Fig. 7
From: Common and distinct transcriptional signatures of mammalian embryonic lethality
Investigation of repeat deregulation. a Schematic representing a region of the genome (red line), a gene on the forward strand (exons are blue boxes and introns are blue lines) and strand-specific repeats (yellow boxes). The area within the grey box shows the genomic stretch where strand-specific reads were considered within exons (green), within introns (brown), intergenic (purple) or within annotated repeats (yellow). b Differential repeat and gene expression for 13 mutant lines (Hmgxb3 acts as a negative control). For each mutant line the number of differentially expressed repeat instances (DERs) is shown on the top x-axis split by genomic location (bars). The number of genes differentially expressed (homozygotes versus siblings) for each mutant line are indicated by a cross and shown on the bottom x-axis. Dhx35 has a large number of DERs in intronic regions (brown bar), whereas for Morc2a they are mostly in intergenic regions (purple bar). c Fold change of repeats and genes in Dhx35 mutant line. Genes enriched for the number of intronic DERs, if greater than 1 instance, compared to all introns for each gene are shown by circles (unique to Dhx35) or triangles (found in Dhx35 and at least one other mutant), ENSMUSG00000107482 has no exon counts and was excluded from the plot. The colour shows the adjusted p value (−log10 scaled) from DESeq2 for the gene with grey as not significant. The log2[fold change] for the gene is on the x-axis with the mean fold change of intronic DERs on the y-axis. d Repeat instance expression in the Morc2a mutant line. Only repeat families enriched for individual DERs against total instances in the genome are shown. Bar shows total repeat instances with DERs in red. Bars in the Location in Reference column display the number of DERs by genomic location relative to gene annotation. Dashed box shows subset of repeat instances ≥4 kb. Mean centred and scaled heatmaps in the Expression column are of expression levels of DERs (L1MdGf_I, MMERGLN-int and MMETn-int families) across heterozygous (het), homozygous (hom) and wild-type (wt) Morc2a embryos. Source data are provided as a Source Data file
