Publications

Kazunori Yamamoto, *Akatsuki Kimura,
An anisotropic attraction model for the diversity and robustness of cell arrangement in nematodes.,
Development 144, 4437-4449 (2017).

[Summary] During early embryogenesis in animals, cells are arranged into a species-specific pattern in a robust manner. Diverse cell arrangement patterns are observed, even among close relatives. In the present study, we evaluated the mechanisms by which the diversity and robustness of cell arrangements are achieved in developing embryos. We successfully reproduced various patterns of cell arrangements observed in various nematode species in Caenorhabditis elegans embryos by altering the eggshell shapes. The findings suggest that the observed diversity of cell arrangements can be explained by differences in the eggshell shape. Additionally, we found that the cell arrangement was robust against eggshell deformation. Computational modeling revealed that, in addition to repulsive forces, attractive forces are sufficient to achieve such robustness. The present model is also capable of simulating the effect of changing cell division orientation. Genetic perturbation experiments demonstrated that attractive forces derived from cell adhesion are necessary for the robustness. The proposed model accounts for both diversity and robustness of cell arrangements, and contributes to our understanding of how the diversity and robustness of cell arrangements are achieved in developing embryos.

Yuki Hara, Kenta Adachi, Shunsuke Kagohashi, Kazuo Yamagata, Hideyuki Tanabe, Shinji Kikuchi, Sei-Ichi Okumura, and *Akatsuki Kimura,
Scaling relationship between intra-nuclear DNA density and chromosomal condensation in metazoan and plant.,
Chromosome Science 19, 43-49 (2017).

[Summary] Because the fundamental structure of chromosomes is conserved across eukaryotes, it might be assumed that an increase in the number of DNA base-pairs in a chromosome would lead to a corresponding increase in the physical length of chromosome. This does not appear to be the case, however. We compared the lengths of mitotic chromosome from several diverse species to determine the relationship between chromosome length, number of base-pairs, and the extent of chromosome packing. We found that all species share the same relationship among these, indicating that as base-pairs are added, chromosomes become more tightly packed so that the overall length increases less than expected. Our results suggest that instead of being related to the number of DNA base-pairs, chromosome length might be proportional to the surface area of the nucleus. This may be due to the need for the chromosomes to fit within a nuclear area known as the metaphase plate during mitosis, which occurs during cellular reproduction. This study provides insight into the features that drive the evolution of genome, chromosome, nucleus, and cell size and indicates that these characteristics are shared across eukaryotes.

Ritsuko Arai, Takeshi Sugawara, Yuko Sato, Yohei Minakuchi, Atsushi Toyoda, Kentaro Nabeshima, Hiroshi Kimura, *Akatsuki Kimura,
Reduction in chromosome mobility accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans.,
Scientific Reports 19, 43-49 (2017).

[Summary] Many of us may imagine the DNA inside our cells as a jumble of noodles. However, DNA is more organized than this inside the nucleus, with chromosomes occupying distinct nuclear territories, for example. It is unclear though whether this organization is always present or whether it appears at some point during development after fertilization of the egg. We studied chromosome organization by observing the mobility of chromosomes inside in the nucleus in developing nematode embryos from the 2-cell to the 48-cell stage. We found that chromosome mobility decreases in 8-cell embryos, suggesting the initiation of chromosome organization at this point. Chromosome organization in the nucleus is important for gene expression and may have other purposes as well. For example, we found that in nematodes, the timing of chromosome organization coincides with the appearance of epigenetic marks, which regulate gene expression, and of a nuclear domain called the nucleolus. Now that we have identified the timeline of nuclear chromosome organization in nematodes, we will be able to conduct future studies to determine the factors responsible for initiating this organization.

Kenji Kimura, Alexandre Mamane, Tohru Sasaki, Kohta Sato, Jun Takagi, Ritsuya Niwayama, Lars Hufnagel, Yuta Shimamoto, Jean-François Joanny, Seiichi Uchida, and Akatsuki Kimura,
Endoplasmic reticulum-mediated microtubule alignment governs cytoplasmic streaming.,
Nature Cell Biology 19, 399-406 (2017).

[Summary] Cytoplasmic streaming refers to a collective movement of cytoplasm observed in many cell types. The mechanism of meiotic cytoplasmic streaming (MeiCS) in C. elegans zygotes was puzzling as the direction of the flow is not predefined by cell polarity and occasionally reverses. The research group demonstrated that the endoplasmic reticulum (ER) network structure is required for the collective flow. Using a combination of RNAi, microscopy, and image processing of C. elegans zygotes, the group devised a theoretical model, which reproduced and predicted the emergence and reversal of the flow. They proposed a positive feedback mechanism, where a local flow generated along a microtubule is transmitted to neighboring regions through the ER. This, in turn, aligns microtubules over a broader area to self-organize the collective flow. The proposed model could be applicable to various cytoplasmic streaming phenomena in the absence of predefined polarity. The increased mobility of cortical granules by MeiCS correlated with the efficient exocytosis of the granules to protect the zygotes from osmotic and mechanical stresses.

