Lost in translation: egg transcriptome reveals molecular signature to predict developmental success and novel maternal-effect genes

Abstract

BackgroundGood quality or developmentally competent eggs result in high survival of progeny. Previous research has shed light on factors that determine egg quality, however, large gaps remain. Initial development of the embryo relies on maternally-inherited molecules, such as transcripts, deposited in the egg, thus, they would likely reflect egg quality. We performed transcriptome analysis on zebrafish fertilized eggs of different quality from unrelated, wildtype couples to obtain a global portrait of the egg transcriptome to determine its association with developmental competence and to identify new candidate maternal-effect genes.ResultsFifteen of the most differentially expressed genes (DEGs) were validated by quantitative real-time PCR. Gene ontology analysis showed that enriched terms included ribosomes and translation. In addition, statistical modeling using partial least squares regression and genetics algorithm also demonstrated that gene signatures from the transcriptomic data can be used to predict reproductive success. Among the validated DEGs, otulina and slc29a1a were found to be increased in good quality eggs and to be predominantly localized in the ovaries. CRISPR/Cas9 knockout mutants of each gene revealed remarkable subfertility whereby the majority of their embryos were unfertilizable. The Wnt pathway appeared to be dysregulated in the otulina knockout-derived eggs.ConclusionsOur novel findings suggested that even in varying quality of eggs due to heterogeneous causes from unrelated wildtype couples, gene signatures exist in the egg transcriptome, which can be used to predict developmental competence. Further, transcriptomic profiling revealed two new potential maternal-effect genes that have essential roles in vertebrate reproduction.

Peer Review #2 of "foxr1 is a novel maternal-effect gene in fish that is required for early embryonic success (v0.2)"

“…In addition, we found that the foxr1 mutant-derived eggs were non-cellularized and did not undergo subsequent cell division despite being fertilized, as also observed for eggs derived from npm2b mutant females [26]. This suggested that their defect did not lie in the capability to be fertilized, as seen in slc29a1a and otulina mutants [3], In this study, we showed that foxr1 is found in a wide-range of vertebrates and is homologous to the foxr1 genes found in other species. In teleosts, foxr1 expression is found predominately in the ovary while in mammals, it appears to be specific to the male germline…”

“…Maternal-effect genes are transcribed from the maternal genome and encode the maternal factors that are deposited into the developing oocytes in order to coordinate embryonic development before MBT [2]. We had previously explored the zebrafish egg transcriptome [3] and proteome [4] in order to gain further understanding of the maternal factors that contribute to good quality or developmentally competent eggs that result in high survival of progeny. However, despite the increasing identification of maternal-effect genes and their functions, large gaps still remain especially the role of genes that regulate early embryogenesis.…”

foxr1is a novel maternal-effect gene in fish that is required for early embryonic success

“…Maternal-effect genes are transcribed from the maternal genome and encode the maternal factors that are deposited into the developing oocytes in order to coordinate embryonic development before MBT ( Lindeman & Pelegri, 2010 ). We had previously explored the zebrafish egg transcriptome ( Cheung et al, 2018 ) and proteome ( Yilmaz et al, 2017 ) in order to gain further understanding of the maternal factors that contribute to good quality or developmentally competent eggs that result in high survival of progeny. However, despite the increasing identification of maternal-effect genes and their functions, large gaps still remain especially the role of genes that regulate early embryogenesis.…”

foxr1is a novel maternal-effect gene in fish that regulates embryonic cell growth viap21andrictor

“…Further, we found that the foxr1 mutant-derived eggs were non-cellularized and did not undergo subsequent cell division despite being fertilized. This suggested that their defect did not lie in the capability to be fertilized, as seen in slc29a1a and otulina mutants [3], but in the cell cycle and proliferation processes. Thus, we investigated the expression profiles of p21 , p27 , and rictor , which are all cell cycle and cell survival regulators, since Santo et al had previously knocked down foxr1 using short hairpin RNAs in mammalian cells and found it to be a transcriptional repressor of them[26].…”

“…Maternal-effect genes are transcribed from the maternal genome and encode the maternal factors that are deposited into the developing oocytes in order to coordinate embryonic development before MBT [2]. We had previously explored the zebrafish egg transcriptome [3] and proteome [4] in order to gain further understanding of the maternal factors that contribute to good quality or developmentally competent eggs that result in high survival of progeny. However, large gaps still remain.…”