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Mušo M, Dumbell R, Pulit S, Sinnott-Armstrong N, Laber S, Zolkiewski L, Bentley L, Claussnitzer M, Cox RD. A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194640. [PMID: 33007465 PMCID: PMC7695619 DOI: 10.1016/j.bbagrm.2020.194640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 11/06/2022]
Abstract
We have prioritised a single nucleotide polymorphism (SNP) rs2645294 as one candidate functional SNP in the TBX15-WARS2 waist-hip-ratio locus using posterior probability analysis. This SNP is located in the 3' untranslated region of the WARS2 (tryptophanyl tRNA synthetase 2, mitochondrial) gene with which it has an expression quantitative trait in subcutaneous white adipose tissue. We show that transcripts of the WARS2 gene in a human white adipose cell line, heterozygous for the rs2645294 SNP, showed allelic imbalance. We tested whether the rs2645294 SNP altered WARS2 RNA stability using three different methods: actinomycin-D inhibition and RNA decay, mature and nascent RNA analysis and luciferase reporter assays. We found no evidence of a difference in RNA stability between the rs2645294 alleles indicating that the allelic expression imbalance was likely due to transcriptional regulation.
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Affiliation(s)
- Milan Mušo
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rebecca Dumbell
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Oxford University, Oxford, UK; Program in Medical Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Samantha Laber
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Louisa Zolkiewski
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Liz Bentley
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Melina Claussnitzer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gerontology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany
| | - Roger D Cox
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK.
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2
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Singh S, Choudhary S, Anand V, Jaswal S, Verma AK, Kumar S, Kaushik JK, Mohanty AK. New insights into the catalytic inactivity of mammary gland protein-40, a chitinase-like protein expressed during mammary gland involution. Mol Biol Rep 2019; 46:2243-2257. [DOI: 10.1007/s11033-019-04679-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
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3
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Lee BP, Lloyd-Laney HO, Locke JM, McCulloch LJ, Knight B, Yaghootkar H, Cory G, Kos K, Frayling TM, Harries LW. Functional characterisation of ADIPOQ variants using individuals recruited by genotype. Mol Cell Endocrinol 2016; 428:49-57. [PMID: 26996131 DOI: 10.1016/j.mce.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/18/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022]
Abstract
Four non-coding GWAS variants in or near the ADIPOQ gene (rs17300539, rs17366653, rs3821799 and rs56354395) together explain 4% of the variation in circulating adiponectin. The functional basis for this is unknown. We tested the effect of these variants on ADIPOQ transcription, splicing and stability respectively in adipose tissue samples from participants recruited by rs17366653 genotype. Transcripts carrying rs17300539 demonstrated a 17% increase in expression (p = 0.001). Variant rs17366653 was associated with disruption of ADIPOQ splicing leading to a 7 fold increase in levels of a non-functional transcript (p = 0.002). Transcripts carrying rs56354395 demonstrated a 59% decrease in expression (p = <0.0001). No effects of rs3821799 genotype on expression was observed. Association between variation in the ADIPOQ gene and serum adiponectin may arise from effects on mRNA transcription, splicing or stability. These studies illustrate the utility of recruit-by-genotype studies in relevant human tissues in functional interpretation of GWAS signals.
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Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Henry O Lloyd-Laney
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Jonathan M Locke
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Laura J McCulloch
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Bridget Knight
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Giles Cory
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Katarina Kos
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.
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4
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Genomic, proteomic and physiological characterization of a T5-like bacteriophage for control of Shiga toxin-producing Escherichia coli O157:H7. PLoS One 2012; 7:e34585. [PMID: 22514640 PMCID: PMC3326045 DOI: 10.1371/journal.pone.0034585] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/07/2012] [Indexed: 11/19/2022] Open
Abstract
Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31 × 10(-9) ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (<60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the L-shaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre- and post-harvest biocontrol agent.
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vsx1 3′ untranlated region-mediated translation difference at differentdevelopmental stages of goldfish embryos. J Genet Genomics 2009; 36:483-90. [DOI: 10.1016/s1673-8527(08)60138-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 03/19/2009] [Accepted: 03/23/2009] [Indexed: 11/18/2022]
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6
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Jacobs GH, Stockwell PA, Tate WP, Brown CM. Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res 2006; 34:D37-40. [PMID: 16381889 PMCID: PMC1347521 DOI: 10.1093/nar/gkj159] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3' and 5' flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at http://uther.otago.ac.nz/Transterm.html.
