Two miRNAs are sufficient for C. elegans embryogenesis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641827 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12089028.fastq.gz | Fastqsanger.gz | |||
| SRR12089029.fastq.gz | Fastqsanger.gz | |||
| SRR12089030.fastq.gz | Fastqsanger.gz | |||
| SRR12089031.fastq.gz | Fastqsanger.gz | |||
| SRR12089032.fastq.gz | Fastqsanger.gz |
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Project description:miRNAs play essential roles in the mechanics of gene regulation, however, on an organismal-scale, the processes in they are deployed are not well understood. Here, we adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both C. elegans and D. melanogaster. We find that, in both species, the miRNA complement of the transcriptome shifts in a punctuated fashion during the previously identified mid-developmental transition specifying two dominant modes of miRNA expression: an early and a late profile. Strikingly, we find that phylogenetically conserved miRNAs are expressed late, while early expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Our work exposes two distinct strategies of miRNA function comprising late-expressed physiological roles and early expressed repressive roles. In summary, the expression of miRNAs throughout embryogenesis in two species implicates their role in the canalization of cell-types during late phases of embryogenesis and repressing targets to lock-down misexpression.
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Project description:Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes.
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Project description:Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes. Various C. elegans embryo samples were generated: mixed embryos by traditional bleaching (Brenner, 1974), early embryos by eFACS (Stoeckius et al., in press). RNA was extracted and length fractionated. Small RNA was subjected to a 5'-dependent ligation protocol to add sequencing adapters. The small RNA samples were sequenced using the Illumina GA I & II.
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Project description:Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis
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Project description:MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants?and increasing studies have been performed on some crops?however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. In this study, we globally identified small RNAs and their related target genes during cotton somatic embryogenesis by the high throughput small RNA and degradome sequencing technology using fresh hypocotyls and EC (embryogenic calli) of Gossypium hirsutum YZ1. A total of 36 differentially expressed conserved miRNA families of which 19 miRNA families represented by 29 precursors and 25 novel miRNAs were identified, with star sequences of 20 known miRNAs and 2 novel miRNAs discovered. 234 genes in EC and 322 genes in CK were identified as targets of 23 and 30 known miRNA families, and 16 genes were found as targets of 8 novel miRNAs. The expression profiles of several miRNAs and their targets were verified by qRT-PCR and 5’RACE were further used to validate the sliced sites of the targets. Interestingly, four TAS3 D6 and D7 were also found in both degradome libaries which can perfectly match their precursors. The profiling of the miRNAs and their target genes provides more information about the regulatory network of miRNAs during somatic embryogenesis in cotton. small RNA and degradome sequencing of CK(fresh hypocotyls) and EC (embryogenic calli) of Gossypium hirsutum YZ1
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