Comparative biology: beyond sequence analysis

Current Opinion in Biotechnology

Volumn 18, Issue 4, 2007, Pages 371-377

  Tirosh, Itay ^a   Bilu, Yonatan ^a   Barkai, Naama ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; FUNCTION EVALUATION; GENE EXPRESSION; PROBABILITY DISTRIBUTIONS;

COMPARATIVE ANALYSIS; COMPARATIVE PARADIGMS; FUNCTIONAL ELEMENTS;

BIOTECHNOLOGY;

COMPARATIVE STUDY; DUPLICATE GENE; GENE EXPRESSION; MOLECULAR BIOLOGY; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MODELS, THEORETICAL; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 34548544672     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2007.07.003     Document Type: Review

References (51)

1. Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., Waterston R., Cohen B.A., and Johnston M. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301 (2003) 71-76
2. Kellis M., Patterson N., Endrizzi M., Birren B., and Lander E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 (2003) 241-254
3. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006, 443:931-949.
4. McCarroll S.A., Murphy C.T., Zou S., Pletcher S.D., Chin C.S., Jan Y.N., Kenyon C., Bargmann C.I., and Li H. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet 36 (2004) 197-204. This study demonstrates how comparison of analogous expression datasets from distant organisms can be used to identify conserved expression programs. In particular, conserved expression programs were identified during aging of flies and worms.
5. Fay J.C., McCullough H.L., Sniegowski P.D., and Eisen M.B. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 5 (2004) R26
6. Gilad Y., Oshlack A., Smyth G.K., Speed T.P., and White K.P. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440 (2006) 242-245. Comparison of gene expression levels in liver cells among humans, chimpanzees, orangutans, and rhesus macaques using a multi-species array. Both conserved and divergent genes were identified and analyzed.
7. Khaitovich P., Hellmann I., Enard W., Nowick K., Leinweber M., Franz H., Weiss G., Lachmann M., and Paabo S. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309 (2005) 1850-1854
8. Kliebenstein D.J., West M.A., van Leeuwen H., Kim K., Doerge R.W., Michelmore R.W., and St Clair D.A. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 172 (2006) 1179-1189
9. Landry C.R., Oh J., Hartl D.L., and Cavalieri D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multicopy and dispensable genes. Gene 366 (2006) 343-351
10. Ranz J.M., Castillo-Davis C.I., Meiklejohn C.D., and Hartl D.L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300 (2003) 1742-1745
11. Rifkin S.A., Kim J., and White K.P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33 (2003) 138-144
12. Sartor M.A., Zorn A.M., Schwanekamp J.A., Halbleib D., Karyala S., Howell M.L., Dean G.E., Medvedovic M., and Tomlinson C.R. 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. Nucl Acids Res 34 (2006) 185-200
13. Tirosh I., Weinberger A., Carmi M., and Barkai N. A genetic signature of interspecies variations in gene expression. Nat Genet 38 (2006) 830-834. Comparison of gene expression among four yeast species subjected to several environmental stresses identified a common signature (TATA-box) in divergent genes from various studies and organisms. This study demonstrates the comparison of expression data from closely related organisms at identical conditions.
14. Yvert G., Brem R.B., Whittle J., Akey J.M., Foss E., Smith E.N., Mackelprang R., and Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35 (2003) 57-64
15. Lemos B., Meiklejohn C.D., and Hartl D.L. Regulatory evolution across the protein interaction network. Nat Genet 36 (2004) 1059-1060
16. Gu Z., Rifkin S.A., White K.P., and Li W.H. Duplicate genes increase gene expression diversity within and between species. Nat Genet 36 (2004) 577-579
17. Berg J., and Lassig M. Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 103 (2006) 10967-10972
18. Bergmann S., Ihmels J., and Barkai N. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2 (2004) E9
19. Stuart J.M., Segal E., Koller D., and Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (2003) 249-255
20. Tirosh I., and Barkai N. Computational verification of protein-protein interactions by orthologous co-expression. BMC Bioinformatics 6 (2005) 40
21. Snel B., van Noort V., and Huynen M.A. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucl Acids Res 32 (2004) 4725-4731
22. Sharan R., Suthram S., Kelley R.M., Kuhn T., McCuine S., Uetz P., Sittler T., Karp R.M., and Ideker T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102 (2005) 1974-1979. Comparison of genome-wide PPI data using "network alignment", and prediction of conserved complexes and pathways.
23. Ihmels J., Bergmann S., Berman J., and Barkai N. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 1 (2005) e39. Describes a general framework for comparative analysis that focuses on the modular network structure. This framework is applied to compare two yeast species (S. cerevisiae and C. albicans) and reveals various similarities and pheonotypic-related differences.
