Figure 5—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 5—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 5—figure supplement 1.
Download figureOpen in new tabFigure 5—figure supplement 1. U-tract length of Alu-exons traced throughout primate orthologues.

We searched for the orthologues of all Alu-exons with a strong 3' splice site in human, either annotated in UCSC or described in this study (2867 Alu-exons in total). We used the following genomes: hg19 (human), panTro4 (chimpanzee), nomLeu1 (gibbon), rheMac3 (rhesus macaque) and calJac3 (marmoset). (A) Human Alu-exons were classified according to the time of emergence of their 3' splice site: (Deininger and Batzer, 2002) before Old and New World monkeys, (Lev-Maor et al., 2003) before split of hominoidea superfamily from other Old World monkeys, or (Sorek et al., 2004) only found in hominoidea. Left: The median length of the longest U-tract is shown with 95% confidence intervals estimated by bootstrapping. Right: Substitutions of the Alu elements from consensus is shown. (B) Alu-exons with orthologues present in gibbon or chimpanzee (nomLeu1 or panTro4, respectively) were classified as described in Figure 5, and progression in predicted 3' splice site strength of the three groups of Alu-exons is shown on the left. The longest U-tract of the Alu elements in each species was identified. U-tract length is shown in each species, as 95% confidence intervals of the median estimated by bootstrapping (middle) similar to Figure 5A and B and the underlying distribution of U-tract lengths as a boxplot (right side). (C) Shown is the distribution of U-tract lengths underlying the summarised data presented in Figure 5B. Alu-exons with orthologues present in marmoset (calJac3) were classified as described in Figure 5, and the longest U-tract of the Alu elements in each species was identified. (D) Shown is the distribution of U-tract lengths underlying the summarised data presented in Figure 5C. Alu-exons with orthologues present in rhesus macaque (rheMac3) were classified as described in Figure 5, and the longest U-tract of the Alu elements in each species was identified. Supplemental Dataset 1. List of exons with sufficient coverage for DEXSeq analysis in our RNAseq data. Deposited at the Dryad repository, doi:10.5061/dryad.7h81d. Source Data of Figure 4D. Percent exon inclusion of Alu-exons in different tissues. Source Data of Figure 5. List of Alu exons across our datasets and UCSC annotation, including cross-species annotation.

DOI: http://dx.doi.org/10.7554/eLife.19545.020