Extended Data Fig. 8: Expression level of genes exhibiting sequence similarity in the different mouse cell line models.

a–c, RNA-seq analysis of genes exhibiting sequence similarity with Fermt2 (a), Actg1 (b) or Actb (c) in knockout compared to wild-type cells. Bold, significantly upregulated in knockout relative to wild-type cells; red, L2F>0, blue, L2F<0; green, P value or adjusted P value ≤ 0.05; purple; genes exhibiting sequence similarity with the mutated gene's mRNA in their promoter region; yellow, genes exhibiting sequence similarity with the mutated gene's mRNA in their 3′UTR region. Other non-coloured genes exhibit sequence similarity with the mutated gene's mRNA in their exons or introns. Boxed, upregulated in knockout but not RNA-less cells; no Fermt2 RNA-less allele was analysed. d, qPCR analysis of Ubapl, Fmnl2, Cdk12 and Actr1a pre-mRNA expression levels in Actg1 knockout relative to wild-type cells. e, qPCR analysis of actb1 mRNA expression levels in 6 hpf wild-type zebrafish injected with uncapped mouse Actb RNA. f, Schematic representation of regions of sequence similarity between hif1ab mRNA and the epas1a locus. Grey shaded triangles represent the alignments; intensity represents the alignment quality; and width at the base represents the length of the similarity region. g, qPCR analysis of epas1a mRNA expression levels in 6 hpf wild-type zebrafish embryos injected with uncapped RNA composed solely of the hif1ab sequences similar to the epas1a promoter, exons, introns or 3′UTR; the same eGFP uncap. control samples were used for all comparisons. n = 2 (a–c) or n = 3 (d, e, g) biologically independent samples. DESeq2 tests were used to test for significance of coefficients in a negative binomial generalized linear model with the Wald test (a–c). P values were not corrected for multiple testing. Wild-type or control expression levels were set at 1 for each assay (d, e, g). Data are mean ± s.d., and a two-tailed Student’s t-test was used to calculate P values.

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