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| Status |
Public on Feb 10, 2024 |
| Title |
Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis [lna_data] |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
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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| Overall design |
Zebrafish embryos were dechorionated and injected at single cell stage with 50mM s4-UTP, plus 20µM of locked nucleic acid against either miR-430 or mismatched sequence. Embryos were kept in the dark until collection time, shield stage (~6 hours post-injection). Total RNA was extracted, and kept away from direct light, alkylated, used for library preparation with QuantSeq 3′ mRNA‐Seq Library Prep Kit for Illumina (FWD).
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| Contributor(s) |
Baia Amaral D, Egidy R, Perera A, Bazzini AA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 15, 2023 |
| Last update date |
Feb 11, 2024 |
| Contact name |
Ariel Alejandro Bazzini |
| Organization name |
Stowers Institute for Medical Research
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| Lab |
Bazzini Lab
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| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platforms (1) |
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| Samples (12)
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| GSM7903215 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r1 |
| GSM7903216 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r2 |
| GSM7903217 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r3 |
| GSM7903218 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r4 |
| GSM7903219 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r5 |
| GSM7903220 |
zebrafish_shield_20µM_lnacontrol_50mM_s4u_r6 |
| GSM7903221 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r1 |
| GSM7903222 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r2 |
| GSM7903223 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r3 |
| GSM7903224 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r4 |
| GSM7903225 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r5 |
| GSM7903226 |
zebrafish_shield_20µM_lnamir430_50mM_s4u_r6 |
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| This SubSeries is part of SuperSeries: |
| GSE247935 |
Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis |
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| Relations |
| BioProject |
PRJNA1040920 |
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