Extended Data Figure 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 K.O. cells compared to wt. L2F: Log₂ Fold change. Bold: Significantly upregulated in K.O. cells relative to wt. Red: L2F>0, blue: L2F<0. Green: P value or P adjusted value ≤ 0.05. Purple: Genes that exhibit sequence similarity with the mutated gene’s mRNA in their promoter region. Yellow: Genes that exhibit sequence similarity with the mutated gene’s mRNA in their 3’UTR region. Other non-colored genes exhibit sequence similarity with the mutated gene’s mRNA in their exons or introns. Boxed: upregulated in K.O. but not RNA-less cells; no Fermt2 RNA-less allele was analyzed. d, qPCR analysis of Ubapl, Fmnl2, Cdk12 and Actr1a pre-mRNA levels in Actg1 K.O. cells relative to wt. e, qPCR analysis of actb1 mRNA levels in 6 hpf wt zebrafish injected with uncapped mouse Actb RNA. f, Schematic representation of regions of sequence similarity between hif1ab mRNA and epas1a locus. TSS: transcription start site. Grey shaded triangles represent the alignments; intensity represents alignment quality and width at the base represents length of the similarity region. g, qPCR analysis of epas1a mRNA levels in 6 hpf wt zebrafish embryos injected with uncapped RNA composed solely of the hif1ab sequences similar to epas1a promoter, exons, introns, or 3’UTR. a-e, g, n = 2 (a-c); 3 (d, e, g) biologically independent samples. a-c, DESeq2 tests for significance of coefficients in a negative binomial GLM (Generalized Linear Model) with the Wald test. P values were not multiple testing corrected. d, e, g, wt or control expression set at 1 for each assay. Error bars, mean, s.d. Two-tailed student’s t-test used to assess P values.