Maeshima Group / Genome Dynamics Laboratory
Kurokawa Group / Genome Evolution Laboratory
Kanemaki Group / Molecular Cell Engineering Laboratory
Kuraku Group / Molecular Life History Laboratory
Cohesin prevents local mixing of condensed euchromatic domains in living human cells
Masa A. Shimazoe†, Shiori Iida†, Katsuhiko Minami†, Koichi Higashi†, Sachiko Tamura, Yoshiaki Kobayashi, Shin Fujishiro, Le Xiong, Kako Nakazato, S. S. Ashwin, Tomoko Nishiyama, Yu Nagata, Masato T. Kanemaki, Akane Kawaguchi, Yasuyuki Ohkawa, Lothar Schermelleh, Atsushi Toyoda, Liangqi Xie, Ken Kurokawa, Hiroshi Ochiai, Masaki Sasai, and Kazuhiro Maeshima*
†co-first authors; *corresponding author
Nature Genetics DOI: 10.1038/s41588-026-02736-2
Press Release（Japanese only）
The human genome is about two meters long, yet it is folded inside a cell nucleus only about 10 micrometers in diameter. In cells, DNA is wrapped around histone proteins to form nucleosomes, which are further organized into chromatin. For decades, chromatin has often been described in textbooks in two simple forms: euchromatin, which is active, open, and accessible (Figure A), and heterochromatin, which is more compact and repressed.
This simple textbook view has long been widely accepted. However, if euchromatin were simply open and loose, neighboring active regions might easily interact and mix with each other (Figure A). How, then, are neighboring regions kept properly separated for gene regulation?
We investigated the physical nature of euchromatin in living human cells, not only from Hi-C genomic maps but also at the level of individual nucleosomes. For this purpose, we first focused on the histone H3 variant H3.3 and fused it to HaloTag (H3.3-Halo) to label euchromatin in human cells. We then combined single-nucleosome imaging and tracking in living cells with super-resolution 3D-structured illumination microscopy (3D-SIM).
Next, we investigated how the cohesin complex is involved in this process. Cohesin is a ring-shaped protein complex widely known for forming chromatin loops and organizing the genome. We rapidly depleted cohesin in living cells and examined how the properties of euchromatin changed. Cohesin depletion increased the mobility of nucleosomes within euchromatic domains, increasing nucleosome-level fluidity within the domains (Figure C). However, this increase in fluidity occurred without altering the overall compaction of euchromatin. Neighboring condensed domains appeared to begin mixing locally.
We then asked what the biological relevance of this local mixing was. We focused on transcription bursts of several gene pairs on chromosome 1 and found that the proximal co-burst frequency of these gene pairs significantly increased after cohesin depletion. This suggests that local domain mixing after cohesin depletion weakened transcriptional insulation (Figure C).
Our study therefore revises the view of euchromatin: Active chromatin is not simply open. It can form condensed, dynamic domains whose local mixing is actively controlled. Cohesin constrains euchromatic domains and helps maintain their integrity, providing a physical basis for transcriptional insulation in living cells (Figure B).
Finally, because cohesin dysfunction is linked to developmental disorders and cancer, understanding this physical role of cohesin may also provide new insight into how genome regulation fails in disease.
This study was conducted by an international collaborative team comprising Masa A. Shimazoe, graduate student at the ROIS National Institute of Genetics (NIG) and SOKENDAI and JSPS Research Fellow DC1; Shiori Iida, Project Researcher at NIG (currently Max Planck Institute for Molecular Biomedicine); Katsuhiko Minami, Project Researcher at NIG (currently Harvard University); Koichi Higashi, Assistant Professor at NIG (currently Associate Professor, Bio Generative AI Research and Development Center, ROIS); Sachiko Tamura, Technical Staff; Kako Nakazato, SOKENDAI graduate student and JSPS Research Fellow DC2; Yu Nagata, SOKENDAI graduate student; Masato T. Kanemaki, Professor; Akane Kawaguchi, Assistant Professor; Atsushi Toyoda, Project Professor; Ken Kurokawa, Professor; and Kazuhiro Maeshima, Professor, at NIG; Yoshiaki Kobayashi, Assistant Professor, Yasuyuki Ohkawa, Professor, and Hiroshi Ochiai, Professor, at Kyushu University; Shin Fujishiro, Researcher, Tomoko Nishiyama, Professor, and Masaki Sasai, Researcher, at Kyoto University; Le Xiong, Researcher, and Liangqi Xie, Group Leader, at Cleveland Clinic, USA; S. S. Ashwin, Associate Professor, at GITAM, India; and Lothar Schermelleh, Professor, at the University of Oxford, UK.
This work was supported by JSPS/MEXT KAKENHI grants JP20H05937, JP23K17398, JP24H00061, JP25K24664, JP22H00406, JP21H04767, JP25H02584, JP24H02326, JP23KJ0996, JP23KJ0998, JP24KJ1161, and JP26KJ1223; the Takeda Science Foundation; JST CREST (JPMJCR23N3); JST SPRING (JPMJSP2104); ROIS; the Kyushu University Medical Research Center Initiative for High Depth Omics; the Cooperative Research Project Program and the Coalition of Universities for Research Excellence Program (CURE, JPMXP1323015486) under the MEXT Project for Formation of a Joint Usage/Research System; an American Cancer Society Postdoctoral Fellowship (PF-25-1409973-01-PFMBB); the National Institutes of Health (1DP2GM154017-01); the Mathers Foundation (MF-2207-02991); the American Cancer Society (DBG-22-112-01-DMC); and the Cooperative Research Project Program of the Joint Usage/Research Center at the Medical Institute of Bioregulation, Kyushu University. Sequencing and analysis support was provided by NIG-JOINT (15R2025, 69A2024, and 42A2025) and the Platform for Advanced Genome Science (PAGS; JP22H04925).
The revised view of active chromatin regions (euchromatin). In the classical view (A), euchromatin regions are often regarded as open and loose. This new study suggests that euchromatin forms condensed loop domains (B), and that cohesin helps keep neighboring domains separated and prevents their local mixing. (C) Cohesin loss caused neighboring condensed domains to mix locally and weakened transcriptional insulation.
Live-cell 3D-SIM imaging of H3.3-Halo-labeled euchromatin in a human cell. The movie shows the condensed organization of active chromatin in the nucleus.