Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

Ramasubramanian Sundaramoorthy; Amanda L. Hughes; Hassane El-Mkami; David Norman; Tom Owen-Hughes

The Chd1 enzyme has the ability to organise spaced arrays of nucleosomes both in vitro and in vivo (Gkikopoulos et al., 2011; Lusser et al., 2005; Robinson & Schultz, 2003) . Enzymes that exhibit this organising activity typically reposition nucleosomes away from the ends of short DNA fragments. This is also true for Chd1 (McKnight et al., 2011; Stockdale et al., 2006) . As a result we would anticipate that Chd1 would be most likely to reposition nucleosomes away from the short (exit) linker, encroaching into the long Inferring the mechanism of Chd1 from NS3 is complicated by the fact these enzymes are not so closely related. Conserved motifs are difficult to align based on sequence alone. In addition some aspects of nucleic acid binding by both Snf2 and Chd1 profoundly differ from NS3. Notably, motifs II and III within lobe 1 contact the opposite, 3'-5' stand, which is not present in NS3. In addition, Snf2 related chromatin remodelling enzymes contain features that extend the nucleic acid binding cleft between the two ATPase lobes and make contacts with both strands ( Figure 6 ). As a result of the extensive contacts with both strands, it is possible that the assignment of guide and tracking strands within remodelling ATPases is not absolute as tracking may be coupled to both strands. Consistent with this experiments that have probed the action of remodelling enzymes using short gaps in either strand of nucleosomal DNA have found them to be sensitive to lesions in either strand (Saha et al., 2005; Zofall et al., 2006) .