Sat, 05 Jul 2008 12:23:19 BST CiteULike: dpollard's variation http://www.citeulike.org/user/dpollard/tag/variation CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/dpollard/article/2318101 <i>Pac Symp Biocomput (2008), pp. 489-500.</i><br /><br />The identification of transcription factor binding sites commonly relies on the interpretation of scores generated by a position weight matrix. These scores are presumed to reflect on the affinity of the transcription factor for the bound sequence. In almost all applications, a cutoff score is chosen to distinguish between functional and non-functional binding sites. This cutoff is generally based on statistical rather than biological criteria. Furthermore, given the variety of transcription factors, it is unlikely that the use of a common statistical threshold for all transcription factors is appropriate. In order to incorporate biological information into the choice of cutoff score, we developed a simple evolutionary model that assumes that transcription factor binding sites evolve to maintain an affinity greater than some factor-specific threshold. We then compared patterns of substitution in binding sites predicted by this model at different thresholds to patterns of substitution observed at sites bound in vivo by transcription factors in S. cerevisiae. Assuming that the cutoff value that gives the best fit between the observed and predicted values will optimally distinguish functional and non-functional sites, we discovered substantial heterogeneity for appropriate cutoff values among factors. While commonly used thresholds seem appropriate for many factors, some factors appear to function at cutoffs satisfied commonly in the genome. This evidence was corroborated by local patterns of rate variation for examples of stringent and lenient p-value cutoffs. Our analysis further highlights the necessity of taking a factor-specific approach to binding site identification. Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. RW Lusk MB Eisen Pac Symp Biocomput (2008), pp. 489-500. 2008-02-01T06:17:57-00:00 2008 Pac Symp Biocomput 1793-5091 489 500 affinity binding_site transcription_factor variation yeast http://www.citeulike.org/user/dpollard/article/899366 <i>Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419.</i><br /><br />Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating. 10.1093/molbev/msg140 The Evolution of Transcriptional Regulation in Eukaryotes Gregory Wray Matthew Hahn Ehab Abouheif James Balhoff Margaret Pizer Matthew Rockman Laura Romano doi:10.1093/molbev/msg140 Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419. 2006-10-16T14:20:09-00:00 2003 Mol Biol Evol 20 9 1377 1419 cis_regulatory_elements regulatory_evolution review variation http://www.citeulike.org/user/dpollard/article/1110638 <i>Nature Reviews Genetics, Vol. 8, No. 3., pp. 206-216.</i> The evolutionary significance of cis-regulatory mutations Gregory Wray doi:10.1038/nrg2063 Nature Reviews Genetics, Vol. 8, No. 3., pp. 206-216. 2007-02-17T21:01:11-00:00 Nature Reviews Genetics 1471-0056 8 3 206 216 Nature Publishing Group cis_regulatory_elements polymorphism regulatory_evolution review variation http://www.citeulike.org/user/dpollard/article/1187466 <i>Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1341-1350.</i><br /><br />We investigated patterns of rate asymmetry in sequence evolution among the gene pairs (ohnologs) formed by whole-genome duplication (WGD) in yeast species. By comparing three species (Saccharomyces cerevisiae, Candida glabrata, and S. castellii) that underwent WGD to a nonduplicated outgroup (Kluyveromyces lactis), and by using a synteny framework to establish orthology and paralogy relationships at each duplicated locus, we show that 56% of ohnolog pairs show significantly asymmetric protein sequence evolution. For ohnolog pairs that remain duplicated in two species there is a strong tendency for the faster-evolving copy in one species to be orthologous to the faster copy in the other species, which indicates that the evolutionary rate differences were established before speciation and hence soon after the WGD. We also present evidence that in cases where one ohnolog has been lost from the genome of a post-WGD species, the lost copy was likely to have been the faster-evolving member of the pair prior to its loss. These results suggest that a significant fraction of the retained ohnologs in yeast species underwent neofunctionalization soon after duplication. 