胡桃坂計画研究代表、による成果が PNAS Nexus 誌に掲載されました!

Asymmetric fluctuation of overlapping dinucleosome studied by cryo-electron microscopy and small-angle X-ray scattering

Masahiro Shimizu, Hiroki Tanaka, Masahiro Nishimura, Nobuhiro Sato, Kayo Nozawa, Haruhiko Ehara, Shun-ichi Sekine, Ken Morishima, Rintaro Inoue, Yoshimasa Takizawa, Hitoshi Kurumizaka, Masaaki Sugiyama

Abstract
Nucleosome remodelers modify the local structure of chromatin to release the region from nucleosome-mediated transcriptional suppression. Overlapping dinucleosomes (OLDNs) are nucleoprotein complexes formed around transcription start sites as a result of remodeling, and they consist of two nucleosome moieties: a histone octamer wrapped by DNA (octasome) and a histone hexamer wrapped by DNA (hexasome). While OLDN formation alters chromatin accessibility to proteins, the structural mechanism behind this process is poorly understood. Thus, this study investigated the characteristics of structural fluctuations in OLDNs. First, multiple structures of the OLDN were visualized through cryo-electron microscopy (cryo-EM), providing an overview of the tilting motion of the hexasome relative to the octasome at the near-atomistic resolution. Second, small-angle X-ray scattering (SAXS) revealed the presence of OLDN conformations with a larger radius of gyration than cryo-EM structures. A more complete description of OLDN fluctuation was proposed by SAXS-based ensemble modeling, which included possible transient structures. The ensemble model supported the tilting motion of the OLDN outlined by the cryo-EM models, further suggesting the presence of more diverse conformations. The amplitude of the relative tilting motion of the hexasome was larger, and the nanoscale fluctuation in distance between the octasome and hexasome was also proposed. The cryo-EM models were found to be mapped in the energetically stable region of the conformational distribution of the ensemble. Exhaustive complex modeling using all conformations that appeared in the structural ensemble suggested that conformational and motional asymmetries of the OLDN result in asymmetries in the accessibility of OLDN-binding proteins.

PNAS Nexus, doi: 10.1093/pnasnexus/pgae484. (2024)
https://academic.oup.com/pnasnexus/advance-article/doi/10.1093/pnasnexus/pgae484/7845919