Figure 4. The 12 bp recruitment motif is enriched on the X. Bound motifs are characterized by DNA-encoded nucleosome occupancy.
(A) The 12 bp recruitment motif identified using high-resolution SDC-2 ChIP-seq data. (B) Motif distribution is plotted for chromosomes I through V (shades of gray) and chromosome X (purple). Motif enrichment is dependent on score-cutoff. Weaker motifs (score <7) are randomly distributed across the chromosomes. Strong motifs (score ≥7) are enriched on the X chromosome. Perfect score motifs (score 10, sequence ATCGCGCAGGGA) show almost complete X-specificity: 10/11 (91%) are on the X. (C) Heatmaps showing H3 ChIP-seq enrichment from wild-type (left) and sdc-2 null (right) embryos, plotted across a 1 kb window centered on all strong motifs of score ≥7. Motifs are sorted by H3 enrichment in wild-type, and divided into three categories: Bound by DCC on the X (n = 50), unbound on the X (n = 45), and unbound on the autosomes (n = 184). Here, we define ‘bound’ as the overlap of both SDC-3 and DPY-27 binding. There are no bound motifs on the autosomes. (D) Heatmap indicates the probability of nucleosome occupancy across a 1 kb window centered on the motifs. As in (C), motifs are sorted by H3 enrichment in wild-type. (E) Boxplot indicates intrinsic nucleosome occupancy for a 150 bp window centered on each motif. Bound motifs (dark purple, median 0.616) have significantly higher DNA-encoded nucleosome occupancy compared to unbound motifs on the X (light purple, median 0.4865) and motifs on the autosomes (grey, median 0.503). Significance calculated using one-tailed students t-test (** p-value<0.01, *** p-value<0.001).