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Fig. 3 | Genome Biology

Fig. 3

From: Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis

Fig. 3

UBP12/13 protect against H3K27me3 removal. a Differential H3K27me3 enrichment in the ubp12/13 mutant minus wild type, for UBP12/13 targets and non-targets (left), for UBP12/13 targets and non-targets marked with H3K27me3 (middle), and for UBP12/13 targets with H3K27me3 on the first 20% or the last 20% of gene bodies (right). Tests for significance (for ac) were done by Mann-Whitney U test; ns p ≥ 0.05, *p < 0.05, **p < 0.01,***p < 0.001; Bonferroni correction was applied with m = 6. b Metagene plot showing the median H3K27me3 coverage-scaled fragment counts in the ubp12/13 mutant (dashed line) and wild type (solid line), for UBP12/13 targets with H3K27me3 (green) and non-targets with H3K27me3 (grey). c REF6 enrichment (median coverage-scaled fragment count) at narrow H2Aub1 peaks (left) and at CTCTGYTY motifs (right). Depicted in the left panel are all significant H2Aub1 peaks (purple), all peaks with at least one CTCTGYTY motif (red) and all peaks that do not possess at least one CTCTGYTY motif (blue). Depicted in the right panel are all CTCTGYTY motifs (purple), all motifs with H2Aub1 (red), and all motifs without H2Aub1 (blue). REF6-HA binding sites and CTCTGYTY data obtained from [25]. d Differential coverage-scaled REF6 fragment counts (mutant-wt) for genes that lose H2Aub1 (“Down”), genes without a change in H2Aub1 (“Stable”), and genes gaining H2Aub1 (“Up”). e Scatterplots made with the coverage-scaled fragment counts of H2Aub1 and REF6 in 50-bp windows (genome-wide). CTCTGYTY motifs were also counted in 600-bp windows around the centre of the windows, and windows were split over separate plots depending on the number of motifs. The x- and y-axes are logarithmic (Log10). Statistics: 0 motifs (m = 0.33, R2 = 0.17, p < 2.2E−16), 1 motif (m = 0.27, R2 = 0.09, p < 2.2E−16), 2 motifs (m = 0.39, R2 = 0.11, p < 2.2E−16), 3 motifs (m = 0.47, R2 = 0.10, p < 2.2E−16), 4 motifs (m = 0.47, R2 = 0.07, p < 2.2E−16), and 5+ motifs (m = 0.41, R2 = 0.05, p < 3.7E−9). The biological material used to generate the data in this figure was 33 DAG rosettes, apart from the REF6-HA data, which was obtained from 12 DAG seedlings

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