Extended Data Fig. 9: Halting loop extrusion activates gene expression at genomic regions enriched for interchromosomal interactions.
From: Nuclear morphology is shaped by loop-extrusion programs
Box plots show log2-transformed fold changes in FKPM reads (+dTAG versus −dTAG treated cells). 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. Genes whose transcription start sites were located in the euchromatic (A) compartment were segregated into 3 groups based on low, median and high gene density. At similar gene density, the euchromatic regions that were enriched for interchromosomal interactions were associated with upregulated gene expression compared to the euchromatic regions without interchromosomal interactions. Two-sample t-test was performed. P = 2.90 × 10−9 (Total), P = 0.0014 (Group 1), P = 1.83 × 10−6 (Group 2), P = 5.18 × 10−10 (Group 3).
