Local DNA motion remains nearly constant during cell interphase

Human genomic DNA is wrapped around core histone proteins to form nucleosomes, the fundamental units of chromatin. During interphase, the period between cell divisions, DNA is replicated and the nucleus becomes larger. At the same time, cells must continuously carry out essential genome functions such as transcription, DNA replication and DNA repair. How the behavior of genomic DNA is maintained during these large changes has remained unclear.

A research team led by Professor Kazuhiro Maeshima at the National Institute of Genetics (NIG) and SOKENDAI, Japan, has now shown that average local DNA motion remains nearly constant throughout interphase in living human cells. Importantly, the researchers also found that this motion is not just constant: it can increase in response to cellular perturbations such as transcription inhibition, replication stress and DNA damage.

In a previous study, the team showed using synchronized human cells that local chromatin motion remained nearly constant throughout G1, S and G2 phases (Iida et al., Science Advances, 2022; https://www.science.org/doi/10.1126/sciadv.abn5626). The present study tested whether this behavior is also observed in asynchronously growing cells without drug-induced synchronization.

To study DNA motion during the cell cycle under physiological conditions, the researchers combined single-nucleosome imaging with fluorescent cell-cycle indicators known as Fucci probes. Fucci probes change their fluorescent color according to cell-cycle progression, allowing the researchers to identify the cell-cycle stage of individual living cells without using prolonged drug treatments to synchronize them.

By labeling the core histone H2B with HaloTag, which can mark bulk DNA, the researchers were able to visualize and track individual nucleosomes in living human cells. They then combined these measurements with Fucci signals to determine how local nucleosome motion changes as cells progress from G1 through S to G2 phase. Using asynchronously growing cells, the team found that average local nucleosome motion remained nearly constant throughout interphase. This means average local DNA motion remained nearly constant throughout interphase.

This stability is notable because major physical changes occur during the same period. As genomic DNA doubles, nuclear volume increases substantially. Nevertheless, local DNA motion is maintained at a similar average level.

The researchers next examined nucleosomes containing the histone variant H3.3, which is enriched in active chromatin, or euchromatin. H3.3-HaloTag nucleosomes showed greater motion than bulk H2B-HaloTag nucleosomes, but this higher level of motion also remained nearly constant throughout interphase. These results suggest that different chromatin environments retain characteristic levels of local motion as the cell cycle progresses.

"Our results show that local DNA motion is maintained at a surprisingly similar level even while DNA is being duplicated and the nucleus is growing," said Yu Nagata. "This near-constant motion may provide similar physical conditions for housekeeping genome functions throughout interphase."

The team also asked whether this steady motion could be altered when cells face different conditions. Transcription inhibition increased nucleosome motion throughout interphase. Replication stress induced by hydroxyurea and DNA damage induced by cisplatin also increased average nucleosome motion.

Cells seem to maintain local DNA motion near a steady level for routine housekeeping tasks, but they can change this motion when necessary. For example, increased DNA motion after DNA damage may help cells perform ad hoc tasks such as recruiting DNA repair factors."

Professor Kazuhiro Maeshima, National Institute of Genetics (NIG) and SOKENDAI, Japan