Fig. 3

TEs are necessary for maintaining conserved higher-order chromosomal structures in humans. a Results of a CRISPR/Cas9-based deletion of an L1M3f element at chr10:26–28 Mb in GM187278 cells. Mega-contact maps (details in “Methods”) generated using Hi-C² technology for the (top) WT locus and (bottom) KO (ΔL1M3f) locus. b Virtual 4C plot displaying total percent interactions emanating from an anchor on a 5-kb window containing the L1M3f element. c Boxplot measuring the percent inter-domain interactions (Additional file 3: Table S2.5) across the targeted domain and a control domain (boundaries unaffected by CRISPR edits) using subsampled contact maps (details in “Methods”). d Results of CRISPR/Cas9-based deletion of an LTR41 element at chr8:70.3–71.8 Mb in GM12878 cells. Mega-contact maps generated in Hi-C² experiments for the (top) WT locus and (bottom) KO (ΔLTR41) locus. e Virtual 4C plot displaying total percent interactions emanating from an anchor on a 5-kb window containing the left anchor CTCF of the conserved loop, and f the LTR41 element