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Species-specific oscillation periods of human and mouse segmentation clocks are due to cell autonomous differences in biochemical reaction parameters

Mitsuhiro Matsuda, Hanako Hayashi, Jordi Garcia-Ojalvo, Kumiko Yoshioka-Kobayashi, Ryoichiro Kageyama, Yoshihiro Yamanaka, Makoto Ikeya, Junya Toguchida, Cantas Alev, Miki Ebisuya

Preprint posted on May 26, 2019 https://doi.org/10.1101/650648

The time is now: understanding developmental timescales by inter-species comparison of the oscillation period in the presomitic mesoderm.

Selected by Teresa Rayon

Summary:

In this preprint, the Ebisuya lab study how are periodic oscillations in the segmentation clock species-specific and what mechanisms explain the differences in tempo of conserved developmental processes. Alongside the spatial control of gene expression, the temporal control in developing tissues remains elusive. Even though most of the patterning processes in development are well conserved between species, the speed of differentiation varies in each one of them. A paradigmatic example of temporal differences in the developing embryo is the vertebrate segmentation clock: a series of periodic oscillations in gene expression in the cells that will form the somites in an elongating embryo. In this preprint, the authors recapitulate the segmentation clock of mouse and human embryos in vitro, and exploit the differences of period in the segmentation clock of mouse (2-3 hours) and humans (5-6 hours) [1,2], to show that it is intrinsic to the species. Importantly, the authors show that the interspecies period difference is cell-autonomous, allowing the study of the phenomena in single cells. To understand what mechanisms account for the differences in oscillation period between mouse and human, they examined the dynamics of the master regulator Hes7. By measuring and fitting degradation rates of HES7 protein and mRNA, and the delays in the feedback loop of HES7, they build a mathematical model where they show that the interspecies period difference depends on the kinetics of transcription and translation.

Why I chose the paper:

How cells keep track of time is one of the fascinating questions in developmental biology that we are trying to answer in the lab [3]. Interestingly enough, the same gene regulatory networks are used repeatedly during development to generate the wide variety of cells found in the adult organism. Therefore, to coordinate the onset of developmental events, mechanisms to track the course of time must exist. We know that there is not a single clock that starts ticking upon fertilization, and there could be different mechanisms that cooperate to explain the flow of time in different tissues. To understand how time is encoded in these gene regulatory networks, one needs to have a good understanding of the dynamics of the network to compare a conserved differentiation process between species. To my knowledge, this is the first piece of work where this inter-species comparison has been used to unravel the temporal mechanisms driving development.

I particularly like the experiments where the authors swap the regulatory landscapes of the mouse and human master regulator Hes7, generating a humanized version of the gene in a mouse context to ask if that is enough to change the period of oscillations. They show that the humanized version of Hes7 in the mouse context behaves just like the mouse version, demonstrating that there is species-specific control of development. In addition, the rigorous measurements of degradation rates, transcription and translation delays of Hes7 combined with mathematical modeling (see Irepan’s preLight) allows them to elegantly show how the slower biochemical reactions in human cells are enough to explain the longer oscillation period of the human segmentation clock.

Figure 1. Ex vivo tail bud cultures of the E10.5 mouse embryos containing the human HES7 locus (Homo swap) show similar Hes7 oscillations. Reproduced from Figure2 of the preprint.

 

How this work moves the field forward:

This preprint provides evidence that the kinetics of biochemical reactions explain how conserved mechanisms of development take longer in humans than in mouse in the segmentation clock. Now, one can ask if these same mechanisms operate in other developmental processes, how they operate in differentiation processes that take longer than the segmentation clock, and whether one can change the speed of processes by manipulating the kinetics of transcription and translation. In addition, by understanding the commonalities of temporal scaling in conserved processes across species, one can ask if species-specific patterning events follow the same temporal dynamics.

References :

1. Diaz-Cuadros, M., Wagner, D. E., Budjan, C., Hubaud, A., Touboul, J., Michaut, A., Tanoury, Z. Al, Yoshioka-Kobayashi, K., Niino, Y., Kageyama, R., et al. (2018). In vitro characterization of the human segmentation clock. bioRxiv 461822. https://doi.org/10.1101/461822

2. Matsuda, M., Yamanaka, Y., Uemura, M., Osawa, M., Saito, M. K., Nagahashi, A., Nishio, M., Guo, L., Ikegawa, S., Sakurai, S., et al. (2019). Modeling the Human Segmentation Clock with Pluripotent Stem Cells. bioRxiv 562447. https://doi.org/10.1101/562447

3. Ebisuya, M. and Briscoe, J. (2018). What does time mean in development? Development 145, dev164368. https://dev.biologists.org/content/145/12/dev164368.long

Irepan and Teresa’s questions to the authors:

Q1.  Since the size and number of somites differ between mouse and human, it would be interesting to know if the identified temporal mechanisms play a role in counting the number or measuring the size of somites. Do the authors think that the in vitro protocol in mouse and human generates the appropriate number of somites? Does the oscillation period vary over time in vitro?

Q2. For the comparative analysis between species, reporter activity has to be normalized. I wonder if the amplitude of Hes7 is different between mouse and human, or if the levels of expression are compensated between species.

Q3. Since the differences in biochemical reaction parameters determine the tempo of the species, do the authors think that each parameter is independent?

Q4. Since the time of development is species-specific, do the authors think that this has any evolutionary advantage for the species?

Q5. Have you considered perturbation analyses (e.g. introduce large introns to increase intron delay or alteration of mRNA turnover rate) as a further validation of the model?

Tags: developmental time, in vitro differentiation, period, segmentation clock

Posted on: 18th June 2019 , updated on: 19th June 2019

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  • Author's response

    Miki Ebisuya shared

    Teresa’s questions:

    Q1. Since the size and number of somites differ between mouse and human, it would be interesting to know if the identified temporal mechanisms play a role in counting the number or measuring the size of somites. Do the authors think that the in vitro protocol in mouse and human generates the appropriate number of somites? Does the oscillation period vary over time in vitro?

    Since the size of somites is determined by the oscillation period (and the speed of PSM cell supply), the size difference between human and mouse somites can be partly explained by the species-specific biochemical reaction speeds we showed in this preprint. The number of somites, by contrast, depends on when the segmentation clock stops (i.e., when the cell supply stops), independently of the oscillation period. Even though I would love to study why human and mouse have 44 and 65 somites, respectively, our current in vitro protocol does not recapitulate somite formation nor slowing down of the oscillation over time.

    Q2. For the comparative analysis between species, reporter activity has to be normalized. I wonder if the amplitude of Hes7 is different between mouse and human, or if the levels of expression are compensated between species.

    The expression level of the HES7 reporter varied even within the same species, depending on the culture conditions. So, we just focused on the oscillation period that showed reproducible results.

    Q3. Since the differences in biochemical reaction parameters determine the tempo of the species, do the authors think that each parameter is independent?

    Great question! Whether the interspecies differences in the degradation rates and the delays in production processes are derived from a single cause is exactly what I am eager to know now.

    Q4. Since the time of development is species-specific, do the authors think that this has any evolutionary advantage for the species?

    Yes, I think that slower tempo gives animals more time to make bigger and more complex structures.

    Irepan’s question:

    Q5. Have you considered perturbation analyses (e.g. introduce large introns to increase intron delay or alteration of mRNA turnover rate) as a further validation of the model?

    Indeed, such perturbations have been done in mice (Harima et al., Cell Rep, 3, 1-7, 2013; Hirata et al., Nat Genet, 36, 750-754, 2004). Currently I would love to perturb the ultimate cause that determines the speeds of those biochemical reactions.

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