The ChAHP complex counteracts chromatin looping at Ctcf sites that have emerged from recent SINE expansions

Ctcf and cohesin are key players in the three dimensional organization of chromatin. Whereas genome-wide Ctcf binding has diverged substantially between species due to transposon-mediated motif expansions, demarcation of topologically associating domains (TADs) by Ctcf is remarkably well conserved. Yet, the Ctcf consensus motif poorly predicts TADs and the majority of Ctcf sites are not at TAD boundaries. Here we demonstrate that the ChAHP complex (Chd4, Adnp, HP1) competes with Ctcf for a common set of genomic binding sites. In absence of ChAHP, novel insulated regions are formed at ChAHP bound sites, whereas proximal canonical boundaries are weakened. These data reveal that Ctcf-mediated loop formation is modulated by a distinct zinc-finger protein complex. Strikingly, ChAHP bound loci are mainly situated within evolutionary young SINE B2 transposable elements. This further implicates ChAHP in maintenance of evolutionary conserved spatial chromatin organization by buffering novel Ctcf binding sites that emerged through SINE expansions. Overall design: Ctcf, cohesin (Rad21) and H3K27ac ChIPs were performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. Hi-C was performed in biological replicates on independent isogenic wild-type (wt) and Adnp knock-out (AdnpKO) ES cell clones. For each biological Hi-C replicate, we performed a technical replicate for which the cells were grown and processed in parallel. 4C experiments were performed in biological duplicates using the same cell lines as for Hi-C.