Global and Stage Specific Patterns of Krüppel-Associated-Box Zinc Finger Protein Gene Expression in Murine Early Embryonic Cells
Figure 5
Distribution of histone-modifications and KAP1 binding over KRAB-ZFP gene bodies and surrounding genomic regions.
The genomic regions contained between the TSS and gene end of mouse KRAB-ZFP genes, plus the regions including 3.5 kb upstream of the TSS and 3.5 kb downstream of the gene were equally divided in 8 “bins”. Identification of enriched sequences for H3K9me3, H3K27me3, H3K9me3 and KAP1 was performed using publicly available ChIP-seq datasets generated in mouse Rex1-GFPd2 ESCs (H3K4me3, H3K27me3, H3K9me3 [55]) and in KAP1 WT ESCs [39]. For details, see Methods section. A) Distribution of H3K4me3- (blue track) and H3K27me3- (red track) enriched regions over targeted KRAB-ZFP genes. B) Distribution of KAP1 (blue track) enriched regions over targeted KRAB-ZFP genes, highlighting the preferential enrichment for KAP1 downstream of the TSS with no spreading over the rest of the genes, as previously described [21], [61], while H3K9me3 (red track) spreads over the gene body up to downstream of the TSS. C) Distance between KRAB-ZFP genes enriched for H3K9me3 in ESCs and nearest ERVs compared with the distance of other KRAB-ZFP genes and other genes. P-values were calculated using a Wilcoxon test. D) Table summarizing RNA-seq RPKM counts in WT and Kap1 KO ESCs and ratio KO/WT [31] for the 20 KRAB-ZFP genes with KAP1 enrichment in the regions contained between 3.5 kb upstream of the TSS and 3.5 kb downstream of the gene end. “N/A” indicates that no reads were detected for the corresponding gene. Highlighted in yellow are genes up-regulated more than 2 folds upon Kap1 KO.
