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 introduction of gaps in nucleosomal DNA has also been used to infer the directionality with which ATPases's move along DNA. Introduction of gaps distal to the SHL 2 location closest to the entry linker DNA has been observed to impede the action of Snf2, Iswi and Chd1 enzymes (McKnight et al., 2011; Saha et al., 2005; Zofall et al., 2006) . This has been used as evidence that . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/290874 doi: bioRxiv preprint the enzyme translocation that drives repositioning initiates from the SHL 2 located distal to the entry DNA. As a consequence it has been proposed that Chd1 bound in the cross gyres conformation, that we and others observe, represents an inactive state in which the interaction of the DNABD with linker DNA is inhibitory (Farnung et al., 2017; Nodelman et al., 2017) . If this were the case, then Chd1 directed repositioning might be expected to be limited once a nucleosome has moved far enough from a DNA end to enable the DNABD to contact linker DNA. On Chd1 bound nucleosomes the DNABD contacts extend to 7bp from the nucleosomes edge. A stall to repositioning after 7bp is not observed, instead Chd1 repositions nucleosomes 23-39 base pairs into a 54 base pair linker in a very similar way to Isw1a and Isw2 The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/290874 doi: bioRxiv preprint Both budding yeast Chd1 and human Chd2 are found to be enriched within coding regions (de Dieuleveult et al., 2016; Gkikopoulos et al., 2011; Lee et al., 2017) . Histone H3 K36me3 is a hallmark of coding region nucleosomes, so we prepared nucleosomes alkylated to mimic trimethylation at this position.