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Bucklin DJ, Wills NM, Gesteland RF, Atkins JF. P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation. J Mol Biol 2005; 345:39-49. [PMID: 15567409 DOI: 10.1016/j.jmb.2004.10.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/11/2004] [Accepted: 10/13/2004] [Indexed: 11/29/2022]
Abstract
Programmed ribosomal bypassing occurs in decoding phage T4 gene 60 mRNA. Half the ribosomes bypass a 50 nucleotide gap between codons 46 and 47. Peptidyl-tRNA dissociates from the "take-off" GGA, codon 46, and re-pairs to mRNA at a matched GGA "landing site" codon directly 5' of codon 47 where translation resumes. The system described here allows the contribution of peptidyl-tRNA re-pairing to be measured independently of dissociation. The matched GGA codons have been replaced by 62 other matched codons, giving a wide range of bypassing efficiencies. Codons with G or C in either or both of the first two codon positions yielded high levels of bypassing. The results are compared with those from a complementary study of non-programmed bypassing, where the combined effects of peptidyl-tRNA dissociation and reassociation were measured. The wild-type, GGA, matched codons are the most efficient in their gene 60 context in contrast to the relatively low value in the non-programmed bypassing study.
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Affiliation(s)
- Douglas J Bucklin
- Department of Human Genetics, University of Utah, 15N 2030E Rm7410, Salt Lake City, UT 84112-5330, USA
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8
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Baranova A, Hammarsund M, Ivanov D, Skoblov M, Sangfelt O, Corcoran M, Borodina T, Makeeva N, Pestova A, Tyazhelova T, Nazarenko S, Gorreta F, Alsheddi T, Schlauch K, Nikitin E, Kapanadze B, Shagin D, Poltaraus A, Ivanovich Vorobiev A, Zabarovsky E, Lukianov S, Chandhoke V, Ibbotson R, Oscier D, Einhorn S, Grander D, Yankovsky N. Distinct organization of the candidate tumor suppressor gene RFP2 in human and mouse: multiple mRNA isoforms in both species- and human-specific antisense transcript RFP2OS. Gene 2004; 321:103-12. [PMID: 14636997 DOI: 10.1016/j.gene.2003.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the present study, we describe the human and mouse RFP2 gene structure, multiple RFP2 mRNA isoforms in the two species that have different 5' UTRs and a human-specific antisense transcript RFP2OS. Since the human RFP2 5' UTR is not conserved in mouse, these findings might indicate a different regulation of RFP2 in the two species. The predicted human and mouse RFP2 proteins are shown to contain a tripartite RING finger-B-box-coiled-coil domain (RBCC), also known as a TRIM domain, and therefore belong to a subgroup of RING finger proteins that are often involved in developmental and tumorigenic processes. Because homozygous deletions of chromosomal region 13q14.3 are found in a number of malignancies, including chronic lymphocytic leukemia (CLL) and multiple myeloma (MM), we suggest that RFP2 might be involved in tumor development. This study provides necessary information for evaluation of the role of RFP2 in malignant transformation and other biological processes.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Chromosome Mapping
- Chromosomes, Human, Pair 13/genetics
- Cloning, Molecular
- DNA/chemistry
- DNA/genetics
- DNA-Binding Proteins/genetics
- Exons
- Female
- Gene Expression
- Genes/genetics
- Humans
- Introns
- Male
- Mice
- Molecular Sequence Data
- Promoter Regions, Genetic/genetics
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Species Specificity
- Transcription, Genetic
- Tumor Suppressor Proteins/genetics
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Affiliation(s)
- Ancha Baranova
- Genome Analysis Laboratory, Institute of General Genetics, Russian Academy of Science, Moscow 119991, Russia.
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9
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Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M. Comprehensive sequence analysis of translation termination sites in various eukaryotes. Gene 2002; 300:79-87. [PMID: 12468089 DOI: 10.1016/s0378-1119(02)01042-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.
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Affiliation(s)
- Y Ozawa
- Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa, Japan
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10
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Abstract
In two Escherichia coli genomes, laboratory strain K-12 and pathological strain O157:H7, tandem termination codons as a group are slightly over-represented as termination signals. Individually however, they span the range of representations, over, as expected, or under, in one or both of the strains. In vivo, tandem termination codons do not make more efficient signals. The second codon can act as a backstop where readthrough of the first has occurred, but not at the expected efficiency. UGAUGA remains an enigma, highly over-represented, but with the second UGA a relatively inefficient back up stop codon.
