Fig. 2: The lamina-associated genome is modified with H3K9me2 in naive pluripotency.
From: The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
a, Averaged genome tracks and HMM domain calls from spike-in controlled lamin B1, LAP2β, H3K9me2 and H3K9me3 CUT&RUN in WT mES cells (n = 3 replicates per condition except for H3K9me3, for which n = 2 replicates were performed), highlighting a 50 Mb section of chromosome 12 (chr 12). b, An UpSet plot showing the overlap between lamin B1 and H3K9me3 on 312.5 Mb of the genome in WT mES cells. H3K9me3 domains separately cover 186.7 Mb, while lamin B1 domains separately cover 998.2 Mb. c, An UpSet plot showing the extensive overlap of lamin B1, LAP2β and H3K9me2 in WT mES cells in domains covering 1081 Mb of the genome (‘LADs’), H3K9me2-only domains covering 439 Mb of the genome (‘KODs’) and lamin B1 and LAP2β-occupied domains covering 167.6 Mb of the genome. d, Analysis of LAD-resident genes, defined as being at least 90% covered by a LAD, in WT mES cells (14,376 genes in total). #long non-coding (lnc)RNAs that are significantly depleted in LADs compared with the mouse genome (P < 0.0001, two-sided chi-squared test). *Protein-coding genes and **pseudogenes significantly enriched in mES cell LADs (P = 0.0334 and P < 0.0001, respectively, two-sided chi-square test). e, The proportion of genes expressed (TPM >5) in non-LADs (n = 28,410 genes), LAP2β+LB1+ domains (n = 5,020 genes), KODs (n = 9,224 genes) and LADs (n = 14,376 genes) in WT mES cells. ****all means are significantly different (P < 0.0001) by one-way ANOVA. TEC, to be experimentally confirmed; snoRNA, small nucleolar RNA; snRNA, small nuclear RNA.