*Yuko Sato, Tomoya Kujirai, Ritsuko Arai, Haruhiko Asakawa, Chizuru Ohtsuki, Naoki Horikoshi, Kazuo Yamagata, Jun Ueda, Takahiro Nagase, Tokuko Haraguchi, Yasushi Hiraoka, Akatsuki Kimura, Hitoshi Kurumizaka, and *Hiroshi Kimura,
A genetically encoded probe for live-cell imaging of H4K20 monomethylation.,
Journal of Molecular Biology 428, 3885-2902 (2016).

[Summary] Eukaryotic gene expression is regulated in the context of chromatin. Dynamic changes in post-translational histone modification are thought to play key roles in fundamental cellular functions such as regulation of the cell cycle, development, and differentiation. To elucidate the relationship between histone modifications and cellular functions, it is important to monitor the dynamics of modifications in single living cells. A genetically encoded probe called mintbody (modification-specific intracellular antibody), which is a single-chain variable fragment tagged with a fluorescent protein, has been proposed as a useful visualization tool. However, the efficacy of intracellular expression of antibody fragments has been limited, in part due to different environmental conditions in the cytoplasm compared to the endoplasmic reticulum where secreted proteins such as antibodies are folded. In this study, we have developed a new mintbody specific for histone H4 Lys20 monomethylation (H4K20me1). The specificity of the H4K20me1-mintbody in living cells was verified using yeast mutants and mammalian cells in which this target modification was diminished. Expression of the H4K20me1-mintbody allowed us to monitor the oscillation of H4K20me1 levels during the cell cycle. Moreover, dosage-compensated X chromosomes were visualized using the H4K20me1-mintbody in mouse and nematode cells. Using X-ray crystallography and mutational analyses, we identified critical amino acids that contributed to stabilization and/or proper folding of the mintbody. Taken together, these data provide important implications for future studies aimed at developing functional intracellular antibodies. Specifically, the H4K20me1-mintbody provides a powerful tool to track this particular histone modification in living cells and organisms.

Ritsuya Niwayama, Hiromichi Nagao, Tomoya Kitajima, Lars Hufnagel, Kyosuke Shinohara, Tomoyuki Higuchi, Takuji Ishikawa, and *Akatsuki Kimura,
Bayesian Inference of Forces Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes.,
PLoS ONE 11, e0159917 (2016).

[Summary] Cellular structures are hydrodynamically interconnected, such that force generation in one location can move distal structures. One example of this phenomenon is cytoplasmic streaming, whereby active forces at the cell cortex induce streaming of the entire cytoplasm. However, it is not known how the spatial distribution and magnitude of these forces move distant objects within the cell. To address this issue, we developed a computational method that used cytoplasm hydrodynamics to infer the spatial distribution of shear stress at the cell cortex induced by active force generators from experimentally obtained flow field of cytoplasmic streaming. By applying this method, we determined the shear-stress distribution that quantitatively reproduces in vivo flow fields in Caenorhabditis elegans embryos and mouse oocytes during meiosis II. Shear stress in mouse oocytes were predicted to localize to a narrower cortical region than that with a high cortical flow velocity and corresponded with the localization of the cortical actin cap. The predicted patterns of pressure gradient in both species were consistent with species-specific cytoplasmic streaming functions. The shear-stress distribution inferred by our method can contribute to the characterization of active force generation driving biological streaming.

*Shigeru Matsumura, Tomoko Kojidani, Yuji Kamioka, Seiichi Uchida, Tokuko Haraguchi, Akatsuki Kimura, and Fumiko Toyoshima,
Interphase adhesion geometry is transmitted to an internal regulator for spindle orientation via caveolin-1.,
Nature Communications 7, 11858 (2016).

[Summary] Despite theoretical and physical studies implying that cell-extracellular matrix adhesion geometry governs the orientation of the cell division axis, the molecular mechanisms that translate interphase adhesion geometry to the mitotic spindle orientation remain elusive. Here, we show that the cellular edge retraction during mitotic cell rounding correlates with the spindle axis. At the onset of mitotic cell rounding, caveolin-1 is targeted to the retracting cortical region at the proximal end of retraction fibres, where ganglioside GM1-enriched membrane domains with clusters of caveola-like structures are formed in an integrin and RhoA-dependent manner. Furthermore, Gαi1-LGN-NuMA, a well-known regulatory complex of spindle orientation, is targeted to the caveolin-1-enriched cortical region to guide the spindle axis towards the cellular edge retraction. We propose that retraction-induced cortical heterogeneity of caveolin-1 during mitotic cell rounding sets the spindle orientation in the context of adhesion geometry.