Evolution of the correlation between expression divergence and protein divergence in mammals

Genome Biology and Evolution

Volumn 5, Issue 7, 2013, Pages 1324-1335

  Warnefors, Maria ^a,b   Kaessmann, Henrik ^a,b  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Amniotes; Correlation analysis; Gene expression evolution; Primates; Protein evolution

Indexed keywords

PROTEIN; TRANSCRIPTOME;

AMINO ACID SEQUENCE; AMNIOTE; ANIMAL; ARTICLE; BIRD; CHEMISTRY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE EXPRESSION EVOLUTION; GENE ONTOLOGY; GENETIC SELECTION; GENETICS; GENOME; HUMAN; MAMMAL; METABOLISM; MOLECULAR EVOLUTION; MOUSE; PHYLOGENY; PRIMATE; PROTEIN EVOLUTION;

AMNIOTES; CORRELATION ANALYSIS; GENE EXPRESSION EVOLUTION; PRIMATES; PROTEIN EVOLUTION;

AMINO ACID SEQUENCE; ANIMALS; BIRDS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE ONTOLOGY; GENOME; HUMANS; MAMMALS; MICE; PHYLOGENY; PROTEINS; SELECTION, GENETIC; TRANSCRIPTOME;

EID: 84891724119     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt093     Document Type: Article

References (50)

1. Bedford T, Hartl DL. 2009. Optimization of gene expression by natural selection. Proc Natl Acad Sci U S A. 106:1133-1138.
2. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Methodol. 57:289-300.
3. Brawand D, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
4. Carmel L, Koonin EV. 2009. A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol. 1:382-390.
5. Chamary JV, Parmley JL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 7:98-108.
6. Chen WH, Minguez P, Lercher MJ, Bork P. 2012. OGEE: an online gene essentiality database. Nucleic Acids Res. 40:D901-D906.
7. Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
8. Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
9. Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74.
10. Eden E, et al. 2009. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48.
11. Fletcher W, Yang Z. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol. 27:2257-2267.
12. Flicek P, et al. 2011. Ensembl 2011. Nucleic Acids Res. 39:D800-D806.
13. Fujita PA, et al. 2011. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39:D876-D882.
14. Gene Ontology Consortium. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25-29.
15. Gibbs RA, et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
16. Gout JF, Kahn D, Duret L. 2010. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet. 6:e1000944.
17. Gu X, Su Z. 2007. Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. Proc Natl Acad Sci U S A. 104: 2779-2784.
18. Harmon LJ, et al. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.
19. Haygood R, Babbitt CC, Fedrigo O, Wray GA. 2010. Contrasts between adaptive coding and noncoding changes during human evolution. Proc Natl Acad Sci U S A. 107:7853-7857.
20. Holloway AK, et al. 2007. Adaptive gene expression divergence inferred from population genomics. PLoS Genet. 3:2007-2013.
21. Hunt BG, Ometto L, Keller L, Goodisman MA. 2013. Evolution at two levels in fire ants: the relationship between patterns of gene expression and protein sequence evolution. Mol Biol Evol. 30:263-271.
22. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
23. Jordan IK, Marino-Ramirez L, Koonin EV. 2005. Evolutionary significance of gene expression divergence. Gene 345:119-126.
24. Khaitovich P, et al. 2005. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
25. Kim SH, Yi SV. 2007. Understanding relationship between sequence and functional evolution in yeast proteins. Genetica 131:151-156.
26. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
27. Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol. 22:1345-1354.
28. Liao BY, Weng MP, Zhang J. 2010. Contrasting genetic paths to morphological and physiological evolution. Proc Natl Acad Sci U S A. 107: 7353-7358.
29. Liao BY, Zhang J. 2006a. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol. 23: 530-540.
30. Liao BY, Zhang J. 2006b. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol. 23:1119-1128.
31. Locke DP, et al. 2011. Comparative and demographic analysis of orangutan genomes. Nature 469:529-533.
32. Löytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.
33. Makova KD, LiWH. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13:1638-1645.
34. Mikkelsen TS, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-177.
35. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
36. Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM. 2004. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol. 21:1308-1317.
37. Pereira V, Waxman D, Eyre-Walker A. 2009. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 183:1597-1600.
38. R Development Core Team. 2011. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
39. Sartor MA, et al. 2006. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles 'uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res. 34:185-200.
40. Scally A, et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.
41. Schluter D, Price T, Mooers AO, Ludwig D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
42. Subramanian S, Kumar S. 2004. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381.
43. Tirosh I, Barkai N. 2008. Evolution of gene sequence and gene expression are not correlated in yeast. Trends Genet. 24:109-113.
44. Vogel C, Marcotte EM. 2012. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 13:227-232.
45. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 10:57-63.
46. Warren WC, et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175-183.
47. Wilson MD, et al. 2008. Species-specific transcription in mice carrying human chromosome 21. Science 322:434-438.
48. Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 8:206-216.
49. Yanai I, et al. 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650-659.
50. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.