Fig. 3: Loss of the 5′ intergenic boundary of Notch affect gene expression.

a Schematic representation of the TAD landscape surrounding Notch and the genes tested for transcriptional changes. b Transcription of Notch as measured by RT-qPCR. Transcriptional quantifications in each CRISPR mutant compared to wild-type using three primer pairs spanning the Notch D1 domain and one pair for the Notch D2 domain. Significant differences between wild-type and CRISPR mutants were calculated using a t-test. n = 3, p-value *p < 0.05, **p < 0.01, ***p < 0.001. Error bars represent the standard error of the mean (s.e.m.) of four replicates (n = 4). Source data are provided as Source Data File. c Transcription of genes located at TADs flanking Notch as measured by RT-qPCR in wild-type and each CRISPR mutant. Significant differences between wild-type and CRISPR mutants were calculated using a t-test. n = 3, p-value *p < 0.05, **p < 0.01, ***p < 0.001. Error bars represent the standard error of the mean (s.e.m.) of four replicates (n = 4). Source data are provided as Source Data File. d Virtual-4C for wild-type and mutant clones using the 5′ UTR (top) and the exon 6 (bottom) as viewpoints. Shown are the percent of interactions between the viewpoints and regions within the kirre domain-2, the Notch D1 domain, the Notch D2 domain, and the dnc domain for both wt and all mutant samples. ChIP-seq tracks for CP190 and RNA Pol II are also shown. e Virtual-4C for wild-type and mutant clones using the promoter of the kirre-full isoform (top) and the promoter of dnc (bottom) as viewpoints. Shown are the percent of interactions between the viewpoints and the TADs in which they are located. Arrows indicate regions with ectopic interactions. ChIP-seq tracks for CP190 and RNA Pol II are also shown.