10.1534/genetics.106.066951 Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication Kevin Byrne Kenneth Wolfe doi:10.1534/genetics.106.066951 Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1341-1350. 2007-03-26T07:00:17-00:00 2007 Genetics 175 3 1341 1350 duplication gene genome rate turnover variation http://www.citeulike.org/user/dpollard/article/1181237 <i>PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e57.</i><br /><br />Recent analyses indicate that differences in protein concentrations are only 20%–40% attributable to variable mRNA levels, underlining the importance of posttranscriptional regulation. Generally, protein concentrations depend on the translation rate (which is proportional to the translational activity, TA) and the degradation rate. By integrating 12 publicly available large-scale datasets and additional database information of the yeast Saccharomyces cerevisiae, we systematically analyzed five factors contributing to TA: mRNA concentration, ribosome density, ribosome occupancy, the codon adaptation index, and a newly developed “tRNA adaptation index.” Our analysis of the functional relationship between the TA and measured protein concentrations suggests that the TA follows Michaelis–Menten kinetics. The calculated TA, together with measured protein concentrations, allowed us to estimate degradation rates for 4,125 proteins under standard conditions. A significant correlation to recently published degradation rates supports our approach. Moreover, based on a newly developed scoring system, we identified and analyzed genes subjected to the posttranscriptional regulation mechanism, translation on demand. Next we applied these findings to publicly available data of protein and mRNA concentrations under four stress conditions. The integration of these measurements allowed us to compare the condition-specific responses at the posttranscriptional level. Our analysis of all 62 proteins that have been measured under all four conditions revealed proteins with very specific posttranscriptional stress response, in contrast to more generic responders, which were nonspecifically regulated under several conditions. The concept of specific and generic responders is known for transcriptional regulation. Here we show that it also holds true at the posttranscriptional level. Posttranscriptional Expression Regulation: What Determines Translation Rates? Regina Brockmann Andreas Beyer Jürgen Heinisch Thomas Wilhelm doi:10.1371/journal.pcbi.0030057 PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e57. 2007-03-23T00:26:32-00:00 2007 PLoS Computational Biology 3 3 e57 translation_rate variation http://www.citeulike.org/user/dpollard/article/904109 <i>Nature Reviews Genetics, Vol. 7, No. 11., pp. 862-872.</i> Genetics of global gene expression Matthew Rockman Leonid Kruglyak doi:10.1038/nrg1964 Nature Reviews Genetics, Vol. 7, No. 11., pp. 862-872. 2006-10-18T20:14:27-00:00 Nature Reviews Genetics 1471-0056 7 11 862 872 Nature Publishing Group association_mapping eisen_journal_club eqtl gene_expression in_depth qtl variation http://www.citeulike.org/user/dpollard/article/766707 <i>Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633.</i><br /><br />Studies of evolutionary conservation of gene regulatory signals have led to a paradox: extensive sequence similarity implies functional conservation in non-coding regions across mammalian species; however, this stands in contrast to our understanding of transcriptional regulatory sites composed of degenerate recognition sequences for transcription factors that can maintain functional equivalence despite considerable sequence divergence. The latter observation provides an explanation for the rapid evolution of new traits through the gain and loss of transcription factor binding sites that bring new genes under the control of an existing genetic regulatory network. The former observation might point to novel mechanisms of gene regulation and/or chromosome function that are currently unappreciated. Recent comparative genome analysis has highlighted extensive conserved sequences in mammalian genomes that are beginning to be functionally characterized. Conserved sequences and the evolution of gene regulatory signals. MD Adams doi:10.1016/j.gde.2005.09.004 Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633. 2006-07-20T15:00:35-00:00 2005 Curr Opin Genet Dev 0959-437X 15 6 628 633 binding_site evolution regulatory_sequence transcription_factor turnover variation http://www.citeulike.org/user/dpollard/article/767600 <i>Heredity, Vol. aop, No. current.