Stage-specific profiling of the transcriptome during oogenesis and identification of a novel type of small RNA within the zebrafish ($\textit{Danio rerio}$)

Developmental biology is an important field of study, as breakthroughs in this field can be used to understand aspects of evolution, more complex biological processes, and even diseases, such as cancer. Pathways and developmental programs are often highly conserved between organisms, especially vertebrates, allowing for studies within model organisms to have implications in humans. Zebrafish have long been used in the study of developmental biology due to their fast replication times, translucent embryos and relatively low cost. Much is known about early zebrafish embryology due to results from mutagenesis studies, however some aspects of development continue to remain unclear. It is known that maternal products control early development, including setting up the axes and providing the transcripts required prior to zygotic genome activation, but the timing of the production of these transcripts is unknown. To be accurately localized within the embryo, these transcripts are deposited prior to fertilization, during egg development (oogenesis). The oocyte goes through many important changes in gene expression, chromatin conformations, meiotic stages and maturation processes during oogenesis, all of which are essential for normal embryonic development. In this thesis, I have used next generation sequencing techniques to profile and characterize the rapidly changing transcriptome during each stage of oogenesis, using the zebrafish as a model organism. Specifically, a method for accurate staging and collection of high quality oocytes was developed based on previous work on zebrafish and Xenopus oogenesis. Once separated into stages the small RNA content of stage I oocytes was closely examined and profiled using RNA-Seq. Following this, the transcriptomes of each stage of oogenesis were characterized using whole molecule polyA RNA-Seq. An in depth analysis of the transcriptomes elucidated the timings of important oogenic events and identified specific expression patterns within each stage. Finally, I compared the small RNA of stage I oocytes with polyA RNA to examine and identify common features.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2016

Author dc:creator

• Stewart, Caitlin

Advisor dc:contributor.advisor

• Stemple, Derek

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/c61df417-a6cf-461e-94ad-2dbb53c88548/download
• https://www.rioxx.net/licenses/all-rights-reserved/
• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/c6792121-812a-466c-8c28-babb58f513ce/download

Language dc:language

en

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.7409

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/262168