Figure 3—figure supplement 3. | 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 3.

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 3.
Download figureOpen in new tabFigure 3—figure supplement 3. Examples of intron-retaining Alu transcripts.

RNAseq data were visualised with IGV. Data were generated from polyA-selected RNA from cells depleted of hnRNPC (siC #1 and #2), UPF1 (siUPF1), or UPF1 and hnRNPC, or control cells (unspecific control oligonucleotide). All traces are scaled according to the total number of reads in each sample. (A) An Alu-exon in intron 16 of the NUP133 gene is associated with intron. The Alu-exon is validated by junction-spanning reads on both sides. Note that although hnRNPC/UPF1 co-depletion restores overall expression of NUP133 in hnRNPC-depleted cells, the coverage of the intron region is not changing compared to the flanking exons, confirming that the intron-retaining Alu transcript itself is not depleted by NMD. (B) Two Alu-exons in intron four of the GMPS gene are associated with partial intron. Both Alu-exons are validated by junction-spanning reads at the 3' splice site while junction-spanning reads at the 5’ splice sites of the Alu-exons are absent. Both exons can be detected by PCR (see Figure 3—figure supplement 2C). Note that although hnRNPC/UPF1 co-depletion restores overall expression of GMPS in hnRNPC-depleted cells, the coverage of the intron region is not changing compared to the flanking exons, confirming that the intron transcript itself is not depleted by NMD. (C) An Alu-exon in intron two of the C8ORF76 gene is associated with intron. The Alu-exon is validated by junction-spanning reads at the 3' splice site but not at the 5' splice site.

DOI: http://dx.doi.org/10.7554/eLife.19545.013