</i> Evolution of cis-regulatory sequence and function in Diptera PJ Wittkopp doi:10.1038/sj.hdy.6800869 Heredity, Vol. aop, No. current. 2006-07-20T21:55:39-00:00 Heredity 0018-067X aop current Nature Publishing Group evolution prediction regulatory_sequence structure variation http://www.citeulike.org/user/dpollard/article/975260 <i>Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 559-564.</i><br /><br />The focus of large genomic studies has shifted from only looking at genes and protein-coding sequences to exploring the full set of elements in each genome. The explosion of comparative sequencing data has led to an increase in methodologies, approaches and ideas on how to analyze the unknown fraction of the genome, namely the non-protein-coding fraction. The main issues relate to the discovery, evolutionary analysis and natural variation of non-coding DNA, and the parameters that prevent us from fully understanding the properties of non-coding DNA. Functional variation and evolution of non-coding DNA Christine Bird Barbara Stranger Emmanouil Dermitzakis doi:10.1016/j.gde.2006.10.003 Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 559-564. 2006-12-05T12:49:53-00:00 2006 Current Opinion in Genetics & Development 16 6 559 564 evolution noncoding_dna regulatory_sequence variation http://www.citeulike.org/user/dpollard/article/1097547 <i>Genetics (4 February 2007)</i><br /><br />Currently, the relevance of common genetic variants--particularly those significantly associated with phenotypic variation in laboratory studies--to standing phenotypic variation in the wild is poorly understood. To address this, we quantified the relationship between achaete-scute complex (ASC) polymorphisms and Drosophila bristle number phenotypes in several new population samples. MC22 is a biallelic, nonrepetitive length polymorphism 97 bp downstream of the scute transcript. It has been previously shown to be associated with sternopleural bristle number variation in both sexes in a set of isogenic lines. We replicated this association in a large cohort of wild-caught Drosophila melanogaster. We also detected a significant association at MC22 in an outbred population maintained under laboratory conditions for ~25 years, but the phenotypic effects in this sample were opposite from the direction estimated in the initial study. Finally, no significant associations were detected in a second large wild-caught cohort, or in a set of 134 Nearly Isogenic Lines. Our ability to repeat the initial association in wild samples suggests that it was not spurious. Nevertheless, inconsistent results from the other three panels suggest the relationship between polymorphic genetic markers and loci contributing to continuous variation is not a simple one. How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila? Jonathan D Gruber Anne Genissel Stuart J Macdonald Anthony D Long doi:10.1534/genetics.106.067108 Genetics (4 February 2007) 2007-02-10T01:26:04-00:00 2007 Genetics 0016-6731 association bristle polymorphism variation http://www.citeulike.org/user/dpollard/article/903958 <i>Genetics (8 October 2006)</i><br /><br />Selection, recombination and the demographic history of a species can all have profound effects on genome wide patterns of variability. To assess the impact of these forces in the genome of Drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. In accordance with recent findings in D. melanogaster, we find that non-coding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in non- coding DNA is significantly skewed towards rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most non-coding DNA is functionally constrained and evolving under purifying selection. However, in contrast to findings in the D. melanogaster species group, we find little evidence of adaptive evolution acting on either coding or non-coding sequences in D. miranda. Levels of linkage disequilibrium (LD) in D. miranda are comparable to those observed in D. melanogaster, but vary considerably among chromosomes. These patterns suggest a significantly lower rate of recombination on autosomes, possibly due to the presence of polymorphic autosomal inversions and/or differences in chromosome sizes. All chromosomes show significant departures from the standard neutral model, including too much heterogeneity in synonymous site polymorphism relative to divergence among loci and a general excess of rare synonymous polymorphisms. These departures from neutral equilibrium expectations are discussed in the context of non-equilibrium models of demography and selection. Selection, recombination and demographic history in Drosophila miranda. Doris Bachtrog Peter Andolfatto doi:10.1534/genetics.106.062760 Genetics (8 October 2006) 2006-10-18T19:01:44-00:00 2006 Genetics 0016-6731 adaptive demography drosophila polymorphism protein recombination selection variation http://www.citeulike.org/user/dpollard/article/846056 <i>BMC Genomics, Vol. 7 (15 September 2006), 235.