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

Abstract

Summary Chromatin remodelers use a helicase-like ATPase motor to reposition and reorganize nucleosomes along genomic DNA. Yet how the ATPase motor communicates with other remodeler domains in the context of the nucleosome has so far been elusive. Here we report for the Chd1 remodeler a unique organization of domains on the nucleosome that reveals direct domain-domain communication. Site-specific cross-linking shows that the chromodomains and ATPase motor bind to adjacent SHL1 and SHL2 sites, respectively, on nucleosomal DNA and pack against the DNA-binding domain on DNA exiting the nucleosome. This domain arrangement spans the two DNA gyres of the nucleosome and bridges both ends of a wrapped, ~90 bp nucleosomal loop of DNA, suggesting a means for nucleosome assembly. This architecture illustrates how Chd1 senses DNA outside the nucleosome core and provides a basis for nucleosome spacing and directional sliding away from transcription factor barriers.

The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

“…The reason for this instability is unclear, but was observed with two different positioning sequences. While present evidence suggests that Chd1 shifts nucleosomes when at SHL2 (Nodelman et al, 2017), two recent studies have shown that remodeler ATPases can also engage with the outer gyre of DNA: the isolated SWI/SNF ATPase, in a cryoEM study, was shown to bind SHL6 as well as SHL2 (Liu et al, 2017), and yeast INO80 was shown to reposition nucleosomes by translocating on DNA around SHL5 (Brahma et al, 2017). For Chd1, reversal of DNA movement may therefore result from translocation of the ATPase at the SHL2 site on the opposite side of the nucleosome (Figure 3G, model 1), or by reorienting to SHL5 or SHL6 on the opposite gyre, which is close to the first SHL2 site (Figure 3G, model 2).…”

“…The ATP-dependent chromatin assembly and remodeling factor (ACF), an ISWI-type remodeler, ensures back-and-forth sliding by cooperatively binding to nucleosomes as dimers, with each remodeler ATPase poised at an SHL2 site (Racki et al, 2009). While the nucleosome can simultaneously accommodate two Chd1 proteins, one at each SHL2 site (Nodelman et al, 2017), here we make the unexpected discovery that back-and-forth movement of nucleosomal DNA can be achieved by a single Chd1 remodeler (Figure 2). After initially shifting the nucleosome away from the short end, however, Chd1 appears unable to stably shift nucleosomes in the reverse direction (Figure 3 and S1).…”

“…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.…”

“…Deletion of the DBD severely impaired nucleosome sliding activity, yet substituting foreign binding domains restored robust sliding, indicating that the DBD is not mechanically required for nucleosome repositioning (McKnight et al, 2011; Nodelman and Bowman, 2013; Patel et al, 2013). More recently, the finding that the DBD communicates with the ATPase motor when bound to DNA flanking the nucleosome has suggested that the DBD also plays a regulatory role (Nodelman et al, 2017). Like SWI/SNF and ISWI remodelers, the ATPase motor of Chd1 translocates on DNA at superhelix location 2 (SHL2), an internal site ~20 bp from the nucleosome dyad (McKnight et al, 2011; Saha et al, 2005; Schwanbeck et al, 2004; Zofall et al, 2006).…”

“…DNA translocation by these remodeler ATPases is believed to be unidirectional, and therefore relative to the SHL2 site where the ATPase motor is engaged, DNA flanking one side of the nucleosome shifts onto the core (entry side) while DNA on the other turn or gyre of DNA shifts further away from the nucleosome core (exit side). The ATPase motor and DBD of Chd1 can therefore be in two distinct organizations on the nucleosome: they can be either on opposite DNA gyres and spatially close together on the same “edge” of the nucleosome, or on the same DNA gyre and separated from each other across the face of the nucleosome (Nodelman et al, 2017). When on the same gyre and across the face of the nucleosome, the DBD can assist the ATPase motor via tethering, but would be too far to directly contact the ATPase motor.…”