Regulatory changes underlying expression differences within and between Drosophila species.

PubWeight™: 3.24‹?› | Rank: Top 1%

🔗 View Article (PMID 18278046)

Published in Nat Genet on February 17, 2008

Authors

Patricia J Wittkopp1, Belinda K Haerum, Andrew G Clark

Author Affiliations

1: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA. wittkopp@umich.edu

Articles citing this

(truncated to the top 100)

Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet (2008) 5.78

The genomic basis of adaptive evolution in threespine sticklebacks. Nature (2012) 5.20

The loci of evolution: how predictable is genetic evolution? Evolution (2008) 4.31

Species-specific transcription in mice carrying human chromosome 21. Science (2008) 4.03

Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science (2009) 2.77

Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res (2010) 2.69

Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet (2011) 2.60

Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A (2012) 2.20

Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet (2008) 2.09

Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet (2012) 1.79

Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A (2010) 1.75

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol (2009) 1.72

Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol (2010) 1.67

Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression. Proc Natl Acad Sci U S A (2008) 1.67

Natural selection on cis and trans regulation in yeasts. Genome Res (2010) 1.65

Cryptic variation between species and the basis of hybrid performance. PLoS Biol (2010) 1.64

Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics (2009) 1.58

MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol (2011) 1.57

Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol (2008) 1.53

High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol (2008) 1.52

Allele-specific expression assays using Solexa. BMC Genomics (2009) 1.41

Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics (2009) 1.40

Enhancer Runaway and the Evolution of Diploid Gene Expression. PLoS Genet (2015) 1.39

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res (2013) 1.35

Genetic architecture of regulatory variation in Arabidopsis thaliana. Genome Res (2011) 1.32

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol (2010) 1.30

Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet (2013) 1.29

Speciation genetics: current status and evolving approaches. Philos Trans R Soc Lond B Biol Sci (2010) 1.28

Complex genetic interactions underlying expression differences between Drosophila races: analysis of chromosome substitutions. Proc Natl Acad Sci U S A (2008) 1.28

Expression quantitative trait loci: present and future. Philos Trans R Soc Lond B Biol Sci (2013) 1.20

Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol (2009) 1.20

Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res (2010) 1.16

Chromatin regulators as capacitors of interspecies variations in gene expression. Mol Syst Biol (2010) 1.14

Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression. Evolution (2010) 1.13

Evolution of transcription networks--lessons from yeasts. Curr Biol (2010) 1.12

Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance. PLoS Genet (2012) 1.07

RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biol Evol (2013) 1.07

The genetic basis of rapidly evolving male genital morphology in Drosophila. Genetics (2011) 1.07

Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet (2012) 1.07

The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res (2009) 1.06

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos Trans R Soc Lond B Biol Sci (2013) 1.06

Evolutionary principles of modular gene regulation in yeasts. Elife (2013) 1.05

Tempo and mode of regulatory evolution in Drosophila. Genome Res (2014) 1.05

Tempo and mode in evolution of transcriptional regulation. PLoS Genet (2012) 1.05

A closer look at the eve stripe 2 enhancers of Drosophila and Themira. PLoS Genet (2008) 1.04

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat Commun (2012) 1.03

Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity (Edinb) (2011) 1.03

Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids. Proc Natl Acad Sci U S A (2008) 1.03

Faster-X evolution of gene expression in Drosophila. PLoS Genet (2012) 1.01

Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep (2012) 1.00

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Mol Syst Biol (2012) 0.99

Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol (2012) 0.99

The genetic basis of evolutionary change in gene expression levels. Philos Trans R Soc Lond B Biol Sci (2010) 0.97

The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Res (2013) 0.95

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers. Nat Commun (2010) 0.94

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol (2012) 0.93

An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. PLoS Genet (2012) 0.93

Candida glabrata PHO4 is necessary and sufficient for Pho2-independent transcription of phosphate starvation genes. Genetics (2009) 0.93

Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet (2012) 0.92

Fungal regulatory evolution: cis and trans in the balance. FEBS Lett (2009) 0.91

A genomic bias for genotype-environment interactions in C. elegans. Mol Syst Biol (2012) 0.90

