Fig. 3: NUP153 influences transcription and binding of CTCF and cohesin at bivalent genes.

a Scatter plot showing expression levels of transcripts in log2[CPM] scale in control and NUP153 KD-1 mouse ES cells. Blue points denote all differentially expressed genes (n = 711) and orange points denote differentially expressed bivalent genes (Supplementary Data 6 and 9). b Table showing number of differentially expressed genes that associate with all, Group I and Group II CTCF-positive TSS (top). Plots showing number of differentially regulated NUP153-positive and NUP153-negative genes that associate with Group I and II CTCF-positive TSS (bottom) (see also Supplementary Data 8). c NUP153 DamID-Seq, CTCF, cohesin, H3K4me3, and H3K27me3 ChIP-Seq, and RNA-Seq tracks are shown for two NUP153-positive Group I genes, Rtn4rl1 (left panel) and Calb2 (right panel) in control (WT) and NUP153 KD ES cells. Rtn4rl1 shows transcriptional upregulation and Calb2 shown transcriptional downregulation. d NUP153 DamID-Seq, CTCF, cohesin, H3K4me3, and H3K27me3 ChIP-Seq tracks are shown for a 145–150 kb region for the HoxA and HoxC loci in control (WT) and NUP153 KD mouse ES cells as indicated. Arrows point to regions where CTCF or SMC3 binding are altered in NUP153 KD mouse ES cells. CTCF sites labeled with asterisk (*) denote CTCF sites that have been reported to regulate transcription at the Hox loci by mediating the formation of TADs48,70. The 2D heat map shows the interaction frequency in mouse ES cells44. Hi-C data was aligned to the mm9 genome showing HoxA cluster residing in a TAD boundary and HoxC cluster in a TAD as published44. H3K4me3 and H3K27me3 (ref. 40) and CBP/P300 (ref. 43) ChIP-Seq data were previously published. CPM, counts per million.