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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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Related in: MedlinePlus

Allelic imbalance of genotype-specific cassette exon inclusion associated withcis-sQTL (a625). Genotype-specific cassette exon that exhibits strong allelic imbalance is shown. The allele-specific exon/intron coverage of genotype-specific splicing event are shown for the F1-hybrids that carried derived (ad) and ancestral (be) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. The plots were created separately for the reads expressed from natural (ab) and tester alleles (de). Only genotypes with estimated ns-Ψ and ts-Ψ-values were considered. cf: The distributions of ns-Ψ (c) and ts-Ψ-values (c) for alleles of cis-sQTL. g: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms are 231 bp and 102 bp, respectively. For other details see the legend to Figure 2.
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Fig4: Allelic imbalance of genotype-specific cassette exon inclusion associated withcis-sQTL (a625). Genotype-specific cassette exon that exhibits strong allelic imbalance is shown. The allele-specific exon/intron coverage of genotype-specific splicing event are shown for the F1-hybrids that carried derived (ad) and ancestral (be) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. The plots were created separately for the reads expressed from natural (ab) and tester alleles (de). Only genotypes with estimated ns-Ψ and ts-Ψ-values were considered. cf: The distributions of ns-Ψ (c) and ts-Ψ-values (c) for alleles of cis-sQTL. g: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms are 231 bp and 102 bp, respectively. For other details see the legend to Figure 2.

Mentions: The coverage plots and distributions of Ψ-values for allele-specific reads are shown for one of genotype-specific splicing events in Figure 4. In this example, a cis-sQTL was associated with the inclusion of a cassette exon in the 5′-untranslated region of the gene Sod3. Plots were created separately for reads expressed from the natural (natural allele-specific reads, Figure 4, upper panels) and tester alleles (tester allele-specific reads, Figure 4, lower panels). Considerable inclusion of the cassette exon was observed only in transcripts expressed from natural alleles carrying the derived variant of the cis-sQTL (Figure 4a). At the same time, almost no inclusion of the cassette exon was detected in transcripts expressed from tester alleles carrying the ancestral variant of the cis-sQTL from the same F1-hybrids (Figure 4d). As a result, a considerable change in the splicing pattern associated with cis-sQTL is observed only for reads expressed from natural alleles (ns-ΔΨ = 0.49, Figure 4abc), and almost no change is observed for reads expressed from tester alleles (ns-ΔΨ = 0.003, Figure 4def). Strong allelic imbalance in heterozygotes implies that the observed inclusion of the cassette exon is regulated in cis, and that the identified cis-sQTL most likely is the causative regulatory variant. An RT-PCR validation experiment confirmed that observable inclusion of the cassette exon occurred only in flies that carried the derived allele of cis-sQTL (A/D and D/D, Figure 4g).Figure 4


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)

Allelic imbalance of genotype-specific cassette exon inclusion associated withcis-sQTL (a625). Genotype-specific cassette exon that exhibits strong allelic imbalance is shown. The allele-specific exon/intron coverage of genotype-specific splicing event are shown for the F1-hybrids that carried derived (ad) and ancestral (be) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. The plots were created separately for the reads expressed from natural (ab) and tester alleles (de). Only genotypes with estimated ns-Ψ and ts-Ψ-values were considered. cf: The distributions of ns-Ψ (c) and ts-Ψ-values (c) for alleles of cis-sQTL. g: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms are 231 bp and 102 bp, respectively. For other details see the legend to Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Allelic imbalance of genotype-specific cassette exon inclusion associated withcis-sQTL (a625). Genotype-specific cassette exon that exhibits strong allelic imbalance is shown. The allele-specific exon/intron coverage of genotype-specific splicing event are shown for the F1-hybrids that carried derived (ad) and ancestral (be) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. The plots were created separately for the reads expressed from natural (ab) and tester alleles (de). Only genotypes with estimated ns-Ψ and ts-Ψ-values were considered. cf: The distributions of ns-Ψ (c) and ts-Ψ-values (c) for alleles of cis-sQTL. g: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms are 231 bp and 102 bp, respectively. For other details see the legend to Figure 2.
Mentions: The coverage plots and distributions of Ψ-values for allele-specific reads are shown for one of genotype-specific splicing events in Figure 4. In this example, a cis-sQTL was associated with the inclusion of a cassette exon in the 5′-untranslated region of the gene Sod3. Plots were created separately for reads expressed from the natural (natural allele-specific reads, Figure 4, upper panels) and tester alleles (tester allele-specific reads, Figure 4, lower panels). Considerable inclusion of the cassette exon was observed only in transcripts expressed from natural alleles carrying the derived variant of the cis-sQTL (Figure 4a). At the same time, almost no inclusion of the cassette exon was detected in transcripts expressed from tester alleles carrying the ancestral variant of the cis-sQTL from the same F1-hybrids (Figure 4d). As a result, a considerable change in the splicing pattern associated with cis-sQTL is observed only for reads expressed from natural alleles (ns-ΔΨ = 0.49, Figure 4abc), and almost no change is observed for reads expressed from tester alleles (ns-ΔΨ = 0.003, Figure 4def). Strong allelic imbalance in heterozygotes implies that the observed inclusion of the cassette exon is regulated in cis, and that the identified cis-sQTL most likely is the causative regulatory variant. An RT-PCR validation experiment confirmed that observable inclusion of the cassette exon occurred only in flies that carried the derived allele of cis-sQTL (A/D and D/D, Figure 4g).Figure 4

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
Related in: MedlinePlus