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It is difficult to assume that the massive number of co-ordinated developmental sequences in a developing embryo is controlled by molecular signalling alone. Is anyone aware of a molecular or developmental clock within the genome which control the on off states of the genes concerned with developmental sequences? If it has not been reported is it likely to exist? (This is not about the molecular clock in evolution.)

Assuming there is a molecular clock, is it possible that the clock is switched on at the time of fertilization, and the zygote transfers the elapsed time to the progressive generations of the cells?

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  • $\begingroup$ You think it is difficult to believe that development is only timed by molecular events, but you are asking whether there is a molecular clock? Seems a bit contradicting... Anyway it has been shown that disruption of clock genes leads to developmental defects: for instance (these are just two random papers I found, but there is surely more) ncbi.nlm.nih.gov/pubmed/22884368 ncbi.nlm.nih.gov/pubmed/17963275 $\endgroup$ – nico Aug 13 '13 at 6:55
  • $\begingroup$ Thanks for the comments Nico, I did not say events, i said molecular signalling and molecular clock. by molecular clock I meant something like a run time clock or a timer for that matter for referance.The circardian rhythm is too slow for temporal refernce control of the fast paced developmental process in an embryo. $\endgroup$ – Ram Manohar M Aug 13 '13 at 18:08
  • $\begingroup$ Ok, now I understand what you mean. In general when speaking about "molecular clock" one refers to a set of genes and their derived proteins that govern circadian rhythms and that indeed act as a "24h timer". See also my explanation here: biology.stackexchange.com/questions/2299/… . Now, although these genes are involved in circadian (~24h) rhythms, they possibly also have a role in shorter (<24h, ultradian) and longer (>24h infradian) rhythms, although this is still very much an unresolved question. $\endgroup$ – nico Aug 13 '13 at 19:01
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I think that the "molecular clock" that you refer to and the "molecular signaling" that you are skeptical of are one and the same thing.

In the 1960s, nuclear transplant experiments established that molecular signals in the cytoplasm can dedifferentiate terminally differentiated nuclei, "resetting" your molecular clock, or in the more common terminology "rerunning" the "developmental program" to yield viable animals.

This "developmental program" metaphor has been frequently used to describe this process, seeing development as a series of gene regulatory cascades; they called it a program because they were thinking of procedural computer programs. It isn't really a clock so much as a complex process by which different sets of genes are turned on and off in a concerted fashion, where one step depends on what happens in the previous step. An undergrad course discussing some of the mechanisms of this is posted here.

We've known for many decades that interrupting cellular processes such as transcription, translation, and DNA replication tend to arrest development at different points (for one early example see here).

A good example of a step/series of steps in the developmental program is the maternal-to-zygotic transition in metazoans, where embryos transition from using maternally deposited mRNAs as molecular raw material to de novo transcription of their own mRNAs.

From the linked review:

As development proceeds, two processes are triggered that together form the maternal-to-zygotic transition (MZT): first, a subset of the maternal mRNAs is eliminated; second, the transcription of the zygotic genome begins. Initially, the destruction of maternal mRNAs is accomplished by maternally encoded products. However, zygotic transcription leads to the production of proteins and microRNAs (miRNAs) that provide feedback to enhance the efficiency of maternal mRNA degradation. In addition, among the earliest mRNAs synthesized de novo in the embryo are transcriptional activators that enhance the efficiency of zygotic transcription. The net result is that the control of development is transferred from the maternal to the zygotic genome.

enter image description here

Figure 1. A comparative overview of the maternal-to-zygotic transition (MZT) in several model organisms. Key embryonic stages for each model organism are depicted schematically above the corresponding cleavage cycle and time after fertilization. The red curves represent the degradation profiles of destabilized maternal transcripts in each species. The light and dark blue curves illustrate the minor and major waves, respectively, of zygotic genome activation. The last embryonic stage presented for each organism is the developmental point at which there is a major requirement for zygotic transcripts.

This transition requires that the developmental steps based on maternally-deposited mRNAs have completed successfully before de novo transcription of embryonic RNAs can begin.

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