24. Lozada-Chavez I., Janga S.C., and Collado-Vides J. Bacterial regulatory networks are extremely flexible in evolution. Nucl Acids Res 34 (2006) 3434-3445
25. Ihmels J., Bergmann S., Gerami-Nejad M., Yanai I., McClellan M., Berman J., and Barkai N. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309 (2005) 938-940. Comparison of the regulatory networks from two yeast species reveals a large-scale difference in the regulation of the mitochondrial ribosomal proteins. This difference was generated by the loss of dozens of regulatory motifs and is implicated in the evolution of the capacity of yeast species for anaerobic growth. This study demonstrates the comparison of co-expression networks and their modular structure.
26. Gasch A.P., Moses A.M., Chiang D.Y., Fraser H.B., Berardini M., and Eisen M.B. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2 (2004) e398
27. Hershberg R., and Margalit H. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biol 7 (2006) R62
28. Tanay A., Regev A., and Shamir R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci USA 102 (2005) 7203-7208. Integration of expression data and promoter sequences from several yeast species revealed that extensive regulatory evolution underlies the conserved co-expression of ribosomal proteins.
29. Bilu Y., and Barkai N. The design of transcription-factor binding sites is affected by combinatorial regulation. Genome Biol 6 (2005) R103
30. Frazer K.A., Elnitski L., Church D.M., Dubchak I., and Hardison R.C. Cross-species sequence comparisons: a review of methods and available resources. Genome Res 13 (2003) 1-12
31. Li L., Stoeckert Jr. C.J., and Roos D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13 (2003) 2178-2189
32. Remm M., Storm C.E., and Sonnhammer E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314 (2001) 1041-1052
33. Sharan R., and Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 24 (2006) 427-433
34. Huminiecki L., and Wolfe K.H. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res 14 (2004) 1870-1879
35. Chain F.J., and Evans B.J. Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genet 2 (2006) e56
36. Byrne K.P., and Wolfe K.H. Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after wholegenome duplication. Genetics (2006)
37. Tirosh I., and Barkai N. Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 8 (2007) R50
38. Woolfe A., and Elgar G. Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biol 8 (2007) R53
39. Kellis M., Birren B.W., and Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428 (2004) 617-624
40. Scannell D.R., Byrne K.P., Gordon J.L., Wong S., and Wolfe K.H. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440 (2006) 341-345. Analysis of gene-loss following the ancient WGD. It is demonstrated that alternative copies were retained in different organisms and this differential gene-loss is proposed to underlie speciation events.
41. Dehal P., and Boore J.L. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3 (2005) e314
42. Man O., and Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet 39 (2007) 415-421. Comparison of codon usage (and the associated translation efficiencies) among nine yeast species. It is shown that differences in translation efficiencies among orthologs are consistent with known phenotypic differences.
43. Dutilh B.E., Huynen M.A., and Snel B. A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics 7 (2006) 10
44. Jensen L.J., Jensen T.S., de Lichtenberg U., Brunak S., and Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443 (2006) 594-597. Comparison of cell cycle regulation among S. cerevisiae, S. pombe, A. thaliana, and H. sapiens. It is shown that different genes are cell cycle regulated in each organism, but these roughly correspond to activation of the same complexes. Furthermore, changes in transcription regulation have co-evolved with changes in post-transcription regulation (i.e. protein phosphorylation).
45. Kopelman N.M., Lancet D., and Yanai I. Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet 37 (2005) 588-589
46. Yanai I., Graur D., and Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics 8 (2004) 15-24
47. Liao B.Y., and Zhang J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23 (2006) 530-540
48. Xie X., Lu J., Kulbokas E.J., Golub T.R., Mootha V., Lindblad-Toh K., Lander E.S., and Kellis M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434 (2005) 338-345. Analysis of conserved non-coding sequences among human, mouse, rat, and dog, discovers numerous known and novel regulatory motifs. This work illustrates the power of evolutionary conservation as a method to identify functional elements.
49. Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature 437 (2005) 1149-1152
50. Khaitovich P., Weiss G., Lachmann M., Hellmann I., Enard W., Muetzel B., Wirkner U., Ansorge W., and Paabo S. A neutral model of transcriptome evolution. PLoS Biol 2 (2004) E132
51. Yanai I., Korbel J.O., Boue S., McWeeney S.K., Bork P., and Lercher M.J. Similar gene expression profiles do not imply similar tissue functions. Trends Genet 22 (2006) 132-138