Figure 4.
Characterization of the Intronic LINE-1 Retrotransposon within SMOC2
(A) Schematic of a full-length canine LINE-1 element consisting of 5′ UTR/3′ UTR, open reading frames 1 and 2 (ORF1/ORF2), and a polyadenylated tail (AAAAn) flanked by target site duplications (TSD). The structural variant within SMOC2 is 1,506 bp in length (in addition to a poly(A) tail) and has a 99.1% match to the consensus sequence of canine LINE-1.
(B and C) Distribution of the SMOC2 LINE-1 fragment for (B) viscerocranium PC1 and neurocranium centroid size (C) across all individuals.
(D) Ventral-dorsal view of the canine hard palate and its constituent bones.
(E) Length and width of the canine palate and constituent bones normalized by the neurocranium centroid for homozygous ancestral (white), heterozygotes (gray), and homozygous-derived (black) individuals for the SMOC2 LINE-1 insertion.
(F) Relative expression levels of SMOC2 both up- and downstream of the LINE insertion (<0.05 ∗; <0.01 ∗∗; <0.001 ∗∗∗). Error bars represent SEM.
(G) RNA sequencing (RNA-seq) data reveal four genes with significant changes in mRNA levels (red) for homozygous SMOC2 LINE-1 carriers compared to non-carriers (three each). Neighboring genes to SMOC2 are colored green.
(H) Schematic of genomic DNA (gDNA) spanning exon 8 and 9 of SMOC2, including the LINE-1 fragment. mRNA transcripts include the canonical splicing of SMOC2 (i) followed by the three most abundant SMOC2 isoforms when the LINE-1 element is present (ii–iv). All isoforms have premature stop codons prior to exon 9. C/T indicates the SNP in exon 8. Schematic is not to scale.
(I) Exons 1–13 of SMOC2 contribute to a follistatin-like module (FS), thyroglobulin-like modules (TY), a unique SMOC module, an extracellular calcium-binding module (EC), and a signal peptide (SP).
See also Figures S5 and S7 and Tables S5 and S6.