Extended Data Fig. 5: Depletion of NIPBL increases chromatin accessibility at neutrophil-specific promoters and enhancers.
From: Nuclear morphology is shaped by loop-extrusion programs
a, NIPBL depletion increases chromatin accessibility across enhancer and promoter elements. NIPBL-FKBP12F36V-EYFP ECOMG progenitors were cultured with β-oestradiol in the absence or presence of dTAG-13. Changes in chromatin accessibility of cells cultured in the absence (0 h) or presence of dTAG-13 (6 and 72 h) were analysed and presented as tornado plots. Clusters were generated using K-means clustering (n = 2). The number of regions associated with neutrophil-specific promoters (H3K4me3), active enhancers (H3K27Ac and H3K4me1) or weak enhancers (H3K4me1) and transcriptionally silent regions are shown. Tornado plots were generated by sorting maximum signal strength intensities for ATAC-seq reads. Colour scale intensities represent normalized read scores (reads per 10 million uniquely mapped reads per base pair). b, Cis elements associated with increased chromatin accessibility at enhancers and promoters are shown. P values for motif enrichment and matched transcription-factor-binding sites are indicated. c, NIPBL depletion decreases chromatin accessibility across a subset of enhancer and promoter elements. Changes in chromatin accessibility of cells cultured in the absence (0 h) or presence of dTAG-13 (6 and 72 h) were analysed and presented as tornado plots. d, Cis elements associated with decreased chromatin accessibility at enhancers and promoters are shown. e, Genome browser tracks depicting RNA-seq, ChIP–seq and ATAC-seq reads at the Myc, Spi1 and Il1b loci are shown.
