Fig. 3

Localization of linker histone H1t at CpG-methylated repeat element chromatin domains. a Annotation of H1t-bound genomic regions using HOMER. b Annotation of H1t peaks at repeat elements showing its predominant association with LINE and LTR subclasses of retrotransposable elements. c Profile of methylated cytosines (SRS557654) across all the H1t peaks. More than 90% of the H1t peaks overlap with methylated CpGs. The y-axis is the count of methylated CpG positions at each peak. Some peaks with more than 100 methylated cytosines have been truncated to 100 for better visualization of the overall plot. d Density plot of H1t peaks overlapping with methylated CpGs (SRS557654). The y-axis represents the density function and the x-axis represents the bandwidth parameter. N represents the number of observations. Co-immunoprecipitation assays showing the coexistence of H1t-containing oligonucleosomes with histone marks H3K9me3 and H4K20me3. e H3K9me3-ChIP showing the co-association with linker histone variant H1t in testicular chromatin. f Linker histone variant H1t is associated with H4K20me3-ChIP elute fraction. g Reciprocal immunoprecipitation assays showing that H1t-positive chromatin fragments to be associated with histone marks H3K9me3 and H4K20me3 in vivo. Information in e–g. The first lane is the input fraction; the second lane is the IP using the non-specific IgG isotype control, the third lane is the IP with the mentioned antibodies (anti-anti-H3K9me3/anti-H4K20me3/anti-H1t). The antibodies labeled alongside the blot refer to the antibodies used for western blotting. Ponceau-stained blots are given for reference