Functional clarification of chromosome-based structures and control of skeletal muscle differentiation

In collaboration with Assistant Professor Kosuke Tomimatsu and Professor Yasuyuki Ohkawa (Medical Institute of Bioregulation, Kyushu University) and Professor Taro Tachibana (Faculty of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University), a research group led by Seiya Hirai (a graduate student in the Department of Biological Sciences, Graduate School of Science, the University of Tokyo) and Professor Hitoshi Kurumizaka (Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, University of Tokyo) has clarified the novel structural mechanism underlying a certain type of DNA folding performed by the mouse histone protein H3mm18, and revealed, for the first time, that H3mm18 regulates muscle differentiation.

In humans and other eukaryotes, DNA is responsible for storing genetic information and is folded around histone proteins. The study group previously found H3mm18 to be a subspecies of a new species of histone H3; however, its function remained unknown. The researchers purified four murine histone proteins, namely H3mm18, H2A, H2B, and H4, and reconstituted the nucleosomes by treating the proteins with DNA in vitro. The reconstituted nucleosome was observed using cryo-electron microscopy to elucidate the detailed three-dimensional structure of the H3mm18 nucleosome.

The conformation that was observed revealed flexibility in the movement of the DNA terminus in H3mm18 nucleosomes compared to that in conventional nucleosomes. The researchers also tested the stability of H3mm18 nucleosomes in response to heat to investigate the structural stability of nucleosomes. Consequently, H3mm18 was found to form extremely unstable nucleosomes.

These results suggest that H3mm18 alters the folding organization of genomic DNA by drastically modifying the structure and properties of nucleosomes. In addition, the regulation of gene expression by this change in folding structure was investigated through cell experiments. H3mm18 was thought to be involved in the genetic control of skeletal muscle differentiation, as cell-specific expression of H3mm18 in murine skeletal muscle tissue had been confirmed previously. Therefore, induction of skeletal muscle differentiation was attempted in mouse myoblasts expressing H3mm18. Subsequently, skeletal muscle differentiation of myoblasts was observed to be suppressed, in addition to decreases in the expression of genes required for skeletal muscle formation, such as those encoding MyHC and Myog.

These results suggest that H3mm18 regulates the key genes involved in muscular development by altering the DNA-folding organization. Most of the histone subspecies that were previously analyzed stably bind to genomic DNA, and H3mm18 nucleosomal instability is prominent among the histone H3 subspecies analyzed till date. Professor Kurumizaka stated "Histone variants and chemical modifications play a central role in epigenetics, which is based on DNA sequence-independent gene regulation." He further added, "We know that malfunctions in epigenetic processes can cause a variety of diseases, including cancer, lifestyle-related diseases, and psychiatric disorders. We intend to understand the underlying mechanisms and contribute to the development of disease prevention and treatment methods."