Extended Data Fig. 3: Depletion of NIPBL interferes with RAD21 occupancy.
From: Nuclear morphology is shaped by loop-extrusion programs
a, NIPBL depletion modulates Rad21 occupancy. NIPBL-FKBP12F36V-EYFP progenitors were cultured with β-oestradiol in the absence or presence of dTAG-13. RAD21 occupancy was analysed using ChIP–seq analysis and presented as tornado plots. Cluster I is comprised of RAD21-binding sites that were enriched upon depletion of NIPBL. Cluster II consists of RAD21-binding sites that were depleted upon removal of NIPBL. In NIPBL-depleted cells 9,293 RAD21-binding sites were lost, 531 binding sites were gained and 7,773 binding sites were shared. RAD21 peaks were generated using FDR <1e-25 and fold enrichment > 5. b, Cis elements associated with 9,293 RAD21-bound sites that were depleted in NIPBL-depleted cells. P values for motif enrichment and matched transcription-factor-binding sites are indicated. c, Cis elements associated with 531 RAD21-bound sites that were gained upon removal of NIPBL expression. d, Genome browser tracks represent ChIP–seq reads in ECOMG progenitors cultured in the absence or presence of dTAG-13. IGV Tracks for Spi1, Nfil3, Ikzf1, Cebpa, Nlrp3 and Lcn2 loci are shown.
