Fig. 2: SnapFISH identified chromatin loops with high accuracy.

A SnapFISH identified a CTCF-CTCF loop in chromosome 2 from mESC DNA seqFISH+ data. The top three tracks are mESC CTCF, mESC H3K4me3 and mESC H3K27ac ChIP-seq data. The middle three tracks represent HiCCUPS-identified loops at 25 Kb bin resolution, HiCCUPS-identified loops at 10 Kb bin resolution, and SnapFISH-identified loops at 25 Kb bin resolution, respectively. The bottom track is the Refseq gene annotation. Both anchors (dashed red boxes) contain mESC CTCF ChIP-seq peaks. Source data are provided as a Source Data file. B SnapFISH identified the Sox2 enhancer-promoter loop from mESC multiplexed DNA FISH data and mESC ORCA data. The top three tracks are mESC CTCF, mESC H3K4me3, and mESC H3K27ac ChIP-seq data. The middle four tracks represent the HiCCUPS-identified loop from mESC bulk Hi-C data³¹, the SnapFISH-identified loop from 1,416 129 alleles and 1416 CAST alleles, and the SnapFISH-identified loop from mESC ORCA data, respectively. All these loops are at 5 Kb bin resolution. The bottom track is the Refseq gene annotation. The red dashed box on the left and the right represents the location of the promoter of the Sox2 gene and its super-enhancer, respectively. We allow for a 5 Kb gap between loop anchors and the Sox2 promoter or super-enhancer (see details in Methods). Source data are provided as a Source Data file. C SnapFISH identified an enhancer-promoter loop in chromosome 15 from DNA seqFISH+ data in mouse excitatory neurons. The top five tracks are ATAC-seq, H3K4me1, H3K4me3, H3K27ac and RNA-seq data from cortical excitatory neurons L2/3 collected from mouse frontal cortex tissue (FC_L2_3 for short)³⁵. The bottom two tracks are SnapFISH-identified 25 Kb bin resolution loops and the Refseq gene annotation. The left anchor (dashed red box on the left) is at gene Myc. The right anchor (dashed red box on the right) is at the transcription end site of gene Pvt1, which contains an ATAC peak. Source data are provided as a Source Data file.