Maeshima Group / Genome Dynamics Laboratory
Kanemaki Group / Molecular Cell Engineering Laboratory
Average local nucleosome motion remains nearly constant during interphase in living human cellsLinker histone H1 functions as a liquid-like glue to organize chromatin in living human cells
Yu Nagata, Shiori Iida, Masa A. Shimazoe, Sachiko Tamura, Kako Nakazato, Kai Shimizu, Yuki Hatoyama, Masato T. Kanemaki and Kazuhiro Maeshima *
*corresponding author
Journal of Cell Science DOI: 10.1242/jcs.265367
Genome Dynamics Laboratory
Genomic DNA in the cell nucleus is wrapped around core histone proteins to form nucleosomes and is organized as chromatin together with other proteins and RNAs. During interphase, DNA content doubles from G1 to G2, and the nuclear volume also increases. At the same time, basic genome functions such as transcription, DNA replication, and DNA repair take place during interphase. However, how the local physical properties of chromatin are maintained during these large changes remains unclear.
A research group led by Yu Nagata (SOKENDAI graduate student), Shiori Iida (Project Researcher; currently a postdoctoral researcher at the Max Planck Institute for Molecular Biomedicine), Masa A. Shimazoe (SOKENDAI graduate student and JSPS DC1 Fellow), Sachiko Tamura (Technical Staff), Kako Nakazato (SOKENDAI graduate student and JSPS DC2 Fellow), Kai Shimizu (SOKENDAI graduate student), and Kazuhiro Maeshima (Professor) at the Genome Dynamics Laboratory, National Institute of Genetics, in collaboration with Masato T. Kanemaki (Professor) and his group at the Molecular Cell Engineering Laboratory, analyzed nucleosome motion throughout interphase in living HeLa cells without drug-induced cell-cycle synchronization.
The researchers tracked individual nucleosomes using H2B-Halo and determined cell-cycle stages using Fucci probes. Average nucleosome motion remained nearly constant throughout G1, S, and G2 phases (Figure). This result is consistent with the finding previously obtained using drug-synchronized cells (Iida et al., Science Advances, 2022; https://www.science.org/doi/10.1126/sciadv.abn5626).
The researchers further labeled the histone variant H3.3, which is enriched in transcriptionally active euchromatin, with HaloTag. H3.3-Halo nucleosomes showed greater motion than H2B-Halo nucleosomes, but this higher motion also remained nearly constant throughout interphase (Figure). Similar results were obtained in human HCT116 cells.
On the other hand, nucleosome motion increased following transcription inhibition, replication stress, and DNA damage. These results show that cells maintain local chromatin motion at a nearly constant level throughout interphase, even though DNA content and nuclear volume substantially change, while still being able to alter the motion when necessary. Our study suggests that interphase chromatin provides a stable physical environment for genome functions such as RNA transcription, DNA replication, and DNA repair. This work was supported by JSPS and MEXT KAKENHI Grants (JP24H00061 and JP25K24664), the Takeda Science Foundation, JSPS Research Fellowships (JP24KJ1161 and JP26KJ1223), and the Research Organization of Information and Systems (ROIS). Sequencing and data analysis were also supported by the Platform for Advanced Genome Science (PAGS; JP22H04925).
The average motion of H2B-Halo nucleosomes remains nearly constant from G1 to G2, despite increases in DNA content and nuclear volume during interphase. Nucleosomes in euchromatin (H3.3-Halo nucleosomes) show greater motion than H2B-Halo nucleosomes, and this difference in motion is also maintained throughout interphase. Nucleosome motion transiently increases in response to perturbations such as DNA damage, replication stress, and transcription inhibition. This suggests that interphase provides a stable physical environment suitable for routine genome functions throughout interphase.
Movements of nucleosomes labeled with H2B-Halo (left) and H3.3-Halo (right) in HeLa cells. Euchromatin nucleosomes (H3.3-Halo) show greater motion than H2B-Halo nucleosomes.