Extended Data Fig. 6: Microcompartments are not artifacts resulting from incomplete ICE balancing nor chromatin accessibility.
From: Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
(a) Comparison of ICE balancing across methods and captured loci. Distributions of the sums of ICE-balanced contact matrix rows at 250 bp resolution are shown at the Klf1, Ppm1g, Fbn2, and Sox2 loci for RCMC, Micro-C12, and Hi-C31, as well as for the subset of RCMC rows containing microcompartment anchors. A sharp unimodal peak is consistent with ICE’s baseline assumption that all contact matrix rows and columns must sum to the same value. (b) Metaplots (above) and heatmaps (below) depicting ATAC signal at microcompartment anchors (left, separated by whether anchors coincide with an ATAC peak) and at all ATAC peaks in the Klf1 and Ppm1g capture loci (right, separated by whether peaks coincide with a microcompartment anchor). Signals are plotted in a 2 kb window centered on the anchor (left) or the ATAC peak (right). (c) RCMC contact maps at the Klf1 (left, 250 bp resolution) and Ppm1g (right, 1.6 kb resolution) loci indicating ATAC peaks that do not form microcompartments (left, magenta arrows) and a microcompartment anchor that does not coincide with an ATAC peak (right, cyan arrow). Black arrows (right) indicate microcompartmental loops involving the ATAC-negative microcompartment anchor. (d) Venn diagram breakdown of the overlap between all manually annotated microcompartment anchors and all ATAC peaks across the Klf1 and Ppm1g capture loci. Of 132 annotated microcompartment anchors, 12 do not coincide with ATAC peaks (cyan) while 120 do (purple, *). Of 353 called ATAC peaks, 187 do not form microcompartment anchors (magenta) while 166 do (purple, **). The apparent discrepancy of 120 microcompartment anchors being anchored by 166 ATAC peaks is due to two close ATAC peaks occasionally anchoring a single microcompartment.
