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Fig. 3 | Epigenetics & Chromatin

Fig. 3

From: Linker histone epitopes are hidden by in situ higher-order chromatin structure

Fig. 3

Large-scale (low resolution) and small-scale (high resolution) comparisons between xChIP and xxChIP sequencing strategies. a H1 epitope “exposure” peak densities over chromosome 7, as measured by scanning with a window of 1000 base pairs: for xChIP H1.2 (dark blue), xChIP H1.5 (magenta), xxChIP H1.2 (orange) and xxChIP H1.5 (green). Black arrowheads show enrichments (compared to surrounding regions) of xChIP-seq reads for H1.2 and H1.5, coupled with deficiencies for xxChIP-seq reads of H1.2 and H1.5 at the same locations. Also indicated are cytogenetic road marks, DNA lengths (mb), the epichromatin track [23], and tracks for the density of peaks enriched with H3K4me1, H3K9ac, H3K27ac, Pol II and SMC3. b Pairwise correlations between xChIP H1.2, xChIP H1.5, xxChIP H1.2 and xxChIP H1.5 signals, averaged over three replicates each, using a 1000-bp sliding window. Note that xChIP H1.2 versus xChIP H1.5 and xxChIP H1.2 versus xxChIP H1.5 reveal clear positive correlations; whereas, the xChIP signals reveal negative correlations with the xxChIP signals. c and d Examples of genomic regions at high resolution, showing distinct patterns of histone occupancy for aligned reads of H1.2 (black) and H1.5 (orange) xChIP-seq. The raw xChIP-seq signal was smoothed by averaging with a 100-bp running window

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