Chromatin Accessibility Dynamics During Zebrafish Early Embryogenesis At The Single-Cell Resolution
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ABSTRACT:
PROVIDER: PRJEB64058 | ENA |
REPOSITORIES: ENA
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Project description:Zebrafish is a popular model for studies of embryonic development. Recent surveys of zebrafish embryogenesis with single-cell transcriptomics have uncovered hundreds of cell types, but the dynamic accessible regions of the genome that determine regulatory programs responsible for the unique identity and function of each cell type during embryogenesis lack detailed study. Here, we present SPATAC-seq: a split-pool ligation-based high-throughput single-cell assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 808,046 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stages in a single experiment. Using this chromatin accessibility map, we identified 604 cell types and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineate development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, transient reporter assays confirmed that a majority of tested cCREs exhibited robust enhanced EGFP expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a comprehensive and valuable open resource for exploring transcriptional regulators that determine cell fate specification in zebrafish embryogenesis.
2024-04-14 | GSE243256 | GEO
Project description:Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq
| PRJNA1017484 | ENA
Project description:The dynamics of gene expression in vertebrate embryogenesis at single cell resolution
| PRJNA449931 | ENA
Project description:Study of transcriptome dynamics using a high-resolution gene-expression time course with 180 individual embryos, obtained from nine different spawns that are profiled from late blastula to mid gastrula stage. All individual embryos of genotype ABTL were photographed and an initial developmental time was estimated using percentage epiboly as a metric.
2017-01-01 | GSE83395 | 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
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 | GSE247930 | GEO
Project description:We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyzed the RNA structure dynamics among different development stages. Also, we studied which factors regulate maternal gene decay by RNA structure switch.
2020-04-14 | GSE120724 | GEO
Project description:We performed plate-based single-nucleus experiments across multiple stages immediately after zygotic genome activation, including 1k, oblong, sphere and dome stages. The first point where cells become distinct at the chromatin level was determined. Many potential enhancers regulating the first cell fate decision were identified.
2023-10-13 | E-MTAB-13115 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
2011-11-17 | E-GEOD-32900 | biostudies-arrayexpress