</i> Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations Debraj Guhathakurta Tao Xie Manish Anand Stephen Edwards Guoya Li Susana Wang Eric Schadt doi:10.1186/1471-2164-7-235 BMC Genomics, Vol. 7 (15 September 2006), 235. 2006-09-15T23:18:54-00:00 2006 BMC Genomics 1471-2164 7 235 cis gene linkage mouse noncoding polymorphism regulation variation http://www.citeulike.org/user/dpollard/article/831971 <i>Genome Res, Vol. 16, No. 9. (September 2006), pp. 1182-1190.</i><br /><br />Although many studies have been conducted to identify single nucleotide polymorphisms (SNPs) in humans, few studies have been conducted to identify alternative forms of natural genetic variation, such as insertion and deletion (INDEL) polymorphisms. In this report, we describe an initial map of human INDEL variation that contains 415,436 unique INDEL polymorphisms. These INDELs were identified with a computational approach using DNA re-sequencing traces that originally were generated for SNP discovery projects. They range from 1 bp to 9989 bp in length and are split almost equally between insertions and deletions, relative to the chimpanzee genome sequence. Five major classes of INDELs were identified, including (1) insertions and deletions of single-base pairs, (2) monomeric base pair expansions, (3) multi-base pair expansions of 2-15 bp repeat units, (4) transposon insertions, and (5) INDELs containing random DNA sequences. Our INDELs are distributed throughout the human genome with an average density of one INDEL per 7.2 kb of DNA. Variation hotspots were identified with up to 48-fold regional increases in INDEL and/or SNP variation compared with the chromosomal averages for the same chromosomes. Over 148,000 INDELs (35.7%) were identified within known genes, and 5542 of these INDELs were located in the promoters and exons of genes, where gene function would be expected to be influenced the greatest. All INDELs in this study have been deposited into dbSNP and have been integrated into maps of human genetic variation that are available to the research community. An initial map of insertion and deletion (INDEL) variation in the human genome. Ryan E Mills Christopher T Luttig Christine E Larkins Adam Beauchamp Circe Tsui W Stephen Pittard Scott E Devine doi:10.1101/gr.4565806 Genome Res, Vol. 16, No. 9. (September 2006), pp. 1182-1190. 2006-09-06T00:04:06-00:00 2006 Genome Res 1088-9051 16 9 1182 1190 human indel polymorphism variation http://www.citeulike.org/user/dpollard/article/758009 <i>Mol Biol Evol (5 June 2006)</i><br /><br />We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative methods of estimating selection. Here, we introduce a simple regression technique for estimating selection pressures on all proteins in a genome, on the basis of limited comparative data. The regression technique does not depend on an underlying population-genetic mechanism. This new approach to estimating selection across a genome should be more powerful and more widely applicable than volatility itself. Estimating Selection Pressures from Limited Comparative Data. Joshua B Plotkin Jonathan Dushoff Michael M Desai Hunter B Fraser doi:10.1093/molbev/msl021 Mol Biol Evol (5 June 2006) 2006-07-13T18:09:16-00:00 2006 Mol Biol Evol 0737-4038 evolution gene method selection variation http://www.citeulike.org/user/dpollard/article/698685 <i>Mamm Genome (12 June 2006)</i><br /><br />Gene expression variation has been the focus of many studies in the past few years. The relevance of gene regulation and gene expression to disease and the development of the technologies used to screen large numbers of genes simultaneously have allowed this rapid development. In this review we discuss issues relating to the biological information one obtains from such studies and the biological significance and use of signals from mapping of gene expression variation. Genetic variation in human gene expression. Emmanouil Dermitzakis Barbara Stranger doi:10.1007/s00335-006-0005-y Mamm Genome (12 June 2006) 2006-06-16T19:59:51-00:00 2006 Mamm Genome 0938-8990 expression gene review