Abstract 

A string of nucleosomes, in which genomic DNA is wrapped around histone proteins, is organized as chromatin within the cell nucleus. Chromatin spans a functional spectrum from transcriptionally active euchromatin (A-compartment) to transcriptionally silent heterochromatin (B-compartment). Understanding the physical differences between these two chromatin states is essential, yet specific labeling methods in living cells have been limited. Here, we introduce replication-dependent histone (Repli-Histo) labeling, a novel technique that marks nucleosomes in euchromatin and heterochromatin based on DNA replication timing. Using this method, we analyzed local nucleosome motion in the four known chromatin classes (IA, IB, II, and III) in living human cells. We found that more euchromatic (earlier-replicated) regions exhibit greater nucleosome motion, whereas more heterochromatic (later-replicated) regions show restricted motion. Nucleosomes in euchromatin domains fluctuate more like a liquid, whereas those in heterochromatin are highly constrained, resembling a gel-like state. Notably, these motion profiles persist throughout interphase. Furthermore, during mitosis, the replicated genome must be faithfully transmitted to two daughter cells as condensed chromosomes. Our single-nucleosome imaging demonstrated that nucleosomes in mitotic chromosomes are much more constrained than interphase chromatin. Condensins and local nucleosome-nucleosome interactions mediated by histone tails are major constraining factors during mitosis.

Biosketch

Kazuhiro Maeshima is currently the Head of the Department of Chromosome Science at the National Institute of Genetics (NIG), Japan, and serves as an Adjunct Professor at the Graduate Institute for Advanced Studies, SOKENDAI. He has held multiple academic and leadership positions at NIG, including Professor since 2019 and Assistant to the Director-General (2022–2024). Prior to this, he served as a Professor at the Structural Biology Center (2009–2019) and held research roles at RIKEN and the University of Geneva. In 1999, hearned his PhD in Medical Science from Osaka University.

Kazuhiro Maeshima is a recipient of the Kihara Memorial Foundation Academic Award (2016) and has been awarded prestigious fellowships including from RIKEN, the Naitoh Foundation, and JSPS.