Figure 1—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 1—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 1—figure supplement 3.
Download figureOpen in new tabFigure 1—figure supplement 3. Alu-exon transcripts are frequently depleted from the cytoplasmic RNA pool.

The relative abundance of the Alu-exon transcripts of AGL, NUP133, TIMM23 and HELLS was measured in cytoplasmic and nuclear RNA of cells depleted of hnRNPC (siC #1 and #2), or control cells (‘no si’: no siRNA; ctrl: unspecific control oligonucleotide). Overall, we observed a tendency for Alu-exon transcripts to be present in the nucleus but lost in the cytoplasm. The relative abundance of Alu-exon transcripts was significantly higher in the nucleus than in the cytoplasm in case of AGL and TIMM23. Note that NUP133 generates two transcripts that contain the Alu-exon sequence, an Alu-exon transcript and a larger 3' intron intron-retaining Alu transcript. The later was not present in the cytoplasm, while the Alu-exon transcript was of equal abundance in both subcellular fractions. The Alu-exon transcript of HELLS did not show consistent depletion in the cytoplasm, but we later found that HELLS produces multiple Alu-exon isoforms (Figure 2—figure supplement 2). Abundance was measured relative to the constitutively spliced transcript by semi-quantitative RT-PCR. Shown are the averages across independent replicates (n = 3–4), error bars represent standard deviation of the mean. To test for significance, two-way ANOVA was performed treating the RNA fraction as confounding factor. Multiple comparison correction was done according to Tukey’s HSD.