Evaluating the Influence of the Nuclear: Cytoplasmic Ratio in the Maternal to Zygotic Transition in Xenopus Embryos
Abstract/Contents
- Abstract
- The maternal to zygotic transition (MZT) is a key developmental transition in rapidly developing vertebrate embryos marked by the initiation of zygotic transcription and degradation of maternal transcripts. This shift from maternal to zygotic control of gene expression requires the coordination of zygotic genome activation (ZGA) across thousands of promoters. Since the 1980s, it has been widely held that the Xenopus laevis MZT occurs due to titration of transcriptional inhibitors against increasing DNA content during rapid early embryonic cell divisions. The influence of increasing DNA content relative to cytoplasm during these rapid division cycles with no intervening cytoplasmic growth is conceptualized as an increasing nuclear-to-cytoplasmic (N:C) ratio. Recent evidence, however, points to N:C ratio-independent onset of the MZT. To better evaluate the influence of N:C ratios on the MZT in Xenopus embryos, I studied the effects of the N:C ratio on the expression of individual genes, rather than bulk radiolabeling methods as have been previously performed. I devised an algorithm to determine an activation time from an RNA-Seq expression time course. I then applied this algorithm to compare activation kinetics in Xenopus embryos engineered to have differing N:C ratios. This analysis revealed that activation times are broadly delayed in embryos with lower N:C ratios, supporting the model that an increase in the N:C ratio has a causal role in the onset of the Xenopus MZT. This work therefore contributes to the study of zygotic genome activation by providing both a rigorous method for analyzing activation kinetics and evidence for the N:C model on a per-gene basis.
Description
| Type of resource | text |
|---|---|
| Date created | June 2021 |
Creators/Contributors
| Author | Kapoor, Rishabh |
|---|---|
| Primary advisor | Skotheim, Jan |
| Advisor | Gozani, Or |
| Advisor | Jukam, David |
| Degree granting institution | Stanford University, Department of Biology, 2021 |
Subjects
| Subject | Biology |
|---|---|
| Subject | Stanford University Department of Biology |
| Subject | Developmental Biology |
| Subject | Molecular Biology |
| Subject | Xenopus |
| Subject | Transcriptomics |
| Genre | Thesis |
Bibliographic information
| Related Publication | Jukam, David and Kapoor, Rishabh and Straight, Aaron and Skotheim, Jan. (2021). The DNA-to-cytoplasm ratio broadly activates zygotic gene expression in Xenopus. bioRxiv 2021.04.18.440334; doi: https://doi.org/10.1101/2021.04.18.440334 |
|---|---|
| Location | https://purl.stanford.edu/mn139cz2068 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Share Alike 3.0 Unported license (CC BY-SA).
Preferred citation
- Preferred Citation
Kapoor, Rishabh and Skotheim, Jan and Gozani, Or and Jukam, David. (2021). Evaluating the Influence of the Nuclear: Cytoplasmic ratio in the Maternal to
Zygotic Transition in Xenopus Embryos. Stanford Digital Repository. Available at: https://purl.stanford.edu/mn139cz2068
Collection
Undergraduate Theses, Department of Biology, 2020-2021
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- Contact
- rishabhk@stanford.edu
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