Figure 3—figure supplement 1. | Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

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Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Figure 3—figure supplement 1.

Affiliation details

UCL Institute of Neurology, United Kingdom; MRC-Laboratory of Molecular Biology, United Kingdom; Institute de Biologie de l’ENS (IBENS), CNRS UMR 8197, France; University College London Genetics Institute, United Kingdom; Goethe University Frankfurt, Germany; Institute of Molecular Biology (IMB), Germany
Figure 3—figure supplement 1.
Download figureOpen in new tabFigure 3—figure supplement 1. Alu-exons with weak splice sites cause formation of intron transcripts.

A modified DEXSeq approach was used to test for significant intron retention (for details, see Methods) in hnRNPC/UPF1 co-depleted cells, covering specifically introns flanking Alu-exons (A and B) or any intron in cells depleted of hnRNPC (C and D). (A) We selected Alu-exons with junction-spanning reads and tested if the intron flanking the Alu-exon is significantly retained in cells co-depleted of hnRNPC and UPF1 (adjusted p-value < 0.01). (B) All Alu-exons were according to which of the flanking introns was retained (upstream or downstream intron, both or none). Shown is the maximum entropy score of the 5' and 3' splice site (SS) of each Alu-exon within the four groups, predicted based on nucleotide sequence (Yeo and Burge, 2004). Similar results were observed if Alu-exons were filtered for junction-spanning reads (data not shown). (C) Retention of all introns not flanking an Alu-exon was monitored and the number of genes with a given number of significantly retained introns is shown. In total, our approach detected sequence retention for 1.52% of introns in hnRNPC-depleted cells. padj: adjusted p-value. (D) All introns flanking an Alu-exon (upstream or downstream) were tested as in (C). Introns flanking Alu-exons were much more likely to be retained than introns not flanking an Alu-exon. Retention is scored based on adjusted p-value < 0.01.

DOI: http://dx.doi.org/10.7554/eLife.19545.011