variation http://www.citeulike.org/user/dpollard/article/691433 <i>Mol Biol Evol (5 June 2006)</i><br /><br />Nucleotide sequence polymorphisms affecting gene expression occur in the regulatory region of genes (in cis) and elsewhere in the genome (in trans). Further study is required to weight the relative importance of cis- and trans-acting mutations in mediating gene expression differences within and between species. Here, microarray hybridization experiments were used to isolate 363 gene expression differences between the female fly head transcriptomes of two D. melanogaster strains. One strain (French) represented the Cosmopolitan M mating race and the other strain (ZS30) represented the Z mating race derived from Zimbabwe, Africa. From chromosomal substitution strains engineered from the two strains we inferred that the expression differences between M and Z alleles largely could be attributed to the genotype of the chromosomes where the differentially expressed genes were located, i.e. cis-regulatory polymorphisms prominently influence gene expression differences between M and Z. The effects of trans-regulatory polymorphisms were apparent yet difficult to quantify. Results have implications for models of gene regulatory evolution as well as experimental studies trying to identify the nucleotide sequence polymorphisms underlying gene expression differences between Drosophila strains. Genomic Inferences of the cis-Regulatory Nucleotide Polymorphisms Underlying Gene Expression Differences between Drosophila melanogaster Mating Races. Naoki Osada Michael H Kohn Chung-I Wu doi:10.1093/molbev/msl023 Mol Biol Evol (5 June 2006) 2006-06-09T21:42:11-00:00 2006 Mol Biol Evol 0737-4038 drosophila evolution expression polymorphism promoter speciation variation http://www.citeulike.org/user/dpollard/article/691427 <i>Mol Biol Evol (6 June 2006)</i><br /><br />The Dobzhansky-Muller model denotes incompatible gene interactions between diverging populations/species and is recognized as the basis of post-zygotic reproductive isolation. Little is known about the molecular nature of such gene interactions. We have carried out comparative gene expression analyses in the testes of three closely related species of the Drosophila melanogaster subgroup and their hybrids (all of which are sterile). We show that in hybrids: (i) a higher proportion of male-biased genes (i.e. genes with a higher level of expression in males) are under-expressed (or not expressed) compared to non-sex-biased genes, (ii) the majority of the under-expressed genes in hybrids appear to be under stabilizing selection by virtue of showing similar levels of expression in the parental species; only a small proportion of genes show signs of directional selection, (iii) very few of the misexpressed genes are shared between species-pairs suggesting that there may not be a common set of "speciation genes", and (iv) Expression of non-testes-specific genes is observed in the testes of interspecific hybrids, and the number of such genes is positively correlated with divergence time. These results suggest that gene regulation divergence of sex- and reproduction-related genes is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila. Gene Regulation Divergence is a Major Contributor to the Evolution of Dobzhansky-Muller Incompatibilities between Species of Drosophila. Wilfried Haerty Rama S Singh Mol Biol Evol (6 June 2006) 2006-06-09T21:27:17-00:00 2006 Mol Biol Evol 0737-4038 drosophila expression speciation variation http://www.citeulike.org/user/dpollard/article/579646 <i>Genetics (2 April 2006)</i><br /><br />When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino-acid divergence due to adaptive evolution - a statistic denoted _bar. But such tests are subject to many biases. Most serious is the possibility that high estimates of _bar reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of _bar from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely-used estimators, and assessing the power of the methods. As part of this process, a new maximum likelihood estimator is introduced. This estimator is applied to a newly compiled dataset of 115 genes from Drosophila simulans, each with each orthologues from D. melanogaster and D. yakuba. In this way, it is estimated that _bar 0.4 +/- 0.1, a value that does not vary substantially between different loci, or over different periods of divergence. The implications of these results are discussed. Estimating the genome-wide rate of adaptive protein evolution in