Extended Data Fig. 20. CTCF-associated cCRE–gene pairs.

a, Enrichment of CTCF binding sites from 8-week-old mouse forebrain³¹ in cCRE modules. b, t-SNE of sn-m3C-seq cells (n = 5,142) coloured by clusters. This panel was replicated from the accompanying paper²⁹ for illustration purposes. c, Percentage of cCRE from module M1 with and without CTCF binding overlapping with contact loops identified from snm3C-seq in hippocampus²⁹. Shuffled loops are generated by randomly flipping one of the anchors. d, Genome browser track⁶⁰ view at the Nsg2 locus as an example for CTCF dependent loops. Displayed are chromatin accessibility profiles for several neuronal and non-neuronal clusters, positively correlated cCRE–gene pairs, H3K27ac in postnatal day 0 (P0) mouse forebrain¹⁰⁸ and CTCF from in cortex from 8-week-old mouse³¹. The triangle heat map (top) shows chromatin contacts in DG neurons and MGC derived from snm3C-seq data (see accompanying manuscript²⁹). DG-specific loops are highlighted by boxes.