Cell-autonomous timing drives the vertebrate segmentation clock’s wave pattern

Reviewer #1 (Public Review):

Summary:
In this manuscript, Rohde et al. discuss how single cells isolated from the presomitic mesoderm of the zebrafish embryo follow a cell-autonomous differentiation "programme", which is dependent on the initial anteroposterior position in the embryo.

Strengths:
This work and in particular the comparison to cellular behaviour in vivo presents a detailed description of the oscillatory system that brings the developmental biology forward in their understanding of somitogenesis.
The main novelty lies in the direct comparison of these isolated single cells to single cells tracked within the developing embryo. This allows them to show that isolated cells follow a similar path of differentiation without direct contact to neighbours or the presence of external morphogen gradients. Based on this, the authors propose an internal timer that starts ticking as cells traverse the presomitic mesoderm, while external signals modify this behaviour.

Weaknesses:
There are a few things that would clarify the current statement or might be added in a reasonable amount of time to further increase the relevance of this study:
- My main point of concern is the precision of dissection. The authors distinguish cells isolated from the tailbud and different areas in the PSM. They suggest that the cell-autonomous timer is initiated, as cells exit the tailbud.
This is also relevant for the comparison of single cells isolated from the embryo and cells within the embryo. The dissection will always be less precise and cells within the PSM4 region could contain tailbud cells (as also indicated in Figure 1A), while in the analysis of live imaging data cells can be selected more precisely based on their location. This could therefore contribute to the difference in noise between isolated single cells and cells in the embryo. This could also explain why there are "on average more peaks" in isolated cells (p. 6, l. 7).
This aspect should be considered in the interpretation of the data and mentioned at least in the discussion.
(It does not contradict their finding that more anterior cells oscillate less often and differentiate earlier than more posterior ones.)

- Here, the authors focus on the question of how cells differentiate. The reverse question is not addressed at all. How do cells maintain their oscillatory state in the tailbud? One possibility is that cells need external signals to maintain that as indicated in Hubaud et al. 2014. In this regard, the definition of tailbud is also very vague. What is the role of neuromesodermal progenitors? The proposal that the timer is started when cells exit the tailbud is at this point a correlation and there is no functional proof, as long as we do not understand how cells maintain the tailbud state. These are points that should be considered in the discussion.

- The authors observe that the number of oscillations in single cells ex vivo is more variable than in the embryo. This is presumably due to synchronization between neighbouring cells via Notch signalling in the embryo. Would it be possible to add low doses of Notch inhibitor to interfere with efficient synchronization, while at the same time keeping single cell oscillations high enough to be able to quantify them?

In the same direction, it would be interesting to test if variation is decreased, when the number of isolated cells is increased, i.e. if cells are cultured in groups of 2,3 or 4 cells, for instance.

- It seems that the initiation of Mesp2 expression is rather reproducible and less noisy (+/- 2 oscillation cycles), while the number of oscillations varies considerably (and the number of cells continuing to oscillate after Mesp2 expression is too low to account for that). How can the authors explain this apparent discrepancy?

- The observation that some cells continue oscillating despite the upregulation of Mesp2 should be discussed further and potential mechanism described, such as incomplete differentiation.

- Fig. 3 supplement 3 B missing

Reviewer #2 (Public Review):

The authors demonstrate convincingly the potential of single mesodermal cells, removed from zebrafish embryos, to show cell-autonomous oscillatory signaling dynamics and differentiation. Their main conclusion is that a cell-autonomous timer operates in these cells and that additional external signals are integrated to tune cellular dynamics. Combined, this is underlying the precision required for proper embryonic segmentation, in vivo. I think this work stands out for its very thorough, quantitative, single-cell real-time imaging approach, both in vitro and also in vivo. A very significant progress and investment in method development, at the level of the imaging setup and also image analysis, was required to achieve this highly demanding task. This work provides new insight into the biology underlying embryo axis segmentation.
The work is very well presented and accessible. I think most of the conclusions are well supported. Here a my comments and suggestions:

1. The authors state that "We compare their cell-autonomous oscillatory and arrest dynamics to those we observe in the embryo at cellular resolution, finding remarkable agreement."

I think this statement needs to be better placed in context. In absolute terms, the period of oscillations and the timing of differentiation are actually very different in vitro, compared to in vitro. While oscillations have a period of ~30 minutes in vivo, oscillations take twice as long in vitro. Likewise, while the last oscillation is seen after 143 minutes in vivo, the timing of differentiation is very significantly prolonged, i.e.more than doubled, to 373min in vitro (Supplementary Figure 1-9). I understand what the authors mean with 'remarkable agreement', but this statement is at the risk of being misleading. I think the in vitro to in vivo differences (in absolute time scales) needs to be stated more explicitly. In fact, the drastic change in absolute timescales, while preserving the relative ones,i.e. the number of oscillations a cell is showing before onset of differentiation remains relatively invariant, is a remarkable finding that I think merits more consideration (see below).