Evolution of splicing regulatory networks in Drosophila. Genome Res (2014) 0.90

The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genet (2015) 0.89

Intra-specific regulatory variation in Drosophila pseudoobscura. PLoS One (2013) 0.89

Genetic influences on translation in yeast. PLoS Genet (2014) 0.89

Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae. Genome Biol Evol (2012) 0.89

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol (2008) 0.89

The ontogeny of color: developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evol Dev (2012) 0.88

Cis-regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans. Dev Dyn (2009) 0.88

Gene duplication and the genome distribution of sex-biased genes. Int J Evol Biol (2011) 0.87

Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Mol Biol Evol (2009) 0.87

Variable transcription factor binding: a mechanism of evolutionary change. PLoS Biol (2010) 0.86

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics (2012) 0.86

Two types of cis-trans compensation in the evolution of transcriptional regulation. Proc Natl Acad Sci U S A (2011) 0.85

The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. BMC Evol Biol (2009) 0.85

Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol (2011) 0.85

Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes. Genome Biol (2010) 0.85

Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PLoS Genet (2014) 0.85

Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana. Mol Biol Evol (2014) 0.84

Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. Genome Biol Evol (2016) 0.84

Social environment influences the relationship between genotype and gene expression in wild baboons. Philos Trans R Soc Lond B Biol Sci (2013) 0.83

Evolution of cichlid vision via trans-regulatory divergence. BMC Evol Biol (2012) 0.83

Divergence of the yeast transcription factor FZF1 affects sulfite resistance. PLoS Genet (2012) 0.83

The Genetic Basis of Pigmentation Differences Within and Between Drosophila Species. Curr Top Dev Biol (2016) 0.82

Allelic expression changes in Medaka (Oryzias latipes) hybrids between inbred strains derived from genetically distant populations. PLoS One (2012) 0.82

Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaoundé Cameroon. Mol Ecol (2014) 0.82

Cis-regulatory variation is typically polyallelic in Drosophila. Genetics (2008) 0.81

Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica (2011) 0.81

Partitioning transcript variation in Drosophila: abundance, isoforms, and alleles. G3 (Bethesda) (2011) 0.81

Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae. Plant Physiol (2015) 0.80

Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility. BMC Genomics (2013) 0.80

Evolution and genetic architecture of chromatin accessibility and function in yeast. PLoS Genet (2014) 0.80

Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill). Heredity (Edinb) (2013) 0.80

Allele-specific gene expression in a wild nonhuman primate population. Mol Ecol (2011) 0.80

Gene regulation and speciation in house mice. Genome Res (2016) 0.80

A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate. J Theor Biol (2015) 0.79

Hybrid male sterility and genome-wide misexpression of male reproductive proteases. Sci Rep (2015) 0.79

Robustness of transcriptional regulatory program influences gene expression variability. BMC Genomics (2009) 0.79

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua. Genome Biol Evol (2016) 0.79

Articles by these authors

Finding the missing heritability of complex diseases. Nature (2009) 67.95

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66

Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84

Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38

A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol (2005) 8.32

Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A (2011) 7.36

Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A (2002) 6.95

Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol (2002) 6.44

Genomic scans for selective sweeps using SNP data. Genome Res (2005) 6.43

Evolutionary changes in cis and trans gene regulation. Nature (2004) 6.24

Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08

Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci U S A (2003) 5.77

Recent explosive human population growth has resulted in an excess of rare genetic variants. Science (2012) 5.58

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet (2003) 5.34

Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11

Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci U S A (2008) 4.76

Recent and ongoing selection in the human genome. Nat Rev Genet (2007) 4.62

The functional spectrum of low-frequency coding variation. Genome Biol (2011) 4.42

Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun (2010) 4.39

Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One (2008) 4.03

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics (2004) 3.65

Linkage disequilibrium and the mapping of complex human traits. Trends Genet (2002) 3.38

Dynamic evolution of the innate immune system in Drosophila. Nat Genet (2007) 3.09

Darwinian and demographic forces affecting human protein coding genes. Genome Res (2009) 3.01

