Translational selection in human: More pronounced in housekeeping genes

Biology Direct

Volumn 9, Issue 1, 2014, Pages

  Ma, Lina ^a   Cui, Peng ^b   Zhu, Jiang ^c   Zhang, Zhihua ^a   Zhang, Zhang ^a  

^a Chinese Academy of Sciences   (China)

^b KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

Codon usage bias; Expression regulation; Housekeeping gene; Tissue specific gene; Translational selection

Indexed keywords

CODON;

ANTIBODY SPECIFICITY; CODON; ESSENTIAL GENE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; PROTEIN SYNTHESIS;

CODON; GENE EXPRESSION REGULATION; GENES, ESSENTIAL; HUMANS; ORGAN SPECIFICITY; PROTEIN BIOSYNTHESIS;

EID: 84903859893     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-9-17     Document Type: Article

References (47)

1. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics 1991, 129:897-907.
2. Akashi H. Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 1997, 205:269-278.
3. Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH. Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A 2004, 101:3480-3485.
4. Hershberg R, Petrov DA. Selection on codon bias. Annu Rev Genet 2008, 42:287-299.
5. Shabalina SA, Spiridonov NA, Kashina A. Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 2013, 41:2073-2094.
6. Xia X. Maximizing transcription efficiency causes codon usage bias. Genetics 1996, 144:1309-1320.
7. Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol 2001, 53:290-298.
8. Duret L. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 2002, 12:640-649.
9. Lynch M. The nucleotide composition landscape. The origins of genome architecture 2007, 127-133. Sinauer Associates Inc: Sunderland, MA, 1.
10. Parmley JL, Hurst LD. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol 2007, 24:1600-1603.
11. Chamary JV, Hurst LD. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 2005, 6:R75.
12. Shabalina SA, Ogurtsov AY, Spiridonov NA. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 2006, 34:2428-2437.
13. Gu W, Zhou T, Wilke CO. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 2010, 6:e1000664.
14. Najafabadi HS, Goodarzi H, Salavati R. Universal function-specificity of codon usage. Nucleic Acids Res 2009, 37:7014-7023.
15. Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson CH. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 2013, 495:116-120.
16. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 1981, 151:389-409.
17. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985, 2:13-34.
18. Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 2011, 12:32-42.
19. Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 1982, 10:7055-7074.
20. dos Reis M, Wernisch L, Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res 2003, 31:6976-6985.
21. Goetz RM, Fuglsang A. Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli. Biochem Biophys Res Commun 2005, 327:4-7.
22. Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13:43.
23. Coghlan A, Wolfe KH. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000, 16:1131-1145.
24. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003, 425:737-741.
25. dos Reis M, Savva R, Wernisch L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 2004, 32:5036-5044.
26. Lavner Y, Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 2005, 345:127-138.
27. Comeron JM. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 2004, 167:1293-1304.
28. dos Reis M, Wernisch L. Estimating translational selection in eukaryotic genomes. Mol Biol Evol 2009, 26:451-461.
29. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. The mosaic genome of warm-blooded vertebrates. Science 1985, 228:953-958.
30. Semon M, Lobry JR, Duret L. No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol Biol Evol 2006, 23:523-529.
31. Doherty A, McInerney JO. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 2013, 30:2263-2267.
32. Urrutia AO, Hurst LD. The signature of selection mediated by expression on human genes. Genome Res 2003, 13:2260-2264.
33. Zhang L, Li WH. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 2004, 21:236-239.
34. Cui P, Lin Q, Ding F, Hu S, Yu J. The transcript-centric mutations in human genomes. Genomics Proteomics Bioinformatics 2012, 10:11-22.
35. Cui P, Ding F, Lin Q, Zhang L, Li A, Zhang Z, Hu S, Yu J. Distinct contributions of replication and transcription to mutation rate variation of human genomes. Genomics Proteomics Bioinformatics 2012, 10:4-10.
36. Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell 2012, 149:202-213.
37. Sharp PM, Tuohy TM, Mosurski KR. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 1986, 14:5125-5143.
38. Qian W, Yang JR, Pearson NM, Maclean C, Zhang J. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet 2012, 8:e1002603.
39. Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 2013, 495:111-115.
40. Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol 2006, 4:e180.
41. Khuu P, Sandor M, DeYoung J, Ho PS. Phylogenomic analysis of the emergence of GC-rich transcription elements. Proc Natl Acad Sci U S A 2007, 104:16528-16533.
42. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.
43. Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y. A role for codon order in translation dynamics. Cell 2010, 141:355-367.
44. Zhu J, He F, Hu S, Yu J. On the nature of human housekeeping genes. Trends Genet 2008, 24:481-484.
45. Prat Y, Fromer M, Linial N, Linial M. Codon usage is associated with the evolutionary age of genes in metazoan genomes. BMC Evol Biol 2009, 9:285.
46. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
47. Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009, 37:D93-D97.