Fig. 2: NUP153 mediates CTCF and cohesin binding at cis-regulatory elements and TAD boundaries in mouse ES cells.

a Distribution of NUP153 peaks in mouse ES cells. Peaks are categorized as promoters (−2 kb from TSS to +100 bp from TSS), gene body (+100 bp from TSS to +1 kb from transcription termination site (TTS)), intergenic sites (<−2 kb from TSS and >+1 kb from TTS). See Supplementary Data 1 for a list of NUP153 binding sites. b Metagene profiles of mean NUP153 binding at NUP153-positive and NUP153-negative TSS and enhancer (±5 kb), and TAD boundaries (±250 kb) (top). Number and percentage of NUP153 binding sites are presented as a table for the indicated genetic elements (bottom). (See Supplementary Data 2 for NUP153 binding sites at different genetic elements.) c Genome-wide CTCF and SMC3 binding sites were compared in control and NUP153 deficient (KD-1, KD-2) mouse ES cells. d Metagene profiles showing mean CTCF and SMC3 binding across CTCF-positive TSS (n = 2164), enhancers (n = 2272), and TAD boundaries (n = 2238) in control and NUP153 deficient mouse ES cells. e Mean CTCF binding in control and NUP153 KD mouse ES cells were compared and CTCF sites were grouped into two. Group I contained CTCF sites that showed greater mean CTCF binding in control cells over NUP153 KD cells. Group II contained CTCF sites that showed equal or lesser mean CTCF binding in control cells over NUP153 KD cells. Number of CTCF-positive sites across TSS and enhancer (±2.5 kb) and TAD boundaries (±250 kb), and the number of NUP153 target genes that associate with each group are shown as a table (top) (see also Supplementary Data 4 and Supplementary Fig. 3d). Metagene profiles showing mean NUP153 binding across CTCF-positive Group I and Group II TSS, enhancer (±2.5 kb) and TAD boundaries (±250 kb) (bottom).