Journal ArticleDOI
Interpreting cDNA sequences: Some insights from studies on translation
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TLDR
This review discusses some rules for assessing the completeness of a cDNA sequence and identifying the start site for translation and includes some advice for using in vitro translation systems for the expression of cDNAs.Abstract:
This review discusses some rules for assessing the completeness of a cDNA sequence and identifying the start site for translation. Features commonly invoked-such as an ATG codon in a favorable context for initiation, or the presence of an upstream in-frame terminator codon, or the prediction of a signal peptide-like sequence at the amino terminus-have some validity; but examples drawn from the literature illustrate limitations to each of these criteria. The best advice is to inspect a cDNA sequence not only for these positive features but also for the absence of certain negative indicators. Three specific warning signs are discussed and documented: (i) The presence of numerous ATG codons upstream from the presumptive start site for translation often indicates an aberration (sometimes a retained intron) at the 5' end of the cDNA. (ii) Even one strong, upstream, out-of-frame ATG codon poses a problem if the reading frame set by the upstream ATG overlaps the presumptive start of the major open reading frame. Many cDNAs that display this arrangement turn out to be incomplete; that is, the out-of-frame ATG codon is within, rather than upstream from, the protein coding domain. (iii) A very weak context at the putative start site for translation often means that the cDNA lacks the authentic initiator codon. In addition to presenting some criteria that may aid in recognizing incomplete cDNA sequences, the review includes some advice for using in vitro translation systems for the expression of cDNAs. Some unresolved questions about translational regulation are discussed by way of illustrating the importance of verifying mRNA structures before making deductions about translation.read more
Citations
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Journal ArticleDOI
A Novel Angiotensin-Converting Enzyme–Related Carboxypeptidase (ACE2) Converts Angiotensin I to Angiotensin 1-9
Mary Donoghue,Frank Y. Hsieh,Elizabeth Baronas,Kevin Godbout,Michael Gosselin,Nancy E. Stagliano,Michael J. Donovan,Betty Woolf,Keith E. Robison,Raju Jeyaseelan,Roger E. Breitbart,Susan L. Acton +11 more
TL;DR: The organ- and cell-specific expression of ACE2 and its unique cleavage of key vasoactive peptides suggest an essential role for ACE2 in the local renin-angiotensin system of the heart and kidney.
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Positional Cloning of the Gene for Multiple Endocrine Neoplasia-Type 1
Settara C. Chandrasekharappa,Siradanahalli C. Guru,Pachiappan Manickam,Shodimu Emmanuel Olufemi,Francis S. Collins,Michael R. Emmert-Buck,Larisa V. Debelenko,Zhengping Zhuang,Irina A. Lubensky,Lance A. Liotta,Judy S. Crabtree,Yingping Wang,Bruce A. Roe,Jane M. Weisemann,Mark S. Boguski,Sunita K. Agarwal,Mary Beth Kester,Young Sik Kim,Christina Heppner,Qihan Dong,Allen M. Spiegel,A. Lee Burns,Stephen J. Marx +22 more
TL;DR: The identification of MEN1 will enable improved understanding of the mechanism of endocrine tumorigenesis and should facilitate early diagnosis of multiple endocrine neoplasia-type 1.
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Serena Nik-Zainal,Serena Nik-Zainal,Helen Davies,Johan Staaf,Manasa Ramakrishna,Dominik Glodzik,Xueqing Zou,Inigo Martincorena,Ludmil B. Alexandrov,Sancha Martin,David C. Wedge,Peter Van Loo,Young Seok Ju,Michiel M. Smid,Arie B. Brinkman,Sandro Morganella,Miriam Ragle Aure,Ole Christian Lingjærde,Anita Langerød,Markus Ringnér,Sung-Min Ahn,Sandrine Boyault,Jane E. Brock,Annegien Broeks,Adam Butler,Christine Desmedt,Luc Dirix,Serge Dronov,Aquila Fatima,John A. Foekens,Moritz Gerstung,Gerrit Gk Hooijer,Se Jin Jang,David Jones,Hyung-Yong Kim,Tari Ta King,Savitri Krishnamurthy,Hee Jin Lee,Jeong-Yeon Lee,Yang Li,Stuart McLaren,Andrew Menzies,Ville Mustonen,Sarah O’Meara,Iris Pauporté,Xavier Pivot,Colin Ca Purdie,Keiran Raine,Kamna Ramakrishnan,Germán Fg Rodríguez-González,Gilles Romieu,Anieta M. Sieuwerts,Peter Pt Simpson,Rebecca Shepherd,Lucy Stebbings,Olafur Oa Stefansson,Jon W. Teague,Stefania Tommasi,Isabelle Treilleux,Gert Van den Eynden,Peter B. Vermeulen,Anne Vincent-Salomon,Lucy R. Yates,Carlos Caldas,Laura Van't Veer,Andrew Tutt,Andrew Tutt,Stian Knappskog,Benita Kiat Tee Bk Tan,Jos Jonkers,Åke Borg,Naoto T. Ueno,Christos Sotiriou,Alain Viari,P. Andrew Futreal,Peter J. Campbell,Paul N. Span,Steven Van Laere,Sunil R. Lakhani,Jorunn E. Eyfjord,Alastair M Thompson,Ewan Birney,Hendrik G. Stunnenberg,Marc J. van de Vijver,John W.M. Martens,Anne Lise Børresen-Dale,Andrea L. Richardson,Gu Kong,Gilles Thomas,Michael R. Stratton +89 more
TL;DR: This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
Journal ArticleDOI
Initiation of translation in prokaryotes and eukaryotes.
TL;DR: The binding of Met-tRNA to ribosomes is mediated by a GTP-binding protein in both prokaryotes and eukaryotes, but the more complex structure of the eukARYotic factor (eIF-2) and its association with other proteins underlie some aspects of initiation unique to eUKaryotes.
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Ancient missense mutations in a new member of the RoRet gene family are likely to cause familial Mediterranean fever
Ivona Aksentijevich,Michael Centola,Zuoming Deng,Raman Sood,James E. Balow,Geryl Wood,Nurit Zaks,Elizabeth Mansfield,Xinguo Chen,S. Eisenberg,Anil Vedula,Neta Shafran,Nina Raben,Elon Pras,M. Pras,DL Kastner,Trevor Blake,Andreas D. Baxevanis,Christiane M. Robbins,David B. Krizman,Francis S. Collins,Paul P. Liu,Xuejun Chen,M. Shohat,Melanie Hamon,T. L. Kahan,A. Cercek,J. I. Rotter,N. FischelGhodsian,N. Richards,D. A. Shelton,D.L. Gumucio,Y. Yokoyama,Marie Mangelsdorf,A. Orsborn,Robert I. Richards,Darrell O. Ricke,J. M. Buckingham,Robert K. Moyzis,L. L. Deaven,N. A. Doggett +40 more
TL;DR: The cloning of the FMF gene promises to shed light on the regulation of acute inflammatory responses and is described as a member of a family of nuclear factors homologous to the Ro52 autoantigen.
References
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Journal ArticleDOI
An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs
TL;DR: 5'-Noncoding sequences have been compiled from 699 vertebrate mRNAs and GCCA/GCCATGG emerges as the consensus sequence for initiation of translation in vertebrates.
Journal ArticleDOI
Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.
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Journal ArticleDOI
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Journal ArticleDOI
A single ataxia telangiectasia gene with a product similar to pi-3 kinase
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Journal ArticleDOI
Signal sequences: The limits of variation
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