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Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [RNA-Seq]

ABSTRACT: Time course analysis of tRNA abundance during zebrafish early embryonic development.

ORGANISM(S): Danio rerio

PROVIDER: GSE241752 | GEO | 2024/10/17

REPOSITORIES: GEO

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Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [Ribo-Seq]

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Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [tRNA-Seq]

Project description:Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition [tRNA-Seq]

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Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.

Project description:Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50%-60%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish.

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Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition

Project description:Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition

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Dynamics of the zebrafish tRNAome during the maternal-to-zygotic transition

Project description:This SuperSeries is composed of the SubSeries listed below.

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Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition

Project description:During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNAbound proteome. This protein constellation consists of many conserved RBPs, with additional embryo- and stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of RBPs in embryogenesis, we focused on hnRNP A1. iCLIP and subsequent mRNA reporter assays revealed a function for hnRNP A1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3’UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that hnRNP A1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-miR-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of hnRNP A1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that hnRNP A1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.

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