Proximity of AUG sequences to initiation codon in genomic 5′ UTR regulates mammalian protein expression

Gene

Volumn 594, Issue 2, 2016, Pages 268-271

  Al Ali, Ruslan ^a   González Sarmiento, Rogelio ^a,b  

^a HOSPITAL UNIVERSITARIO DE SALAMANCA   (Spain)

^b UNIVERSITY OF SALAMANCA   (Spain)

Author keywords

5 UTR; ATG; ATG16L2; AUG; Initiation codon; mRNA; ORF; Protein expression; Upstream AUG (uAUG)

Indexed keywords

TRANSCRIPTOME; 5' UNTRANSLATED REGION; ATG16L1 PROTEIN, HUMAN; AUTOPHAGY RELATED PROTEIN; START CODON;

5' UNTRANSLATED REGION; ANIMAL CELL; AUG GENE; CONTROLLED STUDY; CORRELATION COEFFICIENT; GENE EXPRESSION REGULATION; GENE SEQUENCE; LETTER; NONHUMAN; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; RNA TRANSPORT; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS; START CODON; TRANSCRIPTION REGULATION; ANIMAL; BIOSYNTHESIS; GENETICS; HUMAN; METABOLISM; MUTATION; PROMOTER REGION;

5' UNTRANSLATED REGIONS; ANIMALS; AUTOPHAGY-RELATED PROTEINS; CODON, INITIATOR; GENE EXPRESSION REGULATION; HUMANS; MUTATION; PROMOTER REGIONS, GENETIC;

EID: 84991710827     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2016.08.052     Document Type: Letter

References (20)

1. Andrews, J., Levenson, I., Oliver, B., New AUG Initiation Codons in a Long 5′ UTR Create four Dominant Negative Alleles of the Drosophila C2H2 Zinc-finger Gene Ovo, 207, 1997, 482–487.
2. Araujo, P., Yoon, K., Ko, D., Smith, A., Qiao, M., Suresh, U., Burns, S., Penalva, L.O.F., Before it gets started: regulating translation at the 5′ UTR. Comp. Funct. Genomics, 2012, 2012.
3. Bisio, A., Nasti, S., Jordan, J., Gargiulo, S., Pastorino, L., Provenzani, A., Quattrone, A., Queirolo, P., Bianchi-Scarrà, G., Ghiorzo, P., Inga, A., Functional analysis of CDKN2A/p16INK4a 5′UTR variants predisposing to melanoma. Hum. Mol. Genet. 19:8 (2010), 1479–1491.
4. Calvo, S., Pagliarini, D., Mootha, V., Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. PNAS 106:18 (2009), 7507–7512.
5. Chung, B.Y., Simons, C.S., Firth, A.E., Brown, C.M.B., Hellens, R.P., Effect of 5′UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7:120 (2006), 2164–2167.
6. Damjanovich, K., Langa, C., Blanco, F.J., McDonald, J., Botella, L.M., Bernabeu, C., Wooderchak-Donahue, W., Stevenson, D.A., Bayrak-Toydemir, P., 5′UTR mutations of ENG cause hereditary hemorrhagic telangiectasia. Orphanet J. Rare Dis., 6, 2011, 85.
7. Dvir, S., Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast. Proc. Natl. Acad. Sci. U. S. A. 110:30 (2013), 2792–2801.
8. Ghilardi, N., Wiestner, A., Kikuchi, M., Ohsaka, A., Skoda, R.C., Hereditary thrombocythaemia in a Japanese family is caused by a novel point mutation in the thrombopoietin gene. Br. J. Haematol. 107:2 (2016), 310–316.
9. Gruber, A.R., Lorenz, R., Bernhart, S.H., Neuböck, R., Hofacker, I.L., The Vienna RNA websuite. Nucleic Acids Res. 36 (2008), W70–W74.
10. Ishibashi, K., Fujita, N., Kanno, E., Omori, H., Yoshimori, T., Itoh, T., Fukuda, M., Atg16L2, a novel isoform of mammalian Atg16L that is not essential for canonical autophagy despite forming an Atg12–5-16L2 complex. Autophagy 7 (2011), 1500–1513.
11. Kevil, C., Carter, P., Hu, B., DeBenedetti, A., Translational enhancement of FGF-2 by eIF-4 factors, and alternate utilization of CUG and AUG codons for translation initiation. Oncogene 11 (1995), 2339–2348.
12. Kozak, M., At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J. Mol. Biol. 196:4 (1987), 947–950 (20 Aug.).
13. Matthes, T., Aguilar-Martinez, P., Pizzi-Bosman, L., Darbellay, R., Rubbia-Brandt, L., Giostra, E., Michel, M., Ganz, T., Beris, P., Severe hemochromatosis in a Portuguese family associated with a new mutation. Blood 104:7 (2004), 2181–2183.
14. Mignone, F., Gissi, C., Liuni, S., Pesole, G., Untranslated regions of mRNAs. Genome Biol., 3(3), 2002 (reviews0004-reviews0004.10).
15. Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., Milanesi, L., Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ‘weak’ context of the start codon. Bioinformatics 17:10 (2001), 890–900.
16. Scheper, G., van der Knaap, M., Proud, C., Translation matters: protein synthesis defects in inherited disease. Nat. Rev. Genet. 8 (2007), 711–723.
17. Semler, O., Garbes, L., Keupp, K., Swan, D., Zimmermann, K., Becker, J., Iden, S., Wirth, B., Eysel, P., Koerber, F., Schoenau, E., Bohlander, S.K., Wollnik, B., Netzer, C., A Mutation in the 5′-UTR of IFITM5 Creates an In-frame Start Codon and Causes Autosomal-dominant Osteogenesis Imperfecta Type V with Hyperplastic Callus, vol. 91, 2012, 349–357.
18. Sobczak, K., Krzyzosiak, W., Structural determinants of BRCA1 translational regulation. J. Biol. Chem. 277 (2002), 17349–17358.
19. Suzuki, Y., Ishihara, D., Sasaki, M., Nakagawa, H., Hata, H., Tsunoda, T., Watanabe, M., Komatsu, T., Ota, T., Isogai, T., Suyama, A., Sugano, S., Statistical analysis of the 5′ untranslated region of human mRNA using “oligo-capped” cDNA libraries. Genomics 64:3 (2000), 286–297.
20. Wegrzyn, J., Drudge, T., Valafar, F., Hook, V., Bioinformatic analyses of mammalian 5′-UTR sequence properties of mRNAs predicts alternative translation initiation sites. BMC Bioinf., 9, 2008, 232.