldman E, Groner Y, Harford JB, Hatzglou M, He B, Hellen CU, Hentze MW, Hershey J, Hershey P, Hohn T, Holcik M, Hunter CP, Igarashi K, Jackson R, Jagus R, Jefferson LS, Joshi B, Kaempfer R, Katze M, Kaufman RJ, Kiledjian M, Kimball SR, Kimchi A, Kirkegaard K, Koromilas AE, Krug RM, Kruys V, Lamphear BJ, Lemon S, Lloyd RE, Maquat LE, Martinez-Salas E, Mathews MB, Mauro VP, Miyamoto S, Mohr I, Morris DR, Moss EG, Nakashima N, Palmenberg A, Parkin NT, Pe'ery T, Pelletier J, Peltz S, Pestova TV, Pilipenko EV, Prats AC, Racaniello V, Read GS, Rhoads RE, Richter JD, Rivera-Pomar R, Rouault T, Sachs A, Sarnow P, Scheper GC, Schiff L, Schoenberg DR, Semler BL, Siddiqui A, Skern T, Sonenberg N, Sossin W, Standart N, Tahara SM, Thomas AA, Toulmé JJ, Wilusz J, Wimmer E, Witherell G, Wormington M. New ways of initiating translation in eukaryotes. Mol Cell Biol 2001; 21:8238-46. [PMID: 11710333 PMCID: PMC99989 DOI: 10.1128/mcb.21.23.8238-8246.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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