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Fig. 5 | Genome Biology

Fig. 5

From: Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

Fig. 5

A non-canonically imprinted ERVK LTR drives imprinted expression of Gab1 in placenta. a Screenshot of allelic gene expression, H3K4me3, H3K36me3, and H3K27me3 in B6/CAST and CAST/B6 ExE. ChIP-seq data is quantitated using enrichment normalized RPKM for 1-kb running windows with a 100-bp step (scales in square brackets); paternal (blue) and maternal (red) enrichments are shown on mirrored axes. RNA-seq data is quantitated as RPKM for 1-kb running windows with a 100-bp step. The box denotes the location of the non-canonical imprinted H3K4me3 peak associated with the known non-canonical imprinted gene Gab1. b Screenshot of allelic gene expression, H3K4me3, H3K36me3, and H3K27me3 in matDKO/CAST ExE, quantitated as in a. c Screenshot of H3K4me3, H3K27me3, and DNA methylation in GV oocytes. One-kilobase running windows with a 100-bp step were used; ChIP-seq data was quantitated as RPKM (scales in square brackets). d Screenshot showing allelic gene expression in F/CAST and CAST/F E12.5 placenta across the Gab1 locus. The box depicts the non-canonical imprinted paternal H3K4me3 peak containing an imprinted transcriptionally active ERVK LTR element (RLTR15). RNA-seq data is quantitated as log2RPKM for 1000-bp running windows with a 100-bp step. e Read count for maternal (red) and paternal (blue) transcription is shown for the non-canonically imprinted RLTR15 and exon 1 of the Gab1 gene in E12.5 and E16.5 embryonic (Li, liver; He, heart; Br, brain) and extra-embryonic (Pl, placenta; VE, visceral endoderm) tissues. Only intron-spanning reads were used, and two-tailed t test was used to statistically compare the allelic expression (***p < 0.0005). f Barplot shows the allelic gene expression (allelic ratio = mat/(mat + pat)) for the Gab1 gene in B6/CAST E12.5 yolk sac, placenta, and whole embryos. F4E5 carried CRISPR-targeted deletion of non-canonically imprinted RLTR15 on the paternal allele and was compared to wild-type (WT) controls (N = 3). Two-tailed single sample t test was used to compare the F4E5 value to the WT mean (*p < 0.05). Error bars show standard deviation

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