Genes regulated by mating, sperm, or seminal proteins in mated female Drosophila melanogaster. Curr Biol (2004) 2.84

Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science (2004) 2.80

Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera. Science (2006) 2.64

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46

Genetic basis of natural variation in D. melanogaster antibacterial immunity. Science (2004) 2.38

Evolution of protein-coding genes in Drosophila. Trends Genet (2008) 2.36

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol (2007) 2.33

Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome. Genetics (2013) 2.17

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet (2010) 2.14

Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics (2003) 2.07

Sperm competitive ability in Drosophila melanogaster associated with variation in male reproductive proteins. Genetics (2004) 2.01

Population genetics: malaria variorum. Nature (2002) 1.97

Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet (2009) 1.97

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics (2005) 1.93

Population genetic structure of the people of Qatar. Am J Hum Genet (2010) 1.91

Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease. PLoS One (2007) 1.89

Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genet Epidemiol (2007) 1.87

Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathog (2007) 1.82

Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics (2003) 1.79

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol Biol Evol (2003) 1.75

The evolutionary costs of immunological maintenance and deployment. BMC Evol Biol (2008) 1.74

Low conservation of gene content in the Drosophila Y chromosome. Nature (2008) 1.72

Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69

Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am J Hum Genet (2003) 1.66

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. Am J Hum Genet (2004) 1.61

Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics (2002) 1.57

Conjuring SNPs to detect associations. Nat Genet (2007) 1.57

Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science (2009) 1.56

A genome-wide approach to identifying novel-imprinted genes. Hum Genet (2007) 1.55

Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet (2009) 1.53

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. BMC Genet (2008) 1.53

Estrogen receptor genotypes and haplotypes associated with breast cancer risk. Cancer Res (2004) 1.52

Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res (2005) 1.51

Impact of microRNA regulation on variation in human gene expression. Genome Res (2012) 1.49

Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go? Genetica (2003) 1.49

Mapping multiple Quantitative Trait Loci by Bayesian classification. Genetics (2004) 1.46

Natural genetic variation in male reproductive genes contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster. Mol Ecol (2012) 1.46

Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics (2008) 1.45

Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster. Genetics (2007) 1.45

Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria. Genetics (2006) 1.44

Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Genetics (2009) 1.42

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet (2011) 1.41

Disentangling the relationship between sex-biased gene expression and X-linkage. Genome Res (2012) 1.40

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res (2005) 1.40

Robustness of inference of haplotype block structure. J Comput Biol (2003) 1.38

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36

Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet (2010) 1.36

Post-mating gene expression profiles of female Drosophila melanogaster in response to time and to four male accessory gland proteins. Genetics (2008) 1.33

Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res (2012) 1.31

Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations. PLoS Genet (2012) 1.31

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res (2004) 1.28

Genetic incompatibilities are widespread within species. Nature (2013) 1.28

Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. Mol Biol Evol (2003) 1.27

Larval rearing environment affects several post-copulatory traits in Drosophila melanogaster. Biol Lett (2007) 1.27

Rehabilitation and the single cell. Curr Opin Cell Biol (2006) 1.26

Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A (2013) 1.25

Genes involved in convergent evolution of eusociality in bees. Proc Natl Acad Sci U S A (2011) 1.24

A survey for novel imprinted genes in the mouse placenta by mRNA-seq. Genetics (2011) 1.24

Gene-based testing of interactions in association studies of quantitative traits. PLoS Genet (2013) 1.23

Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand. Proc Natl Acad Sci U S A (2003) 1.23

Contributions of 18 additional DNA sequence variations in the gene encoding apolipoprotein E to explaining variation in quantitative measures of lipid metabolism. Am J Hum Genet (2002) 1.22

The resolution of sexual antagonism by gene duplication. Genetics (2011) 1.18

Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect. Genetics (2013) 1.17

Contrasting the efficacy of selection on the X and autosomes in Drosophila. Mol Biol Evol (2007) 1.16

Mining genetic epidemiology data with Bayesian networks application to APOE gene variation and plasma lipid levels. J Comput Biol (2005) 1.15

Function and evolution of DNA methylation in Nasonia vitripennis. PLoS Genet (2013) 1.14