Living human cells appear to hold the local movement of their DNA at a remarkably steady level through most of the cell cycle, only dialing it up when something goes wrong, according to a new study from a team led by Kazuhiro Maeshima at Japan’s National Institute of Genetics.
Genomic DNA is wrapped around core histone proteins to form nucleosomes, the basic units of chromatin, and this dynamic chromatin behavior, tied to chromatin accessibility, plays a critical role in genome functions such as transcription and DNA replication and repair. During interphase, the period between cell divisions, DNA is replicated and the nucleus expands, all while cells continue these essential functions. How DNA’s physical behavior holds up through these large-scale changes had remained unclear. In an earlier study using synchronized human cells, Professor Maeshima’s team found that local chromatin motion stayed nearly constant across the G1, S, and G2 phases. The new study asked whether the same holds true under more natural conditions, in cells growing asynchronously without drug-induced synchronization.
To find out, the researchers combined single-nucleosome imaging with Fucci probes, fluorescent markers that change color as a cell progresses through the cycle, letting them identify each living cell’s cycle stage without chemical synchronization. Using HeLa and HCT116 cells expressing H2B-HaloTag to mark bulk DNA, they tracked individual nucleosomes and matched that movement to each cell’s Fucci signal. Across asynchronously growing cells, average local nucleosome motion remained nearly constant from G1 through S and into G2, even as the genome doubled in content and the nucleus grew substantially in volume.
The team also examined nucleosomes carrying H3.3, a histone variant enriched in active chromatin, or euchromatin. These nucleosomes moved more than bulk H2B-marked nucleosomes overall, but that elevated level of motion likewise stayed constant across interphase, suggesting different chromatin environments each maintain their own characteristic baseline of movement as the 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, first author of the study published in Journal of Cell Science. “This near-constant motion may provide similar physical conditions for housekeeping genome functions throughout interphase.”
That stability wasn’t absolute, though. When the researchers inhibited transcription, nucleosome motion increased throughout interphase. Replication stress induced with hydroxyurea and DNA damage induced with cisplatin produced the same effect, each raising average nucleosome motion above its steady baseline.
“Cells seem to maintain local DNA motion near a steady level for routine housekeeping tasks, but they can change this motion when necessary,” Professor Maeshima added. “For example, increased DNA motion after DNA damage may help cells perform ad hoc tasks such as recruiting DNA repair factors.”
Genomic DNA is wrapped around core histone proteins to form nucleosomes, the basic units of chromatin, and this dynamic chromatin behavior, tied to chromatin accessibility, plays a critical role in genome functions such as transcription and DNA replication and repair. During interphase, the period between cell divisions, DNA is replicated and the nucleus expands, all while cells continue these essential functions. How DNA’s physical behavior holds up through these large-scale changes had remained unclear. In an earlier study using synchronized human cells, Professor Maeshima’s team found that local chromatin motion stayed nearly constant across the G1, S, and G2 phases. The new study asked whether the same holds true under more natural conditions, in cells growing asynchronously without drug-induced synchronization.
To find out, the researchers combined single-nucleosome imaging with Fucci probes, fluorescent markers that change color as a cell progresses through the cycle, letting them identify each living cell’s cycle stage without chemical synchronization. Using HeLa and HCT116 cells expressing H2B-HaloTag to mark bulk DNA, they tracked individual nucleosomes and matched that movement to each cell’s Fucci signal. Across asynchronously growing cells, average local nucleosome motion remained nearly constant from G1 through S and into G2, even as the genome doubled in content and the nucleus grew substantially in volume.
The team also examined nucleosomes carrying H3.3, a histone variant enriched in active chromatin, or euchromatin. These nucleosomes moved more than bulk H2B-marked nucleosomes overall, but that elevated level of motion likewise stayed constant across interphase, suggesting different chromatin environments each maintain their own characteristic baseline of movement as the 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, first author of the study published in Journal of Cell Science. “This near-constant motion may provide similar physical conditions for housekeeping genome functions throughout interphase.”
That stability wasn’t absolute, though. When the researchers inhibited transcription, nucleosome motion increased throughout interphase. Replication stress induced with hydroxyurea and DNA damage induced with cisplatin produced the same effect, each raising average nucleosome motion above its steady baseline.
“Cells seem to maintain local DNA motion near a steady level for routine housekeeping tasks, but they can change this motion when necessary,” Professor Maeshima added. “For example, increased DNA motion after DNA damage may help cells perform ad hoc tasks such as recruiting DNA repair factors.”