Journal: Human genetics

Article Title: Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches

doi: 10.1007/s00439-021-02326-8

Figure Lengend Snippet: Interaction range detection difference results in the low overlap between DpnII and HindIII. A Distance ranges of intra-chromosomal interaction In DpnII PCC vs. HindIII PCHiC (panels 1–3) and MboI PCHiC vs. HindIII PCHiC (panel 4) in monocyte (Mon), naive B cells (nB), naive CD4 T cells (nCD4) and cardiomyocytes (CM). The distance between mid-points of bait fragment and promoter-interacting region (PIR) was plotted in boxplot for significant cis-interactions (CHiCAGO score > 5). The upper whisker, upper hinge, middle line, middle dot, down hinge and down whisker indicate 95, 75%, median, mean, 25 and 5% percentile. B The number of significant cis-interaction across the different distance between bait and PIR. The significant cis-interactions in DpnII PCC vs. HindIII PCHiC were grouped based on the binned distance (250 k intervals) between mid-points of bait fragment and PIR. Interaction number within each group was plotted. The inset depicts comparative distance interaction distributions of MboI PCHiC vs. HindIII PCHiC. C Venn diagram of genes annotated in DpnII PCC, MboI PCHiC, and HindIII PCHiC datasets. Genes were annotated when the bait of a significant interaction harbors its TSS. Regardless of PIR overlaps, shared (light green), DpnII-specific (dark green), MboI-specific (red), and HindIII-specific (blue) genes were determined based on whether corresponding baits have at least one significant distal interaction in both DpnII and HindIII, MboI and HindIII, or DpnII and MboI datasets. D Distance difference between interactions involving cutter-specific and shared genes. The interaction distance distribution measured by each method (x-axis) was calculated for cutter-specific gene sets (blue) or shared gene sets (red). The labeled p value was determined by two-tailed Wilcoxon rank-sum test. E Example of SERBP1 interacting region range difference between DpnII PCC and HindIII PCHiC in naïve B cells. The DpnII and HindIII baits for SERBP1 were overlapped. Only significant interactions (CHiCAGO score > 5) were shown with arcs in either DpnII PCC (red) and HindIII PCHiC (blue)

Article Snippet: The detection ranges of MboI PCHiC, DpnII PCC and HindIII PCHiC are all consistent with the size of mammalian topologically associating domains (TADs), which range from 100 to 5 Mb with an average of ~ 1Mb ( Rocha et al. 2015 ).

Techniques: Whisker Assay, Labeling, Two Tailed Test