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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Available from: Rita Marie Graze, Sep 29, 2015
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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
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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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    Genome Biology and Evolution 04/2014; 6(4). DOI:10.1093/gbe/evu060 · 4.23 Impact Factor
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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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    Genetics 01/2014; 196(3). DOI:10.1534/genetics.114.161232 · 5.96 Impact Factor
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