Length of the ORF, position of the first AUG and the Kozak motif are important factors in potential dual-coding transcripts

Cell Research

Volumn 20, Issue 4, 2010, Pages 445-457

  Xu, Heng ^a   Wang, Ping ^a   Fu, Yujie ^a   Zheng, Yufang ^c   Tang, Quan ^a   Si, Lizhen ^a   You, Jin ^a   Zhang, Zhenguo ^a   Zhu, Yufei ^a   Zhou, Li ^a   Wei, Zejun ^a   Lin, Bin ^a   Hu, Landian ^a,b   Kong, Xiangyin ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c FUDAN UNIVERSITY   (China)

Author keywords

Dual coding transcripts; First AUG; Kozak motif; Nonsense mediated mRNA decay; Open reading frame

Indexed keywords

STIMULATORY GUANINE NUCLEOTIDE BINDING PROTEIN;

ANIMAL; ARTICLE; BIOLOGY; CELL LINE; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; RAT; START CODON;

ANIMALS; BASE SEQUENCE; CELL LINE; CODON, INITIATOR; COMPUTATIONAL BIOLOGY; GTP-BINDING PROTEIN ALPHA SUBUNITS, GS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RATS;

MAMMALIA; RATTUS;

EID: 77950529397     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2010.25     Document Type: Article

References (33)

1. Klemke M, Kehlenbach RH, Huttner WB. Two overlapping reading frames in a single exon encode interacting proteins-a novel way of gene usage. EMBO J 2001; 20:3849-3860. (Pubitemid 32691796)
2. Liang H, Landweber LF. A genome-wide study of dual coding regions in human alternatively spliced genes. Genome Res 2006; 16:190-196. (Pubitemid 43200267)
3. Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A. A first look at ARFome: dual-coding genes in mammalian genomes. PLoS Comput Biol 2007; 3:e91. (Pubitemid 46827931)
4. Ribrioux S, Brungger A, Baumgarten B, Seuwen K, John MR. Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. BMC Genomics 2008; 9:122. (Pubitemid 351584212)
5. Kozak M. Pushing the limits of the scanning mechanism for initiation of translation. Gene 2002; 299:1-34. (Pubitemid 35379825)
6. Furuno M, Kasukawa T, Saito R, et al. CDS annotation in full-length cDNA sequence. Genome Res 2003; 13:1478-1487. (Pubitemid 36827244)
7. Vilela C, McCarthy JE. Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region. Mol Microbiol 2003; 49:859-867. (Pubitemid 36981334)
8. Kozak M. Context effects and inefficient initiation at non- AUG codons in eucaryotic cell-free translation systems. Mol Cell Biol 1989; 9:5073-5080. (Pubitemid 19275978)
9. Kozak M. Initiation of translation in prokaryotes and eukaryotes. Gene 1999; 234:187-208. (Pubitemid 29298181)
10. Kozak M. Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J 1997; 16:2482-2492. (Pubitemid 27260380)
11. Suzuki Y, Ishihara D, Sasaki M, et al. Statistical analysis of the 5' untranslated region of human mRNA using "oligocapped" cDNA libraries. Genomics 2000; 64:286-297. (Pubitemid 30212629)
12. Kozak M. An analysis of vertebrate mRNA sequences: intimations of translational control. J Cell Biol 1991; 115:887-903. (Pubitemid 21909939)
13. Packham G, Brimmell M, Cleveland JL. Mammalian cells express two differently localized Bag-1 isoforms generated by alternative translation initiation. Biochem J 1997; 328 (Pt 3):807-813. (Pubitemid 28005779)
14. Takayama S, Krajewski S, Krajewska M, et al. Expression and location of Hsp70/Hsc-binding anti-apoptotic protein BAG-1 and its variants in normal tissues and tumor cell lines. Cancer Res 1998; 58:3116-3131. (Pubitemid 28335096)
15. Shyu AB, Wilkinson MF, van Hoof A. Messenger RNA regulation: to translate or to degrade. EMBO J 2008; 27:471-481. (Pubitemid 351225677)
16. Maquat LE. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 2004; 5:89-99.
17. Rehwinkel J, Raes J, Izaurralde E. Nonsense-mediated mRNA decay: target genes and functional diversification of effectors. Trends Biochem Sci 2006; 31:639-646. (Pubitemid 44635264)
18. Zhang J, Sun X, Qian Y, LaDuca JP, Maquat LE. At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol Cell Biol 1998; 18:5272-5283. (Pubitemid 28388111)
19. Lu J, Shen Y, Wu Q, et al. The birth and death of microRNA genes in Drosophila. Nat Genet 2008; 40:351-355. (Pubitemid 351311763)
20. Hartwig A. Zinc finger proteins as potential targets for toxic metal ions: differential effects on structure and function. Antioxid Redox Signal 2001; 3:625-634. (Pubitemid 32785985)
21. Mackay JP, Crossley M. Zinc fingers are sticking together. Trends Biochem Sci 1998; 23:1-4. (Pubitemid 28093984)
22. Kozak M. How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell 1978; 15:1109-1123. (Pubitemid 9109673)
23. Kozak M. The scanning model for translation: an update. J Cell Biol 1989; 108:229-241. (Pubitemid 19065830)
24. Iacono M, Mignone F, Pesole G. uAUG and uORFs in human and rodent 5'untranslated mRNAs. Gene 2005; 349:97-105. (Pubitemid 40501891)
25. Morris DR, Geballe AP. Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol 2000; 20:8635-8642.
26. Abramowitz J, Grenet D, Birnbaumer M, Torres HN, Birnbaumer L. XLalphas, the extra-long form of the alpha-subunit of the Gs G protein, is significantly longer than suspected, and so is its companion Alex. Proc Natl Acad Sci USA 2004; 101:8366-8371. (Pubitemid 38736581)
27. Cojocaru M, Jeronimo C, Forget D, et al. Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J 2008; 409:139-147.
28. Tomer Y, Concepcion E, Greenberg DA. AC/T single-nucle otide polymorphism in the region of the CD40 gene is associated with Graves' disease. Thyroid 2002; 12:1129-1135. (Pubitemid 36114821)
29. Jacobson EM, Concepcion E, Oashi T, Tomer Y. A Graves' disease-associated Kozak sequence single-nucleotide polymorphism enhances the efficiency of CD40 gene translation: a case for translational pathophysiology. Endocrinology 2005; 146:2684-2691. (Pubitemid 40695571)
30. Kozak M. Extensively overlapping reading frames in a second mammalian gene. EMBO Rep 2001; 2:768-769. (Pubitemid 32982742)
31. Nagy E, Maquat LE. A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci 1998; 23:198-199. (Pubitemid 28302613)
32. Scofield DG, Hong X, Lynch M. Position of the final intron in full-length transcripts: determined by NMD? Mol Biol Evol 2007; 24:896-899. (Pubitemid 46536703)
33. Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD. Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. PLoS Genet 2005; 1:e18.