Relationship between 5′ UTR length and gene expression pattern in chicken

Genetica

Volumn 141, Issue 7-9, 2013, Pages 311-318

  Rao, You S ^a,b   Wang, Zhang F ^a   Chai, Xue W ^a   Nie, Qing H ^b   Zhang, Xi Q ^b  

^a Jiangxi Key Laboratory of Genetic Improvement of Indigenous Chicken Breeds   (China)

^b SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

5 UTR length; Gallus gallus; Gene expression pattern; Selection

Indexed keywords

GALLUS GALLUS; MAMMALIA; VERTEBRATA;

5' UNTRANSLATED REGION; ANIMAL; ANTIBODY SPECIFICITY; ARTICLE; CHICKEN; GENETIC TRANSCRIPTION; GENETICS; GENOME; TRANSCRIPTION INITIATION;

5' UNTRANSLATED REGIONS; ANIMALS; CHICKENS; GENOME; ORGAN SPECIFICITY; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

5' UNTRANSLATED REGION;

EID: 84885837123     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-013-9730-9     Document Type: Article

References (38)

1. Akashi H (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11: 660-666.
2. Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M (2010) Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res 20: 1451-1458.
3. Carmel L, Koonin E (2009) A universal nonmonotonic relationship between gene compactness and expression level in muticellular eukaryotes. Genome Biol Evol 1: 382-390.
4. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31: 415-418.
5. Chen CH, Lin HY, Pan CL, Chen FC (2011) The plausible reason why the length of 5′ untranslated region is unrelated to organismal complexity. BMC Res Notes 4: 312.
6. Comeron JM (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 67(3): 1293-1304.
7. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci 103: 5320-5325.
8. Eisenberg E, Levanon EY (2003) Human housekeeping genes are compact. Trends Genet 19(7): 362-365.
9. Flicek P, Amode MR, Barrell D et al (2011) Ensembl. Nucleic Acids Res 39: D800-D806.
10. Holm S (1979) A simple sequentially rejective Bonferroni test procedure. Scand J Stat 6: 65-70.
11. Hughes MJ, Andrews DW (1997) A single nucleotide is a sufficient 5′untranslated region for translation in an eukaryotic in vitro system. FEBS Lett 414: 19-22.
12. Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5: R2.
13. Iida Y, Kanagu D (2000) Quantification analysis of translation initiation signal in vertebrate mRNAs: effect of nucleotides at positions +4(-) +6 upon efficiency of translation initiation. Nucleic Acids Symp Ser 44: 77-78.
14. International Chicken Genome Sequencing Consortium (ICGSC) (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
15. International Chicken Polymorphism Map Consortium (ICPMC) (2004) A genetic variation map for chicken with 2. 8 million single-nucleotide polymorphisms. Nature 432: 717-725.
16. Iwabe N, Miyata T (2001) Overlapping genes in parasitic protist Giardia lamblia. Gene 280: 16-167.
17. Kozak M (1987) An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15: 8125-8148.
18. Kozak M (1996) Interpreting cDNA sequences: some insights from studies on translation. Mamm Genome 7(8): 563-574.
19. Li SW, Feng L, Niu DK (2007) Selection for the miniaturization of highly expressed genes. Biochem Biophy Res Commun 360(3): 586-592.
20. Lin Z, Li WH (2012) Evolution of 5′untranslated region length and gene expression reprogramming in yeasts. Mol Biol Evol 29: 81-89.
21. Liston DR, Johnson PJ (1999) Analysis of a ubiquitous promoter element in a primitive eukaryote: early evolution of the initiator element. Mol Cell Biol 19: 2380-2388.
22. Lynch M, Scofield DG, Hong X (2005) The evolution of transcription-initiation sites. Mol Biol Evol 22: 1137-1146.
23. Maicas E, Shago M, Friesen JD (1990) Translation of the Saccharomyces cerevisiae tcm1 gene in the absence of a 5′untranslated leader. Nucleic Acids Res 18: 5823-5828.
24. Meijer HA, Thomas AA (2002) Control of eukaryotic protein synthesis by upstream open reading frames in the 5′- untranslated region of an mRNA. Biochem J 367: 1-11.
25. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
26. Niu DK, Hou WR, Li SW (2005) mRNA-mediated intron losses: evidence from extraordinarily large exons. Mol Biol Evol 22: 1475-1481.
27. Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S (2001) Structural and functional features of eukaryotic mRNA untranslated regions. Gene 276: 73-81.
28. Radford A, Parish JH (1997) The genome and genes of Neurospora crassa. Fungal Genet Biol 21: 258-266.
29. Rao YS, Chai XW, Wang ZF, Nie QH, Zhang XQ (2013) Impact of GC content on gene expression pattern in chicken. Genet Sel Evol 45: 9.
30. Rao YS, Wang ZF, Zhou M, Shen X, Xia MN, Zhang XQ (2007) Comparative study of SNP diversity and calculation of the effective size of population in chicken. Hereditas (Beijing) 29(9): 1083-1088.
31. Rao YS, Wang ZF, Chai XW, Wu GZ, Zhou M, Nie QH, Zhang XQ (2010) Selection for the compactness of highly expressed genes in Gallus gallus. Biol Direct 5: 35.
32. Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV (2009) Evolution of alternative and constitutive regions of mammalian 5′ UTRs. BMC Genomics 10: 162.
33. Reuter M, Engelsta J, Fontanillas P, Hurst LD (2008) A test of the null model for 5′ utr evolution based on gc content. Mol Biol Evol 25: 801-804.
34. Urrutia AO, Hurst LD (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159: 1191-1199.
35. Vinogradov AE (2006) Genome design' model: evidence from conserved intronic sequence in human- mouse comparison. Genome Res 16: 347-354.
36. Wang X, Zhao Y, Wong K, Ehlers P, Kohara Y, Jones S, Marra MA, Holt RA, Moerman DG, Hansen D (2009) Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics 10: 213.
37. Yanai I, Benjamin H, Shmoish M (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650-659.
38. Zhang W, Morris OD, Chang R et al (2004) The functional landscape of mouse gene expression. J Biol 3: 21.