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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 alternative donor site associated withcis-sQTL in canonical splicing dinucleotide.De novo donor site and inclusion of an 84 bp segment that was associated with cis-sQTL in canonical splicing dinucleotide. a-b: Exon/intron coverage plots of the genotype-specific splicing event are shown for the F1-hybrids that carried derived (a) and ancestral (b) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. c: The distributions of Ψ-values for alleles of this cis-sQTL. d: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms were 234 bp and 150 bp, respectively. For other details see the legend to Figure 2.
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Fig3: Genotype-specific alternative donor site associated withcis-sQTL in canonical splicing dinucleotide.De novo donor site and inclusion of an 84 bp segment that was associated with cis-sQTL in canonical splicing dinucleotide. a-b: Exon/intron coverage plots of the genotype-specific splicing event are shown for the F1-hybrids that carried derived (a) and ancestral (b) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. c: The distributions of Ψ-values for alleles of this cis-sQTL. d: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms were 234 bp and 150 bp, respectively. For other details see the legend to Figure 2.

Mentions: An example of a genotype-specific splicing event associated with cis-sQTL in canonical dinucleotides is shown on Figure 3 (a1219). We observed a de novo donor site (mutation from GC to GT) in the first intron of the gene dbi. Creation of this splice site resulted in inclusion of a 84 bp intron segment to the first exon. In genotypes that carried the ancestral allele, no junction reads corresponding to this splice site were observed. The altered exon was located in the 5′-untranslated region of the gene and most probably did not affect the structure of the encoded protein. The RT-PCR validation experiment confirmed that the transcripts that utilized the new splice site (235 bp band) were expressed only in flies that carried the derived allele of cis-sQTL (A/D and D/D, Figure 3d). However, the homozygous D/D-inbred line was still expressing the short isoform (151 bp band), i.e. we did not observe a complete switch of isoforms.Figure 3


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 alternative donor site associated withcis-sQTL in canonical splicing dinucleotide.De novo donor site and inclusion of an 84 bp segment that was associated with cis-sQTL in canonical splicing dinucleotide. a-b: Exon/intron coverage plots of the genotype-specific splicing event are shown for the F1-hybrids that carried derived (a) and ancestral (b) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. c: The distributions of Ψ-values for alleles of this cis-sQTL. d: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms were 234 bp and 150 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

Fig3: Genotype-specific alternative donor site associated withcis-sQTL in canonical splicing dinucleotide.De novo donor site and inclusion of an 84 bp segment that was associated with cis-sQTL in canonical splicing dinucleotide. a-b: Exon/intron coverage plots of the genotype-specific splicing event are shown for the F1-hybrids that carried derived (a) and ancestral (b) variants of cis-sQTL on natural alleles. Tester alleles of all F1-hybrids carried ancestral variant of cis-sQTL. c: The distributions of Ψ-values for alleles of this cis-sQTL. d: RT-PCR validation of gene models. The predicted lengths of PCR-products corresponding to the long and short isoforms were 234 bp and 150 bp, respectively. For other details see the legend to Figure 2.
Mentions: An example of a genotype-specific splicing event associated with cis-sQTL in canonical dinucleotides is shown on Figure 3 (a1219). We observed a de novo donor site (mutation from GC to GT) in the first intron of the gene dbi. Creation of this splice site resulted in inclusion of a 84 bp intron segment to the first exon. In genotypes that carried the ancestral allele, no junction reads corresponding to this splice site were observed. The altered exon was located in the 5′-untranslated region of the gene and most probably did not affect the structure of the encoded protein. The RT-PCR validation experiment confirmed that the transcripts that utilized the new splice site (235 bp band) were expressed only in flies that carried the derived allele of cis-sQTL (A/D and D/D, Figure 3d). However, the homozygous D/D-inbred line was still expressing the short isoform (151 bp band), i.e. we did not observe a complete switch of isoforms.Figure 3

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