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Natural variation of gene models in Drosophila melanogaster.

Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV - BMC Genomics (2015)

Bottom Line: Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects.The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences.To our knowledge, this is the first sQTL mapping study in Drosophila.

View Article: PubMed Central - PubMed

Affiliation: University of Southern California, Los Angeles, CA, USA. kurmanga@usc.edu.

ABSTRACT

Background: Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns.

Results: Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments.

Conclusions: Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila.

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Genotype-specific transcriptomes. a: Common reference design. 81 inbred lines, which were derived from natural populations (natural lines), were crossed with one common line (tester line). Each heterozygous F1-hybrid had the same tester allele (green bars) and variable natural allele (dark blue bars). Transcriptomes of these F1-hybrids were sequenced and used to annotate and quantify genotype-specific splicing patterns. b: Annotation and quantification of alternative splicing events. We focused on two most common types of alternative splicing events, namely, alternative donor/acceptor sites and cassette exons. The counts of inclusion (i) and exclusion (e) junction reads were used to quantify each alternative splicing event in each F1-hybrid. Ψ-value represented fraction of the longer isoform among two alternate transcripts.
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Fig1: Genotype-specific transcriptomes. a: Common reference design. 81 inbred lines, which were derived from natural populations (natural lines), were crossed with one common line (tester line). Each heterozygous F1-hybrid had the same tester allele (green bars) and variable natural allele (dark blue bars). Transcriptomes of these F1-hybrids were sequenced and used to annotate and quantify genotype-specific splicing patterns. b: Annotation and quantification of alternative splicing events. We focused on two most common types of alternative splicing events, namely, alternative donor/acceptor sites and cassette exons. The counts of inclusion (i) and exclusion (e) junction reads were used to quantify each alternative splicing event in each F1-hybrid. Ψ-value represented fraction of the longer isoform among two alternate transcripts.

Mentions: We analyzed a panel of RNA-seq datasets from 81 D. melanogaster heterozygotes with known genotypes [Lehmann et al., manuscript submitted]. The flies were crossbred following a common reference design [16], such that multiple inbred strains from natural populations (natural lines) were crossed with a single common tester strain (w[1118]). The resulting transcriptomes of F1-hybrids were subsequently sequenced (Figure 1a, see Methods). The measurement of allelic imbalance in a splicing patterns allowed us to partition cis- and trans- genetic effects ([16], see below). In total, the dataset consisted of 800 million uniquely mapped paired-end RNA-Seq reads. The total coverage varied from 1.3 to 41 million reads per genotype (Additional file 1: Table S1).Figure 1


Natural variation of gene models in Drosophila melanogaster.

Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV - BMC Genomics (2015)

Genotype-specific transcriptomes. a: Common reference design. 81 inbred lines, which were derived from natural populations (natural lines), were crossed with one common line (tester line). Each heterozygous F1-hybrid had the same tester allele (green bars) and variable natural allele (dark blue bars). Transcriptomes of these F1-hybrids were sequenced and used to annotate and quantify genotype-specific splicing patterns. b: Annotation and quantification of alternative splicing events. We focused on two most common types of alternative splicing events, namely, alternative donor/acceptor sites and cassette exons. The counts of inclusion (i) and exclusion (e) junction reads were used to quantify each alternative splicing event in each F1-hybrid. Ψ-value represented fraction of the longer isoform among two alternate transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373058&req=5

Fig1: Genotype-specific transcriptomes. a: Common reference design. 81 inbred lines, which were derived from natural populations (natural lines), were crossed with one common line (tester line). Each heterozygous F1-hybrid had the same tester allele (green bars) and variable natural allele (dark blue bars). Transcriptomes of these F1-hybrids were sequenced and used to annotate and quantify genotype-specific splicing patterns. b: Annotation and quantification of alternative splicing events. We focused on two most common types of alternative splicing events, namely, alternative donor/acceptor sites and cassette exons. The counts of inclusion (i) and exclusion (e) junction reads were used to quantify each alternative splicing event in each F1-hybrid. Ψ-value represented fraction of the longer isoform among two alternate transcripts.
Mentions: We analyzed a panel of RNA-seq datasets from 81 D. melanogaster heterozygotes with known genotypes [Lehmann et al., manuscript submitted]. The flies were crossbred following a common reference design [16], such that multiple inbred strains from natural populations (natural lines) were crossed with a single common tester strain (w[1118]). The resulting transcriptomes of F1-hybrids were subsequently sequenced (Figure 1a, see Methods). The measurement of allelic imbalance in a splicing patterns allowed us to partition cis- and trans- genetic effects ([16], see below). In total, the dataset consisted of 800 million uniquely mapped paired-end RNA-Seq reads. The total coverage varied from 1.3 to 41 million reads per genotype (Additional file 1: Table S1).Figure 1

Bottom Line: Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects.The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences.To our knowledge, this is the first sQTL mapping study in Drosophila.

View Article: PubMed Central - PubMed

Affiliation: University of Southern California, Los Angeles, CA, USA. kurmanga@usc.edu.

ABSTRACT

Background: Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns.

Results: Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments.

Conclusions: Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila.

Show MeSH