Abstract
ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single rate-limiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome.
Highlights
ATP-dependent chromatin remodelling enzymes regulate DNA accessibility in eukaryotic genomes
Using both Chd[1] and the catalytic subunit of an ISWI-type remodeler, SNF2h, we show a clear delay between translocation of DNA onto and off of the nucleosome, with DNA first shifting onto the entry side
Chromatin remodellers translocate on DNA from a fixed position on the nucleosome, which results in a global shift of DNA around the histone octamer
Summary
ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. A key question in the field is how ATP-dependent nucleosome sliding is achieved This includes not just the initial phase of DNA translocation or a single catalytic cycle of the motor, but how local perturbations by the ATPase domain of the remodeller result in a global shift of DNA with respect to the histone octamer. We present the simultaneous detection of DNA movement on both sides of the nucleosome by three-colour smFRET48–51, which reveals a distinct order of DNA translocation Using both Chd[1] and the catalytic subunit of an ISWI-type remodeler, SNF2h, we show a clear delay between translocation of DNA onto and off of the nucleosome, with DNA first shifting onto the entry side. Using site-specific cross-linking, we observe that Chd[1] can shift the DNA to the exit side by 4 bp even in the presence of a gap that blocks ATPase translocation after 4–5 bp
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