# The embryo’s first genes

> Every animal embryo starts on its mother’s instructions, then switches on its own genes. When this hand-over happens differs between species.

Source: https://khushisingh.in/explore/08-the-embryos-first-genes/
Author: Khushi Singh (khushisingh.in). Licence: CC BY 4.0 for text and original illustrations, unless a credit says otherwise.
Evidence labels used on this site: established, strong evidence, emerging, hypothesis, debated. Where a page has Simple, Curious and Expert versions, all three follow.

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[Biology made simple](https://khushisingh.in/explore/) · Ideas from my research · 8 of 8

About 2 minutes

An egg is packed with its mother’s mRNAs and proteins, and the young embryo runs on them while its own genes are mostly silent. Then control passes over: maternal mRNAs are cleared and the embryo switches on its own genes. This **maternal-to-zygotic transition** happens in every animal studied (Tadros & Lipshitz 2009; Vastenhouw et al. 2019), at different times: after about 12 cell divisions in frogs (Newport & Kirschner 1982), at the 2-cell stage in mice and around the 4–8-cell stage in humans. (evidence: established)

In the fruit fly, the embryo’s nuclei divide 13 times in about two hours, then form cells at stage 5, when its own genes switch on strongly. Open data from FlyBase show the hand-over:

The mother’s mRNAs fade, the embryo’s own genes switch on (fruit fly)

- oskar (mother’s)
- bicoid (mother’s)
- even-skipped (embryo’s own)
- fushi tarazu (embryo’s own)
- zerknüllt (embryo’s own)

Source: FlyBase gene RPKM matrix (modENCODE developmental RNA-seq; Graveley et al. 2011), CC BY 4.0, retrieved 2026-10-03. Each gene scaled to its own maximum.

**Show the numbers**

| Stage | oskar (mother’s) | bicoid (mother’s) | even-skipped (embryo’s own) | fushi tarazu (embryo’s own) | zerknüllt (embryo’s own) |
| --- | --- | --- | --- | --- | --- |
| 0–2 h | 100 | 100 | 5 | 5 | 13 |
| 2–4 h | 6 | 47 | 100 | 100 | 100 |
| 4–6 h | 2 | 18 | 11 | 16 | 4 |
| 6–8 h | 1 | 14 | 6 | 18 | 0 |
| 8–10 h | 1 | 19 | 6 | 14 | 2 |
| 10–12 h | 1 | 10 | 6 | 3 | 0 |

*[Here the web page has an interactive activity; open the source URL to use it.]*

## My question

In mouse embryos, lactate and a lactyl tag on histones help the first genes switch on (Li et al. 2024). (evidence: emerging) I am asking whether metabolism shapes histone marks at this moment in the fly embryo. (evidence: hypothesis) More on my [current project](https://khushisingh.in/research/gut-to-germline/).

**In my research:** [The fly from egg chamber to stage 5, step by step →](https://khushisingh.in/research/model-system/#fly-stages)

## Sources

1. Tadros W, Lipshitz HD (2009) The maternal-to-zygotic transition: a play in two acts. Development 136:3033–3042. [doi:10.1242/dev.033183](https://doi.org/10.1242/dev.033183)
2. Vastenhouw NL, Cao WX, Lipshitz HD (2019) The maternal-to-zygotic transition revisited. Development 146:dev161471. [doi:10.1242/dev.161471](https://doi.org/10.1242/dev.161471)
3. Newport J, Kirschner M (1982) A major developmental transition in early Xenopus embryos: I. Characterization and timing of cellular changes at the midblastula stage. Cell 30:675–686. [doi:10.1016/0092-8674(82)90272-0](https://doi.org/10.1016/0092-8674(82)90272-0)
4. Graveley BR, et al. (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471:473–479 (via FlyBase, CC BY 4.0). [doi:10.1038/nature09715](https://doi.org/10.1038/nature09715)
5. Li J, et al. (2024) Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. National Science Review 11:nwad295. [doi:10.1093/nsr/nwad295](https://doi.org/10.1093/nsr/nwad295)