Partitioning Transcript Variation in Drosophila: Abundance, Isoforms, and Alleles

G3-Genes Genomes Genetics (Impact Factor: 3.2). 11/2011; 1(6):427-36. DOI: 10.1534/g3.111.000596
Source: PubMed


Multilevel analysis of transcription is facilitated by a new array design that includes modules for assessment of differential expression, isoform usage, and allelic imbalance in Drosophila. The ∼2.5 million feature chip incorporates a large number of controls, and it contains 18,769 3' expression probe sets and 61,919 exon probe sets with probe sequences from Drosophila melanogaster and 60,118 SNP probe sets focused on Drosophila simulans. An experiment in D. simulans identified genes differentially expressed between males and females (34% in the 3' expression module; 32% in the exon module). These proportions are consistent with previous reports, and there was good agreement (κ = 0.63) between the modules. Alternative isoform usage between the sexes was identified for 164 genes. The SNP module was verified with resequencing data. Concordance between resequencing and the chip design was greater than 99%. The design also proved apt in separating alleles based upon hybridization intensity. Concordance between the highest hybridization signals and the expected alleles in the genotype was greater than 96%. Intriguingly, allelic imbalance was detected for 37% of 6579 probe sets examined that contained heterozygous SNP loci. The large number of probes and multiple probe sets per gene in the 3' expression and exon modules allows the array to be used in D. melanogaster and in closely related species. The SNP module can be used for allele specific expression and genotyping of D. simulans.

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    • "- additive inheritance . McManus et al . ( 2010 ) also found that regulatory diver - gence contributes to hybrid incompatibilities in hybrids between D . melanogaster and D . sechellia . A custom array has been designed for Drosophila on an Affymetrix plat - form that can be used to detect allele - specific variation in expression within species ( Yang et al . 2011 ) . This array can measure 3′ expression , exon expression ( and , thus , alterna - tive splicing ) , and allelic imbalance . The test on this array showed an amount of sex bias , alternative exon usage , and allelic imbalance ."
    Dataset: JAG-13-Gaur

    Full-text · Dataset · Apr 2015
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    • " . There were a total of 61 , 752 SNP probe sets on the array developed from population geno - mic data ( DPGP , http : / / www . dpgp . org , last accessed April 2 , 2014 ; Begun et al . 2007 ) with 24 probes in each SNP probe set , all four bases , forward and reverse strands are represented for three positions in the probe set ( 0 , +4 , À4 ) ( Yang et . al . 2011 ; Affymetrix array 520726 ) . The SNP alleles were assigned to perfect match 1 ( PM1 ) , perfect match 2 ( PM2 ) , and MM probes . For each cross and probe set combination , if the rese - quencing data ( Begun et al . 2007 ) showed an SNP between the two parents , the PM1 and PM2 probes were assigned to the matching parental alleles ( s"
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    ABSTRACT: The mechanistic basis of regulatory variation and the prevailing evolutionary forces shaping that variation are known to differ between sexes and between chromosomes. Regulatory variation of gene expression can be due to functional changes within a gene itself (cis) or in other genes elsewhere in the genome (trans). The evolutionary properties of cis mutations are expected to differ from mutations affecting gene expression in trans. We analyze allele-specific expression across a set of X substitution lines in intact adult Drosophila simulans to evaluate whether regulatory variation differs for cis and trans, for males and females, and for X-linked and autosomal genes. Regulatory variation is common (56% of genes), and patterns of variation within D. simulans are consistent with previous observations in Drosophila that there is more cis than trans variation within species (47% vs. 25%, respectively). The relationship between sex-bias and sex-limited variation is remarkably consistent across sexes. However, there are differences between cis and trans effects: cis variants show evidence of purifying selection in the sex toward which expression is biased, while trans variants do not. For female-biased genes, the X is depleted for trans variation in a manner consistent with a female-dominated selection regime on the X. Surprisingly, there is no evidence for depletion of trans variation for male-biased genes on X. This is evidence for regulatory feminization of the X, trans-acting factors controlling male-biased genes are more likely to be found on the autosomes than those controlling female-biased genes.
    Full-text · Article · Apr 2014 · Genome Biology and Evolution
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    • "We emphasize three points concerning the interpretation of these variance components. First, the among-line variance for each expression trait from model (1) differs from that commonly estimated for standard quantitative traits because it is based on samples of pooled RNA from 20–30 individuals , an approach commonly used for individually small organisms, such as vinegar flies (Rifkin et al. 2005; Ayroles et al. 2009; Yang et al. 2011). Individuals within an inbred line are assumed to be genetically nearly identical after .15 "
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    ABSTRACT: The nature and extent of mutational pleiotropy remain largely unknown, despite the central role that pleiotropy plays in many areas of biology, including human disease, agricultural production and evolution. Here, we investigate the variation in 11,604 gene expression traits among 41 mutation accumulation (MA) lines of Drosophila serrata. We first confirmed that these expression phenotypes were heritable, detecting genetic variation in 96% of them in an outbred, natural population of D. serrata. Among the MA lines, 3,385 (29%) of expression traits were variable, with a mean mutational heritability of 0.0005. In most traits, variation was generated by mutations of relatively small phenotypic effect; putative mutations with effects of greater than one phenotypic standard deviation were observed for only 8% of traits. With most (71%) traits unaffected by any mutation, our data provide no support for universal pleiotropy. We further characterized mutational pleiotropy in the 3,385 variable traits using sets of five, randomly assigned, traits. Covariance among traits chosen at random with respect to their biological function is only expected if pleiotropy is extensive. Taking an analytical approach in which the variance unique to each trait in the random 5-trait sets was partitioned from variance shared among traits, we detected significant (at 5% FDR) mutational covariance in 21% of sets. This frequency of statistically supported covariance implied that at least some mutations must pleiotropically affect a substantial number of traits (>70; 0.6% of all measured traits).
    Full-text · Article · Jan 2014 · Genetics
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