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Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis

ABSTRACT: Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis

PROVIDER: PRJNA768450 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16195500_1.fastq.gz	Fastqsanger.gz
	SRR16195500_2.fastq.gz	Fastqsanger.gz
	SRR16195501_1.fastq.gz	Fastqsanger.gz
	SRR16195501_2.fastq.gz	Fastqsanger.gz
	SRR16195502_1.fastq.gz	Fastqsanger.gz

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Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis

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Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis [titration_data]

Project description:Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. Results: By employing Slam-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA430 function, a key post-transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression, which highlights that Slam-seq can be used to disentangle transcriptional and post-transcriptional regulation of mRNA levels. Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.

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Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse_data]

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Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis [lna_data]

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Time-resolved phosphoproteomic analysis of ZIKV-infected cells

Project description:To investigate cellular pathway dysregulation upon ZIKV infection, time-resolved phosphoproteomics LC-MS/MS analysis was used. ZIKV-infected SK-N-BE2 cells or mock-treated cells were harvested 24, 48 and 72 hours post virus infection and their phosphoproteome was quantitatively analyzed by label-free LC-MS/MS.

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