Drosophila. John J Welch doi:10.1534/genetics.106.056911 Genetics (2 April 2006) 2006-04-07T17:57:03-00:00 2006 Genetics 0016-6731 adaptive drosophila evolution gene variation http://www.citeulike.org/user/dpollard/article/572007 <i>Genetics (17 March 2006)</i><br /><br />Fluctuations in base composition appear to be prevalent in Drosophila and mammal genome evolution, but their time-scale, genomic breadth, and causes remain obscure. Here, we study base composition evolution within the X chromosomes of Drosophila melanogaster and five of its close relatives. Substitutions were inferred for 14 telomeric and nine non-telomeric X chromosome loci on six extant and two ancestral lineages using a maximum likelihood method. Heterogeneity in GC content evolution is highly localized both within the genome and within the phylogenetic tree. In the lineages leading to D. yakuba and D. orena, GC content at silent sites is increasing rapidly near telomeres, but is decreasing in more proximal (non-telomeric) regions. D. orena shows a 17-fold excess of GC-increasing synonymous changes within a small (~130kb) telomeric region. Intron GC content increases are consistent with fluctuations in mutational processes, but greater GC elevation at synonymous sites suggest contributions of biased gene conversion and/or natural selection. The D. yakuba lineage shows a less extreme elevation of GC content distributed over a wider genetic region (~1.2Mb). A lack of change in GC content for most introns within this region suggests a role of natural selection in regional base composition evolution. Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome. Wen-Ya Ko Shengfu Piao Hiroshi Akashi doi:10.1534/genetics.105.054346 Genetics (17 March 2006) 2006-03-31T22:48:36-00:00 2006 Genetics 0016-6731 base composition drosophila evolution gene nonstationary rate reconstruction tree variation http://www.citeulike.org/user/dpollard/article/447368 <i>Nature (21 December 2005)</i> Origins of extrinsic variability in eukaryotic gene expression Dmitri Volfson Jennifer Marciniak William Blake Natalie Ostroff Lev Tsimring Jeff Hasty doi:10.1038/nature04281 Nature (21 December 2005) 2005-12-22T22:43:36-00:00 2005 Nature 0028-0836 Nature Publishing Group expression extrinsic gene noise variation yeast http://www.citeulike.org/user/dpollard/article/559089 <i>Gene, Vol. 366, No. 2. (1 February 2006), pp. 343-351.</i><br /><br />One of the most important aspects of the evolution of development and physiology is the interplay between gene expression and the environment, by which traits become altered in response to environmental triggers. This feature is known as phenotypic plasticity. When different genotypes show different levels of plasticity for a trait, then they show genotype-by-environment interaction, or GEI. It is now clear that gene expression plays an important role in organismic-level phenotypic plasticity, but we know very little about whether gene expression itself is subject to genetic variation for phenotypic plasticity (GEI). Given that gene regulation is likely to have evolved to respond to environmental changes, it is of central importance to understand how environmental and genetic variation interact to produce variation in gene expression. Here we investigate genetic variation for phenotypic plasticity in the yeast transcriptome for the whole genome. Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions. Using DNA-microarray data and an ANOVA analysis with a stringent criterion of significance, we found significant genetic variation for transcriptional plasticity (GEI) among strains for approximately 5% of the genes in the genome. There are about twice as many genes that show genetic variation for phenotypic plasticity as show genetic variation in transcription level independent of the environment. We also found that genes with genetic variation for plasticity were less likely to be essential and were significantly biased towards genes that have paralogs. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. CR Landry J Oh DL Hartl D Cavalieri doi:10.1016/j.gene.2005.10.042 Gene, Vol. 366, No. 2. (1 February 2006), pp. 343-351. 2006-03-21T19:19:47-00:00 2006 Gene 0378-1119 366 2 343 351 gene genetic multi-copy non-essential placticity transcription variation yeast http://www.citeulike.org/user/dpollard/article/556246 <i></i> PLoS Computational Biology: Differentiating Positive Selection from Acceleration and Relaxation in Human and Chimp 2006-03-17T20:58:05-00:00 adaptive evolution gene rate variation