The Chd1 chromatin remodeler can sense both entry and exit sides of the nucleosome

Abstract

Chromatin remodelers are essential for establishing and maintaining the placement of nucleosomes along genomic DNA. Yet how chromatin remodelers recognize and respond to distinct chromatin environments surrounding nucleosomes is poorly understood. Here, we use Lac repressor as a tool to probe how a DNA-bound factor influences action of the Chd1 remodeler. We show that Chd1 preferentially shifts nucleosomes away from Lac repressor, demonstrating that a DNA-bound factor defines a barrier for nucleosome positioning. Rather than an absolute block in sliding, the barrier effect was achieved by altered rates of nucleosome sliding that biased redistribution of nucleosomes away from the bound Lac repressor site. Remarkably, in addition to slower sliding toward the LacO site, the presence of Lac repressor also stimulated sliding in the opposite direction. These experiments therefore demonstrate that Chd1 responds to the presence of a bound protein on both entry and exit sides of the nucleosome. This sensitivity to both sides of the nucleosome allows for a faster and sharper response than would be possible by responding to only the entry side, and we speculate that dual entry/exit sensitivity is also important for regularly spaced nucleosome arrays generated by Chd1 and the related ISWI remodelers.

The Chd1 chromatin remodeler shifts hexasomes unidirectionally

“…How Chd1 might sense unwrapping on the entry side is not yet clear, but loss of DNA wrapping from an H2A/H2B dimer may alter dynamics of histone-histone and the remaining histone-DNA contacts, providing a means for Chd1 to indirectly determine the state of the nucleosome prior to sliding. Sensitivity to DNA unwrapping is consistent with slower nucleosome sliding activity of Chd1 when a transcription factor is bound on the entry side of the nucleosome (Nodelman et al, 2016). Transcription factors compete with histone-DNA contacts and can dramatically unwrap nucleosomal DNA when their binding sites are located within the histone footprint (Li and Widom, 2004; North et al, 2012).…”

Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome

“…Coupling the availability of exit DNA to dampening ATPase activity makes sense for a nucleosome spacing factor such as Chd1, as increasing activity when exit-side DNA is occupied would bias nucleosome sliding away from bound factors or other nucleosomes. This model for exit-side inhibition would explain the faster nucleosome sliding we observed when one side of the nucleosome was bound by LacI (Nodelman et al, 2016). In that study, the presence of LacI at a LacO(−11) site, which would displace the Chd1 DBD from its position on exit DNA described here, increased the rate that Chd1 shifted nucleosomes away from the LacO site by 5- to 6-fold.…”

“…It is well established that Chd1 and ISWI remodelers slide nucleosomes away from bound transcription factors (Kang et al, 2002; Li et al, 2015; Nodelman et al, 2016; Pazin et al, 1997) and generate evenly spaced arrays (Gkikopoulos et al, 2011; Ito et al, 1997; Lusser et al, 2005; Ocampo et al, 2016; Pointner et al, 2012; Tsukiyama et al, 1999). These characteristics are reflected by a preference for sliding mononucleosomes away from DNA ends, and indicate the ability to respond to DNA outside the nucleosome core (Kagalwala et al, 2004; McKnight et al, 2011; Stockdale et al, 2006; Yang et al, 2006).…”

“…The wrapping of DNA into nucleosomes is antagonistic to most transcription factors, both for reducing accessibility but also accelerating dissociation of bound factors (Luo et al, 2014). Thus, rapidly shifting the histone core away from DNA-bound factors at the nucleosome edge would greatly increase transcription factor occupancy (Nodelman et al, 2016). The sensitivity of Chd1 for exit-side availability would also be expected to promote regular nucleosome spacing by shifting closely packed or overlapping nucleosomes away from their neighbors.…”

The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

“…In contrast, when the DBD and ATPase are on opposite DNA gyres and therefore physically close, these domains can communicate with each other. As suggested by faster nucleosome sliding away from Lac repressor and dampening of ATPase activity (Nodelman et al, 2017; Nodelman et al, 2016), this cross-gyre communication appears to interfere with nucleosome sliding. The dynamics by which Chd1 switches between active and inhibited states has not previously been examined.…”