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Affiliation(s)
- Louise L Major
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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11
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Jacobs GH, Rackham O, Stockwell PA, Tate W, Brown CM. Transterm: a database of mRNAs and translational control elements. Nucleic Acids Res 2002; 30:310-1. [PMID: 11752323 PMCID: PMC99085 DOI: 10.1093/nar/30.1.310] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transterm is a database that facilitates studies of translation and the translational control of protein synthesis. It contains a curated collection of elements in mRNAs that control translation, and biologically relevant mRNA regions extracted from GenBank. It is organised largely on a taxonomic basis with files and summaries for each species. Global patterns that may affect translation in particular species, for example bias in the context of initiation codons (Kozak's consensus or Shine-Dalgarno sequences) or termination codons, can be detected in the consensus and information content bias summaries. Several types of access are provided via a web browser interface. Transterm defined elements may be matched in a user's sequence or in the database. Alternatively, elements can be entered by the user to search specific sections of the database (for example, coding regions or 3' flanking regions or the 3'-UTRs) or the user's sequence. Each Transterm defined element has an associated biological description with references. The database is accessible at http://uther.otago.ac.nz/Transterm.html.
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Affiliation(s)
- Grant H Jacobs
- Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand
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12
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Namy O, Hatin I, Rousset JP. Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep 2001; 2:787-93. [PMID: 11520858 PMCID: PMC1084031 DOI: 10.1093/embo-reports/kve176] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The efficiency of translation termination is influenced by local contexts surrounding stop codons. In Saccharomyces cerevisiae, upstream and downstream sequences act synergistically to influence the translation termination efficiency. By analysing derivatives of a leaky stop codon context, we initially demonstrated that at least six nucleotides after the stop codon are a key determinant of readthrough efficiency in S. cerevisiae. We then developed a combinatorial-based strategy to identify poor 3' termination contexts. By screening a degenerate oligonucleotide library, we identified a consensus sequence -CA(A/G)N(U/C/G)A-, which promotes >5% readthrough efficiency when located downstream of a UAG stop codon. Potential base pairing between this stimulatory motif and regions close to helix 18 and 44 of the 18S rRNA provides a model for the effect of the 3' stop codon context on translation termination.
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Affiliation(s)
- O Namy
- Laboratoire de génétique moléculaire de la traduction, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France
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13
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Chrzanowska-Lightowlers Z, Lightowlers RN. Fending off decay: a combinatorial approach in intact cells for identifying mRNA stability elements. RNA (NEW YORK, N.Y.) 2001; 7:435-444. [PMID: 11333023 PMCID: PMC1370099 DOI: 10.1017/s1355838201001339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The strategy of systematic evolution, whereby nucleic acid sequences or conformers can be selected and amplified from a randomized population, has been exploited by many research groups for numerous purposes. It is, however, a technique largely performed in vitro, under nonphysiological conditions. We have now modified this in vitro approach to accomplish selection in growing cells. Here, we report that this new methodology has been used in vivo to select RNA elements that confer increased transcript stability. A randomized cassette was embedded in a 3'-untranslated region (UTR), downstream from the luciferase reporter open reading frame. A heterogeneous population of capped luciferase mRNA was then generated by in vitro transcription. Human liver Hep G2 cells were electroporated with this population of luciferase mRNA and total cytoplasmic RNA was isolated after varying lengths of incubation. Following RT-PCR, the 3' UTR was used to reconstruct a new population of luciferase templates, permitting subsequent cycles of in vitro transcription, electroporation, RNA isolation, and RT-PCR. Increasing the incubation time at each cycle before RNA isolation imposed selection for stable transcripts. The functional half-life of the luciferase mRNA population increased from 55 to 140 min after four cycles. Subsequent sequencing of the selected 3' UTRs revealed G-U rich elements in clones with extended chemical and functional half-lives.
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Affiliation(s)
- Z Chrzanowska-Lightowlers
- Department of Neurology, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne, United Kingdom.
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14
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Cassan M, Rousset JP. UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals. BMC Mol Biol 2001; 2:3. [PMID: 11242562 PMCID: PMC29092 DOI: 10.1186/1471-2199-2-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2000] [Accepted: 02/27/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Translation termination is mediated through an interaction between the release factors eRF1 and eRF3 and the stop codon within its nucleotide context. Although it is well known that the nucleotide contexts both upstream and downstream of the stop codon, can modulate readthrough, little is known about the mechanisms involved. RESULTS We have performed an in vivo analysis of translational readthrough in mouse cells in culture using a reporter system that allows the measurement of readthrough levels as low as 10(-4). We first quantified readthrough frequencies obtained with constructs carrying different codons (two Gln, two His and four Gly) immediately upstream of the stop codon. There was no effect of amino acid identity or codon frequency. However, an adenine in the -1 position was always associated with the highest readthrough levels while an uracil was always associated with the lowest readthrough levels. This could be due to an effect mediated either by the nucleotide itself or by the P-site tRNA. We then examined the importance of the downstream context using eight other constructs. No direct correlation between the +6 nucleotide and readthrough efficiency was observed. CONCLUSIONS We conclude that, in mouse cells, the upstream and downstream stop codon contexts affect readthrough via different mechanisms, suggesting that complex interactions take place between the mRNA and the various components of the translation termination machinery. Comparison of our results with those previously obtained in plant cells and in yeast, strongly suggests that the mechanisms involved in stop codon recognition are conserved among eukaryotes.
