Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers

• Published in: bioRxiv
• Main Authors: Kim, Jee Min, Carcamo, Claudia C, Jazani, Sina, Xie, Zepei, Feng, Xinyu A, Yamadi, Maryam, Poyton, Matthew, Holland, Katie L, Grimm, Jonathan B, Lavis, Luke D, Ha, Taekjip, Wu, Carl
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 15.01.2024
• Subjects: Chromatin; Deoxyribonucleic acid; Diffusion; DNA; Fluorophores; Gene expression; Low density lipoprotein; Nucleosomes; Patent applications; Translocation
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2023.06.13.544671

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.