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Genomics and gene regulation in allotetraploid Xenopus embryos

Phelps, Wesley (2023) Genomics and gene regulation in allotetraploid Xenopus embryos. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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During early embryogenesis, key regulatory factors initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this pluripotency transition across animals, suggesting that pervasive regulatory remodeling over evolution has shaped the earliest stages of development; however it is unclear when and how such major modifications arose. For my dissertation, I have dissected the regulatory mechanisms underlying embryonic genome activation and pluripotency in the allotetraploid African-clawed frog, Xenopus laevis, and have additionally revealed key similarities in the pluripotency program across vertebrates despite many regulatory differences. First, I adapted two high-throughput sequencing methods for X. laevis embryos, which have traditionally been difficult to perform genomics on. These methods allow for genome-wide interrogation of gene expression and gene regulation using the limited number of cells present in early embryos. Second, I have demonstrated that the two distinct X. laevis “subgenomes” are activated independently to coordinate pluripotency induction, via subgenome-specific regulatory regions that drive differential gene expression. Maternal homologs of the mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis. However, comparisons with other taxa reveal broad gene expression conservation despite high regulatory sequence turnover. Thus, my dissertation project both elucidates the previously uncharacterized mechanisms underlying genome activation for a long-established research model system and supports the existence of a core pluripotency program regulated by factors conserved across vertebrates.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Phelps, Wesleywap22@pitt.eduwap220000-0002-4056-2345
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee MemberCarlson, Anne E.acarlson@pitt.eduacarlson
Committee MemberArndt, Karen M.arndt@pitt.eduarndt
Committee MemberBerman, Andrea J.AJB190@pitt.eduAJB190
Committee MemberCarvunis, Anne-Ruxandraanc201@pitt.eduanc201
Committee ChairLee, Miler T.miler@pitt.edumiler
Date: 10 May 2023
Date Type: Publication
Defense Date: 29 November 2022
Approval Date: 10 May 2023
Submission Date: 9 February 2023
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 157
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Biological Sciences
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Xenopus, genome activation, pluripotent, genomics, polyploid
Date Deposited: 10 May 2023 16:37
Last Modified: 10 May 2023 16:37

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