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Affiliation(s)
- Michel Cassan
- Centre de Génétique Moléculaire, Bâtiment 26, Avenue de la Terrasse, Gif sur Yvette, France
| | - Jean-Pierre Rousset
- Institut de Génétique et Microbiologie, Bâtiment 400, Université Paris-Sud, France
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15
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Jenkins ZA, Hååg PG, Johansson HE. Human eIF5A2 on chromosome 3q25-q27 is a phylogenetically conserved vertebrate variant of eukaryotic translation initiation factor 5A with tissue-specific expression. Genomics 2001; 71:101-9. [PMID: 11161802 DOI: 10.1006/geno.2000.6418] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Eukaryotic translation initiation factor 5A (eIF5A) is an essential protein tightly linked to cellular polyamine homeostasis. It receives the unique spermidine-derived posttranslational modification hypusine that is necessary for eIF5A's biochemical activity and cellular proliferation. The eIF5A protein stimulates ribosomal peptidyl-transferase and may be involved in nucleocytoplasmic mRNA transport. Little is known about the molecular genetics of eIF5A. Here we report on the sequence and molecular characterization of human EIF5A2, a novel phylogenetically conserved gene for eIF5A. EIF5A2 stretches over 17 kb and consists of five exons and four introns. It is localized at 3q25-q27, often noted for chromosomal instability in cancers. EIF5A2 is highly expressed in testis and colorectal adenocarcinoma and at moderate levels in the brain, in contrast to the ubiquitously expressed EIF5A1 gene. Two EIF5A2 mRNAs share a 129-nt 5' UTR and a coding sequence for the 153-amino-acid eIF5AII protein, but possess two alternative 3' UTRs of 46 and 890 nt that arise through differential polyadenylation. The protein is 84% identical and 94% similar to eIF5AI. Both EIF5A genes are conserved in vertebrates. Our findings lend further support for a specialized gene expression program of polyamine metabolic proteins and regulators that function to maintain polyamine homeostasis at elevated levels during spermatogenesis.
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Affiliation(s)
- Z A Jenkins
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, SE-751 24, Sweden
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16
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Meijer HA, Dictus WJ, Thomas AA. Cloning and analysis of the untranslated regions of the Xenopus laevis Connexin30 mRNA. Gene 2000; 258:71-6. [PMID: 11111044 DOI: 10.1016/s0378-1119(00)00423-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The full-length 5' and 3' untranslated regions (UTRs) of Xenopus laevis Connexin30 (Cx30) mRNA were cloned and sequenced. The Cx30 messenger contains a 148 nt 5' UTR and a 480 nt 3' UTR. Four different constructs were made to enable the analysis of the role of the Cx30 UTRs in translation efficiency and in protein localization in the early Xenopus embryo. Transcripts encoded the Green Fluorescent Protein (GFP) reporter and contained the 5' and 3' UTR of either Cx30 or globin. In vivo analyses after injection of the transcripts into one cell-stage Xenopus embryos showed that the Cx30 3' UTR enables very efficient translation. The 5' UTR was slightly inhibitory compared with the globin 5' UTR. The localization of the produced GFP was analyzed. GFP was ubiquitously expressed in all parts of the embryo. Based on this observation we conclude that neither the 5' UTR nor the 3' UTR confers specific localization of the translation of the Cx30 mRNA in the embryo.
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Affiliation(s)
- H A Meijer
- Department of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Ivanov IP, Gesteland RF, Atkins JF. Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit. Nucleic Acids Res 2000; 28:3185-96. [PMID: 10954585 PMCID: PMC110703 DOI: 10.1093/nar/28.17.3185] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2000] [Revised: 06/30/2000] [Accepted: 07/07/2000] [Indexed: 12/11/2022] Open
Abstract
The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.
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Affiliation(s)
- I P Ivanov
- Department of Human Genetics, University of Utah, 15N 2030E, Room 7410, Salt Lake City, UT 84112-5330, USA
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