A genetic signature of interspecies variations in gene expression

Nature Genetics

Volumn 38, Issue 7, 2006, Pages 830-834

  Tirosh, Itay ^a   Weinberger, Adina ^a   Carmi, Miri ^a   Barkai, Naama ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TATA BINDING PROTEIN;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE CONTROL; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES KUDRIAVZEVII; SACCHAROMYCES MIKATAE; SACCHAROMYCES PARADOXUS; SPECIES DIFFERENCE; STRESS; TATA BOX; TRANSCRIPTION REGULATION;

DNA; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENES, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES; SPECIES SPECIFICITY; TATA BOX;

EUKARYOTA; MAMMALIA; NEMATODA;

EID: 33745583768     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1819     Document Type: Article

References (30)

1. Khaitovich, P. et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309, 1850-1854 (2005).
2. Ranz, J.M., Castillo-Davis, C.I., Meiklejohn, C.D. & Hartl, D.L. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300, 1742-1745 (2003).
3. Rifkin, S.A., Houle, D., Kim, J. & White, K.P. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature 438, 220-223 (2005).
4. Rifkin, S.A., Kim, J. & White, K.P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33, 138-144 (2003).
5. Denver, D.R. et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat. Genet. 37, 544-548 (2005).
6. Vuylsteke, M., van Eeuwijk, F., Van Hummelen, P., Kuiper, M. & Zabeau, M. Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171, 1267-1275 (2005).
7. Kliebenstein, D.J. et al. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 172, 1179-1189 (2006).
8. Gasch, A.P. et al. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2, e398 (2004).
9. Tanay, A., Regev, A. & Shamir, R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc. Natl. Acad. Sci. USA 102, 7203-7208 (2005).
10. Ihmels, J. et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309, 938-940 (2005).
11. Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 (2003).
12. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
13. Edwards-Ingram, L.C. et al. Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex. Genome Res. 14, 1043-1051 (2004).
14. Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31, 370-377 (2002).
15. Townsend, J.P., Cavalieri, D. & Hartl, D.L. Population genetic variation in genome-wide gene expression. Mol. Biol. Evol. 20, 955-963 (2003).
16. Butler, J.E. & Kadonaga, J.T. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 16, 2583-2592 (2002).
17. Basehoar, A.D., Zanton, S.J. & Pugh, B.F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709 (2004).
18. Patikoglou, G.A. et al. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13, 3217-3230 (1999).
19. Gasch, A.P et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
20. Su, A.I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101, 6062-6067 (2004).
21. Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755 (2002).
22. Fay, J.C., McCullough, H.L., Sniegowski, P.D. & Eisen, M.B. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol. 5, R26 (2004).
23. Landry, C.R., Oh, J., Hartl, D.L. & Cavalieri, D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 366, 343-351 (2006).
24. Chin, C.S., Chuang, J.H. & Li, H. Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence. Genome Res. 15, 205-213 (2005).
25. Huisinga, K.L. & Pugh, B.F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573-585 (2004).
26. Zhang, H., Roberts, D.N. & Cairns, B.R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123, 219-231 (2005).
27. Raser, J.M. & O'Shea, E.K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814 (2004).
28. Blake, W.J., Kaern, M., Cantor, C.R. & Collins, J.J. Noise in eukaryotic gene expression. Nature 422, 633-637 (2003).
29. Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl. Acad. Sci. USA 95, 8420-8427 (1998).
30. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).