Fig. 6: Xist deletion leads to increase in YY1 binding at the cis-regulatory elements on the Xi. | Nature Communications

Fig. 6: Xist deletion leads to increase in YY1 binding at the cis-regulatory elements on the Xi.

From: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis

Fig. 6: Xist deletion leads to increase in YY1 binding at the cis-regulatory elements on the Xi.

a Bar graphs show percentages of increased, decreased, and unchanged YY1 peaks at TSS-proximal and TSS-distal regions on the X chromosome and autosomes in Lin− cells. b Bar graphs show percentages of increased, decreased, and unchanged X-linked YY1 (left) and H3K27ac (right) peaks at TSS-proximal and TSS-distal regions in MEFs. c Pie graphs show the number of increased YY1 peaks that overlap with increased, decreased, or unhanged H3K27ac peaks at TSS-proximal or TSS-distal regions of the X chromosome. d Bar graphs show comparison of the percentages of increased, decreased, and unchanged YY1 peaks at promoters of upregulated cDEGs and lsDEGs to nonDEGs on the X chromosome and autosomes in Lin− cells. e Bar graphs show comparison of the percentages of increased, decreased, and unchanged YY1 peaks at promoters and enhancers of the indicated gene sets on the X chromosome in MEFs. f Representative genome tracks show YY1 ChIP-seq signal across typical X-linked upregulated cDEGs associated with increased promoter YY1 binding (e.g., Ddx3x) in Lin− cells. g Representative genome tracks show YY1 ChIP-seq signal across typical Xist-dependent XCI subjective genes within increased YY1 binding at promoter (e.g., Vbp1) and enhancer (e.g., Zfp18) regions in MEFs upon Xist depletion. Firre exemplifies a typical Xist-independent gene associated with increased enhancer YY1 binding. h Violin and box plots show comparison of d-scores of promoter and enhancer YY1 peaks of indicated gene sets in WT MEFs. Analyzed peak numbers are indicated above each bar graph (a, b, d, e). See Supplementary Data 9 for a list of peaks for each group (h). Biological replicates of sequencing data (n ≥ 2) were merged to maximize sequencing depth for allele-specific analysis (b, c, e, h). Boxplots are described in “Methods”. P-values were calculated using two-tailed Chi-squared test (d, when peak number >300), two-tailed Fisher’s exact test (d, e), or two-tailed unpaired Student’s t-test (h).

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