Fig. 3

L1 activation by vitC depends on KDM4 H3K9me2/3 demethylases. A qRT-PCR data showing the expression (relative to untreated shScr) of L1s in shKdm3a/b double knockdown cells, with and without vitC treatment. B Using published ChIP-seq data [20], the enrichment of H3K9me2 at young full-length L1s (> 5 kb; uniquely aligned reads) was compared with that at downstream regions (5 kb long) from the same elements. In vitC-treated cells (72 h), where there is genome-wide H3K9me2 loss [20], L1s preserve more H3K9me2 relative to surrounding regions. C Cumulative KDM4A [46] and KDM4C [45] ChIP-seq signal at full-length L1s. For KDM4A, the dashed line represents the ChIP signal in Kdm4a KO cells; for KDM4C it represents the input signal. D qRT-PCR data in shKdm4a/c KD compared to untreated shScr, with and without vitC. E ChIP-qPCR data for H3K9me3 (left-hand chart) and H3K9me2 (right-hand chart) at the 5′ UTR of young L1s in Kdm4a/c KD mESC. The data show ChIP signals in vitC-treated cells normalised to their respective untreated controls. All p-values shown refer to the effect of the ‘sample’ variable from an ANOVA model using ‘sample’ and ‘amplicon/target’ as independent variables