Natural selection on cis and trans regulation in yeasts

Genome Research

Volumn 20, Issue 6, 2010, Pages 826-836

  Emerson, J J ^a   Hsieh, Li Ching ^a,b   Sung, Huang Mo ^c   Wang, Tzi Yuan ^a,d   Huang, Chih Jen ^d,e,f   Lu, Henry Horng Shing ^g   Lu, Mei Yeh Jade ^a,d   Wu, Shu Hsing ^h   Li, Wen Hsiung ^a,d,i  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^c NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^d BIODIVERSITY RESEARCH CENTER   (Taiwan)

^e ACADEMIA SINICA   (Taiwan)

^f NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^g NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^h INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

ⁱ UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FUNGAL GENE; GENE EXPRESSION; INTRASPECIFIC VARIATION; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; REGULATORY MECHANISM; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS;

DNA, FUNGAL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SACCHAROMYCES CEREVISIAE; SELECTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 77952982347     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.101576.109     Document Type: Article

References (49)

1. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007. (Pubitemid 34856032)
2. Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Belle WV, Beisel C, van Nimwegen E. 2009. Methods for analyzing deep sequencing expression data: Constructing the human and mouse promoterome with deepCAGE data. Genome Biol 10: R79. doi: 10.1186/gb-2009-10-7-r79.
3. Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. 2009. Measuring differential gene expression by short read sequencing: Quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 10: 221. doi: 10.1186/1471-2164-10-221.
4. Bolstad BM, Irizarry RA, Astrand M, Speed TP. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. (Pubitemid 36181903)
5. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755. (Pubitemid 34442007)
6. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. 2002. The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
7. Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25-36.
8. Collins SR, Kemmeren P, Zhao X-C, Greenblatt JF, Spencer F, Holstege FCP, Weissman JS, Krogan NJ. 2007. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450.
9. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. 2009. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25: 3207-3212.
10. Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, Thomas WK. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet 37: 544-548. (Pubitemid 40617285)
11. Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G. 2005. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169: 1915-1925. (Pubitemid 40695608)
12. Edgar RC. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. doi: 10.1186/1471-2105-5- 113.
13. Emerson JJ, Kaessmann H, Betran E, Long M. 2004. Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540. (Pubitemid 38120854)
14. Fisher R. 1922. On the dominance ratio. Proc R Soc Edinb 42: 321-341.
15. Haldane J. 1927. A mathematical theory of natural and artificial selection, Part V: Selection and mutation. Proc Camb Philol Soc 23: 838-844.
16. Halder G, Callaerts P, Gehring WJ. 1995. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267: 1788-1792.
17. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
18. Kent WJ. 2002. BLAT - the BLAST-like alignment tool. Genome Res 12: 656-664.
19. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100: 11484-11489. (Pubitemid 37205962)
20. Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217: 624-626.
21. Kimura M, Ota T. 1971. Protein polymorphism as a phase of molecular evolution. Nature 229: 467-469.
22. King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
23. Kohrer K, Domdey H. 1991. Preparation of high molecular weight RNA. Methods Enzymol 194: 398-405.
24. Kreitman ME, Aguade M. 1986. Excess polymorphism at the Adh locus in Drosophila melanogaster. Genetics 114: 93-110. (Pubitemid 16022488)
25. Kvitek DJ, Will JL, Gasch AP. 2008. Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4: e1000223. doi: 10.1371/journal.pgen.1000223.
26. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654. (Pubitemid 21896661)
27. Mortimer RK, Romano P, Suzzi G, Polsinelli M. 1994. Genome renewal: A new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast 10: 1543-1552.
28. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
29. R Development Core Team. 2009. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
30. Rockman MV, Kruglyak L. 2006. Genetics of global gene expression. Nat Rev Genet 7: 862-872.
31. Ronald J, Akey JM. 2007. The evolution of gene expression QTL in Saccharomyces cerevisiae. PLoS One 2: e678. doi: 10.1371/journal.pone.0000678.
32. Ronald J, Brem RB, Whittle J, Kruglyak L. 2005. Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25. doi: 10.1371/journal.pgen.0010025.
33. Seoighe C, Nembaware V, Scheffler K. 2006. Maximum likelihood inference of imprinting and allele-specific expression from EST data. Bioinformatics 22: 3032-3039. (Pubitemid 44884078)
34. Springer NM, Stupar RM. 2007. Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19: 2391-2402.
35. Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34: D535-D539.
36. Sung H-M, Wang T-Y, Wang D, Huang Y-S, Wu J-P, Tsai H-K, Tzeng J, Huang C-J, Lee Y-C, Yang P, et al. 2009. Roles of trans and cis variation in yeast intraspecies evolution of gene expression.Mol Biol Evol 26: 2533-2538.
37. Tirosh I, Reikhav S, Levy AA, Barkai N. 2009. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324: 659-662.
38. Tu Y, Stolovitzky G, Klein U. 2002. Quantitative noise analysis for gene expression microarray experiments. Proc Natl Acad Sci 99: 14031-14036. (Pubitemid 35257619)
39. Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5: 247-252.
40. Wang D, Sung H-M, Wang T-Y, Huang C-J, Yang P, Chang T, Wang Y-C, Tseng D-L, Wu J-P, Lee T-C, et al. 2007. Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Res 17: 1161-1169.
41. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG. 2008. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 3: e3839. doi: 10.1371/journal.pone.0003839.
42. Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61. (Pubitemid 47373776)
43. Warton DI, Wright IJ, Falster DS, Westoby M. 2006. Bivariate line-fitting methods for allometry. Biol Rev Camb Philos Soc 81: 259-291.
44. Wittkopp PJ, Haerum BK, Clark AG. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
45. Wittkopp PJ, Haerum BK, Clark AG. 2008. Regulatory changes underlying expression differences within and between Drosophila species. Nat Genet 40: 346-350.
46. Yang Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556. (Pubitemid 27480216)
47. Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591. (Pubitemid 47236688)
48. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L. 2003. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57-64. (Pubitemid 37048596)
49. Zhang Z, Schwartz S, Wagner L, Miller W2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.