Abstract
In higher eukaryotic cells, a string of nucleosomes, where long genomic DNA is wrapped around core histones, are rather irregularly folded into a number of condensed chromatin domains, which have been revealed by super-resolution imaging and Hi-C technologies. Inside these domains, nucleosomes fluctuate and locally behave like a liquid. The behavior of chromatin may be highly related to DNA transaction activities such as transcription and repair, which are often upregulated in cancer cells. To investigate chromatin behavior in cancer cells and compare those of cancer and non-cancer cells, we focused on oncogenic-HRAS (Gly12Val)-transformed mouse fibroblasts CIRAS-3 cells and their parental 10T1/2 cells. CIRAS-3 cells are tumorigenic and highly metastatic. First, we found that HRAS-induced transformation altered not only chromosome structure, but also nuclear morphology in the cell. Using single-nucleosome imaging/tracking in live cells, we demonstrated that nucleosomes are locally more constrained in CIRAS-3 cells than in 10T1/2 cells. Consistently, heterochromatin marked with H3K27me3 was upregulated in CIRAS-3 cells. Finally, Hi-C analysis showed enriched interactions of the B-B compartment in CIRAS-3 cells, which likely represents transcriptionally inactive chromatin. Increased heterochromatin may play an important role in cell migration, as they have been reported to increase during metastasis. Our study also suggests that single-nucleosome imaging provides new insights into how local chromatin is structured in living cells.
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Data availability
Raw sequencing datasets for Hi-C analysis generated in this study are available in the DDBJ Sequenced Read Archive under the accession numbers DRA017367.
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Acknowledgements
We are grateful to Dr. K.M. Marshall for critical reading and editing of this manuscript. We thank Dr. S. Kuraku for supporting the Hi-C experiment, Dr. J.R. Davie for providing CIRAS-3 and 10T1/2 cells, Dr. H. Kimura for providing his antibodies, Dr. T. Yugawa for valuable comments, Dr. K. Hibino, Ms. S. Iida, Mr. M. A. Shimazoe, and Maeshima laboratory members for their helpful discussions and support. A.O. thanks Progress Committee members Dr. K. Saito, Dr. M. Kanemaki, Dr. J. Kitano, Dr. A. Kimura for their support. This work was supported by JSPS grants JP21H02453 (K.Maeshima), JP20H05936 (K.Maeshima), JP23K17398 (K.Maeshima and S.I.), JP23K05798 (A.K.), JP22H05606 (S.I.), JP21H02535 (S.I.), JP22H04925 (PAGS) (K.Maeshima), The Naito Foundation (A.K.), Takeda Science Foundation (K.Maeshima) . A.O. is a SOKENDAI Special Researcher (JST SPRING JPMJSP2104). K.Minami was a SOKENDAI Special Researcher and is currently a JSPS Fellow (23KJ0998). M.J.H. is supported by a Canada Research Chair.
Funding
This work was supported by JSPS grants JP21H02453 (K.Maeshima), JP20H05936 (K.Maeshima), JP23K17398 (K.Maeshima and S.I.), JP23K05798 (A.K.), JP22H05606 (S.I.), JP21H02535 (S.I.), JP22H04925 (PAGS) (K.Maeshima), The Naito Foundation (A.K.), Takeda Science Foundation (K.Maeshima). A.O. is a SOKENDAI Special Researcher (JST SPRING JPMJSP2104). K.Minami was a SOKENDAI Special Researcher and is currently a JSPS Fellow (23KJ0998). M.J.H. is supported by a Canada Research Chair.
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K.Maeshima, A.O., and K.Minami designed the project. A.O. and S.T. created the cell lines with the help of S.I. A.O. and K.Minami performed single-nucleosome imaging, tracking, and analysis. A.O. performed most of the cell biology experiments with help of S.I. A.K. performed the Hi-C experiment. K.H., K.K., and A.O. analyzed Hi-C data. S.T. contributed to the scientific illustrations. M.H. provided essential resources. K.Maeshima, K.Minami, and A.O. wrote the manuscript with input from all other authors.
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Otsuka, A., Minami, K., Higashi, K. et al. Chromatin organization and behavior in HRAS-transformed mouse fibroblasts. Chromosoma (2024). https://doi.org/10.1007/s00412-024-00817-x
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DOI: https://doi.org/10.1007/s00412-024-00817-x