Gene promoter evolution targets the center of the human protein interaction network

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Planas, Jordi ^a   Serrat, Josep M ^a  

^a UNIVERSITY OF VIC CENTRAL UNIVERSITY OF CATALONIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE FREQUENCY; GENE FUNCTION; GENETIC CODE; GENETIC REGULATION; GENETIC SELECTION; GENOME ANALYSIS; HUMAN; MOLECULAR EVOLUTION; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN LOCALIZATION; GENETICS; PHYSIOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING;

EVOLUTION, MOLECULAR; HUMANS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN INTERACTION MAPPING;

EID: 77955402458     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011476     Document Type: Article

References (49)

1. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188(4184): 107-116.
2. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20(9): 1377-1419.
3. Wray GA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8(3): 206-216.
4. Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet 39(9): 1140-1144.
5. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, et al. (2003) Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302(5652): 1960-1963.
6. Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, et al. (2009) Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet 5(8): e1000592.
7. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296(5568): 750-752.
8. Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 13(10): 2229-2235.
9. Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314(5807): 1938-1941.
10. Kim PM, Korbel JO, Gerstein MB (2007) Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A 104(51): 20274-20279.
11. Lemos B, Meiklejohn CD, Hartl DL (2004) Regulatory evolution across the protein interaction network. Nat Genet 36(10): 1059-1060.
12. Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM (2006) Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 16(1): 1-10.
13. Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, et al. (2007) Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One 2(8): e807.
14. Koudritsky M, Domany E (2008) Positional distribution of human transcription factor binding sites. Nucleic Acids Res 36(21): 6795-6805.
15. Berglund J, Pollard KS, Webster MT (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol 7(1): e26.
16. Loytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A 102(30): 10557-10562.
17. Loytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320(5883): 1632-1635.
18. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, et al. (2003) PANTHER: A library of protein families and subfamilies indexed by function. Genome Res 13(9): 2129-2141.
19. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA (2003) Global functional profiling of gene expression. Genomics 81(2): 98-104.
20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Geneontology: Tool for the unification of biology. the gene ontology consortium. Nat Genet 25(1): 25-29.
21. UniProt Consortium (2010) The universal protein resource (UniProt) in 2010. Nucleic Acids Res 38(Database issue): D142-D418.
22. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35(Database issue): D561-D565.
23. Brandes U. Network analysis.: Springer Berlin/Heidelberg.
24. R Development Core Team. (2009) R: A language and environment for statistical computing.
25. Drummond DA, Raval A, Wilke CO (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23(2): 327-337.
26. Plotkin JB, Fraser HB (2007) Assessing the determinants of evolutionary rates in the presence of noise. Mol Biol Evol 24(5): 1113-1121.
27. 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(1): 68-74.
28. 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(5): 1345-1354.
29. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH (2005) Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A 102(40): 143380-14343.
30. Subramanian S, Kumar S (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168(1): 373-381.
31. Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, et al. (2008) Species-specific transcription in mice carrying human chromosome 21. Science 322(5900): 434-438.
32. Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM (2006) Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 16(1): 1-10.
33. Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, et al. (2008) Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res 18(3): 380-392.
34. Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary changes in cis and trans gene regulation. Nature 430(6995): 85-88.
35. Ronald J, Brem RB, Whittle J, Kruglyak L (2005) Local regulatory variation in saccharomyces cerevisiae. PLoS Genet 1(2): e25.
36. Davidson EH (2006) The regulatory genome: Gene regulatory networks in development and evolution.
37. Wolf JB, Kunstner A, Nam K, Jakobsson M, Ellegren H (2009) Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol 2009: 308-319.
38. 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(17): 7853-7857.
39. Hoffman MM, Birney E (2010) An effective model for natural selection in promoters. Genome Res 20(5): 685-692.
40. Pagel A, Pomiankowski A, eds (2008) Evolutionary genomics and proteomics. Sunderland MA USA, Sinauer Associates, Inc. Publishers.
41. Bloom JD, Adami C (2004) Evolutionary rate depends on number of proteinprotein interactions independently of gene expression level: Response. BMC Evol Biol 4: 14.
42. Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23(9): 1751-1761.
43. Franzosa EA, Xia Y (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 26(10): 2387-2395.
44. Fraser HB (2005) Modularity and evolutionary constraint on proteins. Nat Genet 37(4): 351-352.
45. Wolf MY, Wolf YI, Koonin EV (2008) Comparable contributions of structuralfunctional constraints and expression level to the rate of protein sequence evolution. Biol Direct 3: 40.
46. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. (2004) A neutral model of transcriptome evolution. PLoS Biol 2(5): E132.
47. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, et al. (2005) BioMart and bioconductor: A powerful link between biological databases and microarray data analysis. Bioinformatics 21(16): 3439-3440.
48. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2008) Ensembl 2008. Nucleic Acids Res 36(Database issue): D707-D714.
49. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21(5): 650-659.