Figure 1: 5C approach to identify looping interactions.
From: The long-range interaction landscape of gene promoters
a, 5C design28. Reverse 5C primers were designed for HindIII fragments that contain a TSS (red; according to the GENCODE v720) and forward 5C primers for all other ‘distal’ HindIII fragments (blue). b, Heat map of all interrogated TSS–distal fragment interactions in 14 ENCODE regions (ENm001–ENm014) in K562 cells. Fragments are displayed in their genomic order. Each dark rectangular area in the heat map denotes interactions within a single ENCODE region whereas remaining areas denote interactions between regions. ENCODE regions that are on the same chromosome show a higher interaction frequency (arrow) than regions that were on different chromosomes. c, d, Examples of 5C interaction profiles for two TSSs indicated by vertical orange bars (left, ACSL6 gene located in ENm002; right, γ-δ-globin located in ENm009). The solid red lines show the expected interaction level (Lowess line, Methods); dashed red lines above and below indicate Lowess ± 1 standard deviation. 5C signals that are significantly higher than expected in both biological replicates (green circles, FDR = 1%) are considered looping interactions. Interactions that are significant in only one replicate (blue circles) are not considered as a high-confidence 5C looping interaction. 5C peak calling detects a long-range interaction between the TSS of ACSL6 and a distal CTCF-bound element in GM12878 cells. The approach identifies the known long-range interactions of γ-δ-globin to HS3, HS4, HS5 and HS-111 and several additional DHS and CTCF sites in K562 cells2 (labelled).
