FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation
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ABSTRACT:
PROVIDER: PRJNA553260 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using ChIP-Seq we examined the targets of FoxH1 in zebrafish embryos at the 6hpf epiboly-stage. The revealed reads could be mapped to more than 16,000 peaks included also the known targets like ndr1, lft2, pitx2, flh, foxa3 and lhx1a. Relevant for our study, we identify the conserved microRNA-430 family (miR-430) as a novel target of FoxH1.
2019-07-18 | GSE133990 | GEO
Project description: Not available
| S-EPMC6664792 | biostudies-literature
Project description:MicroRNAs comprise 1-3% of all vertebrate genes, but their in vivo functions and mechanisms of action remain largely unknown. Zebrafish miR-430 is expressed at the onset of zygotic transcription and regulates morphogenesis during early development. Using a microarray approach and in vivo target validation, we find that miR-430 directly regulates several hundred target mRNAs. Targets are highly enriched for maternal mRNAs that accumulate in the absence of miR-430. We also show that miR-430 accelerates the deadenylation of target mRNAs. These results suggest that miR-430 facilitates the deadenylation and clearance of maternal mRNAs during early embryogenesis. Keywords: Dicer, MZdicer, miR-430, miRNA target, maternal, zygotic
2006-02-17 | GSE4201 | GEO
Project description:Sinorhizobium medicae 430 Resequencing
| PRJNA499411 | ENA
Project description:MicroRNAs comprise 1-3% of all vertebrate genes, but their in vivo functions and mechanisms of action remain largely unknown. Zebrafish miR-430 is expressed at the onset of zygotic transcription and regulates morphogenesis during early development. Using a microarray approach and in vivo target validation, we find that miR-430 directly regulates several hundred target mRNAs. Targets are highly enriched for maternal mRNAs that accumulate in the absence of miR-430. We also show that miR-430 accelerates the deadenylation of target mRNAs. These results suggest that miR-430 facilitates the deadenylation and clearance of maternal mRNAs during early embryogenesis. Experiment Overall Design: As a first step towards the identification of miR-430 targets, we compared the rate of mRNA degradation in wild type and maternal-zygotic (MZ) dicer mutant embryos, which are deficient in miRNA processing. We found that the rate of degradation of a target mRNA with partial complementarity to miR-430 is significantly reduced in MZdicer mutants. Providing miR-430 duplexes to MZdicer mutants restores the rate of target decay. These results indicate that miR-430 enhances the decay of target mRNAs. Experiment Overall Design: To identify miR-430 in vivo targets, we compared the mRNA expression profile of embryos that were wild-type, MZdicer, or MZdicer rescued with miR-430 (MZdicer+miR-430). This analysis identified ~600 genes that were upregulated in MZdicer, but not in MZdicer+miR-430. Experiment Overall Design: We have also analyzed the expression profile of the genes in the array at three different time points, one maternal stage(16 cell), and two Zygotic stages 5 hours and 9 hours
2007-10-05 | E-GEOD-4201 | biostudies-arrayexpress
Project description:Rhizobium leguminosarum SEMIA 430 genome sequencing
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Project description:A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs
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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.
2024-02-10 | GSE247930 | GEO
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.
2024-02-10 | GSE247933 | GEO
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.
2024-02-10 | GSE247934 | GEO