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. 2022 Aug 12;11:e77848. doi: 10.7554/eLife.77848

Figure 7. Stag2 deletion impairs the formation of total and promoter-anchored loops in oligodendrocytes.

(A) Loop counts (left panel) and length (right panel) in the indicated categories of Stag2f/y and Stag2f/y;NesCre oligodendrocytes (OLs). ***p < 0.001. (B) Loop counts plotted against loop length (from 0 to 5 Mb) of Stag2f/y and Stag2f/y;NesCre OLs. (C) Normalized contact counts for loops across different genomic distances in Stag2f/y and Stag2f/y;NesCre OLs. (D) Representative snapshots of contact maps at the Mal gene locus.hic files generated by HiC-Pro were converted to.cool format for plotting at 5 kb resolution. Tracks and narrow peaks from STAG2 and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) as well as the loops are plotted below. Transcription direction is indicated by the black arrow. (E) Pile-up analysis of loop ‘dots’-centered local maps for the promoter-anchored loops of genes in the indicated categories. The maps are balanced, normalized by distance, and plotted at 5 kb resolution. The numbers indicate the enrichment of the central pixel over the upper left and bottom right corners. (F) Pile-up analysis of the local contact maps centered around the transcription start site (TSS) of genes in the indicated categories. Transcription directions are indicated below. 1000 stable genes are chosen randomly and used for the analysis. The maps are balanced, normalized by distance, and plotted at 5 kb resolution. Diagonal pixels are omitted.

Figure 7.

Figure 7—figure supplement 1. Stag2 deletion reduces chromatin loops in oligodendrocytes.

Figure 7—figure supplement 1.

(A) Loop numbers of the indicated categories. (B) Aggregate peak analysis on the replicates of 10 kb Hi-C matrices using loops called from the merged samples of Stag2f/y or Stag2f/y;NesCre mice. Aggregate peak analysis performed on the replicates of 10 kb Hi-C matrices using the group-specific loops. Stag2f/y-specific loops are used in (C) and Stag2f/y;NesCre-specific loops are used in (D). The log2 fold change over Stag2f/y #1 is plotted on the top panels. (E) Pile-up analysis of loop ‘dots’-centered local contact maps for loops specific to Stag2f/y or Stag2f/y;NesCre oligodendrocytes (OLs). (F) Hexbin plot of contact counts of common loops in Stag2f/y and Stag2f/y;NesCre OLs. (G) Scatter plot of contact counts of common loops in Stag2f/y and Stag2f/y;NesCre OLs. Loops with significantly changed strength in Stag2f/y;NesCre OLs are highlighted in red (increased) and blue (decreased). Log2FC threshold of 1 was used. (H) Normalized contact counts for loops in the indicated categories across different genomic distances.
Figure 7—figure supplement 2. STAG2 controls local chromatin looping at differentially expressed genes.

Figure 7—figure supplement 2.

(A–C) Snapshots of the contact maps at the indicated differentially expressed genes. Tracks and peaks from STAG2 and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) as well as loops are shown below. Transcription directions are indicated by arrows. (D) Representative snapshots of contact maps of the replicate samples at Mal and Nkx6-2 genomic loci.hic files generated by HiC-Pro were converted into.cool format. Graphs were plotted with pyGenomeTracks at 5 kb resolution. Transcription orientations are indicated with the black arrows.
Figure 7—figure supplement 3. STAG2 regulates the formation of promoter-anchored loops in oligodendrocytes.

Figure 7—figure supplement 3.

(A) Loop counts (left panel) and fractions (right panel) of loops anchored at promoter or nonpromoter regions in the indicated categories. (B) Loop score of the loops in Figure 7E. Loop score from Stag2f/y oligodendrocytes (OLs) was used for common loops on the left, and loop score from Stag2f/y;NesCre OLs was used for common loops on the right. The unpaired Wilcoxon test was used for the statistical analysis. ***p < 0.001. (C, D) Loop score of loops anchored at differentially expressed genes (DEGs) and stable gene promoters with or without STAG2 enrichment. Loops from Stag2f/y OLs are used for the analysis in (C) and loops from Stag2f/y;NesCre OLs are used for the analysis in (D). Unpaired Wilcoxon test was used for the statistical analysis. *p < 0.05; **p < 0.01; ***p < 0.001; ns, not significant. (E) Profile plot of the average enrichment score for the bottom half of each graph panel in Figure 7F. Diagonal pixels were omitted.