Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling

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.

CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

“…Overall, these data demonstrate that nucleosome binding by CHD4 induces significant slowtimescale changes into extra-nucleosomal DNA, and that this process probably involves either twisting or sliding of the extra-nucleosomal DNA towards the histone octamer. The data also point towards a binding mode for CHD4 that is distinct from that of CHD1 (Sabantsev et al, 2019), in that there is not a significant displacement of several turns of DNA away from the nucleosome surface upon CHD4 binding. Schematic showing the labelling scheme for 9 AF555 w60 Bio and the two possible remodelling directions after treating with CHD4, depending on whether the '9' end acts as an entry or an exit side.…”

Chromatin fibers stabilize nucleosomes under torsional stress

“…For example, it was demonstrated by Vlijm et al 43 that tetrasomes (complexes of 80 base pairs of DNA wrapped around a (H3-H4) 2 tetramer) spontaneously flip between left-and right-handed wrapped states of the DNA, suggesting that they could contribute to the torsional plasticity of chromatin 44 . Similar transient states were not detected in nucleosomes; yet, isolated nucleosomes can absorb some of the imposed torsional stress by buffering the twist defects in the DNA helix and thereby reduce the build-up of torque 43,45 . Earlier, Sheinin et al 46 investigated the force-induced unfolding of single nucleosomes from a rotationally constrained DNA template.…”

CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

“…The "twist diffusion" model proposes that the remodeller changes the structure of the DNA helix, causing a twist defect, and hydrolysis of ATP results in directional transfer of a few base pairs to the adjacent DNA segment 19,20 . Both models hypothesise that the entry site movement happens prior to DNA exiting the nucleosome, a concept that is supported by a recent three-fluorophore smFRET analysis of CHD1 and ISWI activity 21 .…”