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. 2022 Mar 9;2(3):100102. doi: 10.1016/j.xgen.2022.100102

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© 2022 The Author(s)

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

PMC Copyright notice

Structural variations affecting expression of Srp54, Lpp, and Wdfy1

(A) Variation in copy number in a SegDup region is associated with expression of Srp54. The read coverage in these SegDup regions is used to infer the number of copies of the intersecting genes. The bars with similar lengths and colors indicate corresponding SegDup regions. Yellow bars indicate more than 98% sequence similarity; orange bars indicate more than 99% sequence similarity.

(B) A duplication involving the first two exons of Lpp in two substrains of C57BL/10 is associated with an increase in Lpp expression. Duplication of the TSS and the promoter site is the most likely cause.

(C) A segmental duplication region that intersects with three exons in Wdfy1 and is present in C57BL/6J is associated with reduction of expression of Wdfy1 in C57BL/6J. All the other substrains lack this duplication.

(D) Sashimi plots⁴³ for C57BL/6BomTac (a closely related substrain to C57BL/6J), C57BL/6J, Upf2^+/+, and Upf2^−/− cell lines from C57BL/6J highlighting the junction between 6a and 4b exons across the segmental duplication region. Because C57BL/6BomTac lacks the duplication, it does not have any junctions between those exons, whereas the relative number of junctions in the Upf2^−/− cell line is significantly larger than the other wild-type C57BL/6J samples.

(E) The bar plot shows the ratio of the normalized number of junctions between 6a and 4b exons (normalized by the total number of junctions in each sample) in Upf2^−/− over Upf2^+/+ cell lines. It shows a significant increase in the relative number of junctions between the two segmental duplications in the Upf2^−/− cell line. The numbers on top of the bars show p values obtained by the chi-square test.

(F) The expression level of Wdfy1 in the Upf2^−/− cell line is significantly higher than in the Upf2^+/+ cell line. This supports our hypothesis that the reduction of gene expression in C57BL/6J is due to the nonsense-mediated decay (NMD) mechanism.