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. 2022 Jun 15;41(13):e110600. doi: 10.15252/embj.2022110600

Figure 4. Generation of minimal LADs.

Figure 4

  1. Correlation between compartment score and ChIP‐seq enrichment at 50 kb resolution.
  2. Correlation between differential compartment score and differential ChIP‐seq enrichment between mESCs and GSCs at 50 kb resolution.
  3. Representative chromosome‐wide distributions of compartment score and lamin B1 enrichment for mESCs and GSCs.
  4. LAD occupancies in different cell types (Peric‐Hupkes et al, 2010; Robson et al, 2016; Poleshko et al, 2017; Yattah et al, 2020).
  5. Venn diagram of LADs called in GSCs, the union of LADs called in all other cell types in this study, and union of LADs identified from all other studies (Peric‐Hupkes et al, 2010; Robson et al, 2016; Poleshko et al, 2017; Yattah et al, 2020).
  6. UpSet plot for the union set of LADs in different studies (Peric‐Hupkes et al, 2010; Robson et al, 2016; Poleshko et al, 2017; Yattah et al, 2020). A majority of regions correspond to constitutive LADs.
  7. IF analysis for lamin B1 in (left) EpiLCs and d4c7 mPGCLCs, as well as (right) EpiLCs and GSCs. Symbols for each cell type are as indicated. Scale bars, 10 μm.
  8. Western blot for lamin B1 in different cell types (bottom) and quantification normalized by β‐actin (top).
  9. Average distributions of lamin B1 enrichment across all chromosomes (1–19, X). Ribbons correspond to 95% confidence intervals of fitted GAMs.
  10. Lamin B1 ChIP‐seq enrichment in the first (left/p‐ter) and the last (right/q‐ter) 300 kb of each chromosome. The point marks the median while the thick and thin lines correspond to 66% and 95% intervals, respectively. Number of chromosomes = 20 (autosomes and chromosome X).
  11. Representative chromosome‐wide distributions of ChIP‐seq enrichment for lamin B1 and H3K9me3/me2.
  12. (top) Representative images of FISH against major satellite repeats in EpiLCs and GSCs. Scale bars, 10 μm; (bottom) percentage of the pericentromeres detached from the nuclear lamina in EpiLCs and GSCs. The point marks the median while the thick and thin lines correspond to 66% and 95% intervals, respectively. Number of cells = 18/22 for EpiLC/GSC.