1. One timer vs. many timers
   The authors show that the oscillation clock slowing down and the timing of differentiation, i.e. the time it takes to activate the gene mesp, are in principle dissociable processes. In physiological conditions, these are however linked. We are hence dealing with several processes, each controlled in time (and hereby space). Rather than suggesting the presence of 'a timer', I think the presence of multiple timing mechanisms would reflect the phenomenology better. I would hence suggest separating the questions more consistently, for instance into the following three:
   a. what underlies the slowing down of oscillations?
   b. what controls the timing of onset of differentiation?
   c. and finally, how are these processes linked?

Currently, these are discussed somewhat interchangeably, for instance here: "Other models posit that the slowing of Her oscillations arise due to an increase of time-delays in the negative feedback loop of the core clock circuit (Yabe, Uriu, and Takada 2023; Ay et al. 2014), suggesting that factors influencing the duration of pre-mRNA splicing, translation, or nuclear transport may be relevant. Whatever the identity, our results indicate the timer ought to exert control over differentiation independent of the clock."(page 14). In the first part, the slowing down of oscillations is discussed and then the authors conclude on 'the timer', which however is the one timing differentiation, not the slowing down. I think this could be somewhat misleading.

1. From this and previous studies, we learn/know that without clock oscillations, the onset of differentiation still occurs. For instance in clock mutant embryos (mouse, zebrafish), mesp onset is still occurring, albeit slightly delayed and not in a periodic but smooth progression. This timing of differentiation can occur without a clock and it is this timer the authors refer to "Whatever the identity, our results indicate the timer ought to exert control over differentiation independent of the clock." (page 14). This 'timer' is related to what has been previously termed 'the wavefront' in the classic Clock and Wavefront model from 1976, i.e. a "timing gradient' and smooth progression of cellular change. The experimental evidence showing it is cell-autonomous by the time it has been laid down,, using single cell measurements, is an important finding, and I would suggest to connect it more clearly to the concept of a wavefront, as per model from 1976.

2. Regarding question a., clearly, the timer for the slowing down of oscillations is operating in single cells, an important finding of this study. It is remarkable to note in this context that while the overall, absolute timescale of slowing down is entirely changed by going from in vivo to in vitro, the relative slowing down of oscillations, per cycle, is very much comparable, both in vivo and in vivo. To me, while this study does not address the nature of this timer directly, the findings imply that the cell-autonomous timer that controls slowing down is, in fact, linked to the oscillations themselves. We have previously discussed such a timer, i.e. a 'self-referential oscillator' mechanism (in mouse embryos, see Lauschke et al., 2013) and it seems the new exciting findings shown here in zebrafish provide important additional evidence in this direction. I would suggest commenting on this potential conceptual link, especially for those readers interested to see general patterns.

3. Regarding question c., i.e. how the two timing mechanisms are functionally linked, I think concluding that "Whatever the identity, our results indicate the timer ought to exert control over differentiation independent of the clock." (page 14), might be a bit of an oversimplification. It is correct that the timer of differentiation is operating without a clock, however, physiologically, the link to the clock (and hence the dependence of the timescale of clock slowing down), is also evident. As the author states, without clock input, the precision of when and where differentiation occurs is impacted. I would hence emphasize the need to answer question c., more clearly, not to give the impression that the timing of differentiation does not integrate the clock, which above statement could be interpreted to say.

4. A very interesting finding presented here is that in some rare examples, the arrest of oscillations and onset of differentiation (i.e. mesp) can become dissociated. Again, this shows we deal here with interacting, but independent modules. Just as a comment, there is an interesting medaka mutant, called doppelkorn (Elmasri et al. 2004), which shows a reminiscent phenotype "the Medaka dpk mutant shows an expansion of the her7 expression domain, with apparently normal mesp expression levels in the anterior PSM.". The authors might want to refer to this potential in vivo analogue to their single cell phenotype.

5. One strength of the presented in vitro system is that it enables precise control and experimental perturbations. A very informative set of experiments would be to test the dependence of the cell-autonomous timing mechanisms (plural) seen in isolated cells on ongoing signalling cues, for instance via Fgf and Wnt signaling. The inhibition of these pathways with well-characterised inhibitors, in single cells, would provide important additional insight into the nature of the timing mechanisms, their dependence on signaling and potentially even into how these timers are functionally interdependent.