Extended Data Fig. 6: Halting loop extrusion leads to widespread changes in chromatin folding to orchestrate an inflammatory gene program.
From: Nuclear morphology is shaped by loop-extrusion programs
a, Scatter plot shows A versus B compartmentalization (50 kbp resolution) in NIPBL-FKBP12F36V-EYFP ECOMG cells cultured in the absence (x axis) or presence of dTAG-13 (y axis). b, Box plot represents differential segregation scores (50 kbp resolution) for cells cultured in the absence versus presence of dTAG-13. one-sided P < 0.05. In each box, the upper edge, horizontal centre line and lower edge represent the 75th percentile, median and 25th percentile, respectively. The upper whiskers represent the 75th percentile + 1.5× the IQR. The lower whiskers represent the 25th percentile - 1.5× the IQR. c, Venn diagram indicates number of gained or lost chromatin loops in NIPBL-FKBP12F36V-EYFP ECOMG cultured in the absence versus presence of dTAG-13. d, Transcript abundance correlates with the assembly of loops in NIPBL-FKBP12F36V-EYFP cells cultured in the absence versus the presence of dTAG-13. Mean change and corresponding distribution of loops associated with transcriptional silencing or activation log2 FC > = 2 or log2 FC < = −2) in NIPBL-depleted cells are shown. e, GO-based functional classification of differentially expressed transcripts that are associated with gained paired promoter and enhancer elements in NIPBL-depleted cells. f, 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. g, Genome browser tracks indicate RNA-seq, ATAC-seq and Hi-C reads across the Myc locus for NIPBL-FKBP12F36V-EYFP ECOMG cells cultured in the absence or presence of dTAG-13. h, Genome browser tracks indicate RNA-seq, ATAC-seq and Hi-C reads across the Nlrp3 and Nfil3 loci for NIPBL-FKBP12F36V-EYFP cells cultured in the absence or presence of dTAG-13.
