Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA212741 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR941632.fastq.gz | Fastqsanger.gz | |||
| SRR941633.fastq.gz | Fastqsanger.gz | |||
| SRR941634.fastq.gz | Fastqsanger.gz | |||
| SRR941635.fastq.gz | Fastqsanger.gz | |||
| SRR941636.fastq.gz | Fastqsanger.gz |
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Project description:The complexity of metazoan organisms requires precise spatiotemporal regulation of gene expression during development. To identify different modes of developmental gene regulation we measured the transcriptome throughout development of the nematode Caenorhabditis elegans by mRNA sequencing with high temporal resolution. We find that approximately 2,000 transcripts undergo expression oscillations synchronized with larval transitions while thousands of genes are expressed in temporal gradients, similar to known timing regulators. By counting transcripts in individual animals, we show that the pulsatile expression of the microRNA (miRNA) lin-4 maintains the temporal gradient of its target lin-14 by dampening its expression oscillations. Our results demonstrate that this insulation is optimal when pulsatile expression of the miRNA and its target is synchronous. We propose that such a miRNA-mediated incoherent feed-forward loop is a potent filter that prevents propagation of potentially deleterious gene expression fluctuations during the development of an organism.
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Project description:Degradome sequencing reveals an endogenous microRNA target in C. elegans
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Project description:The complexity of metazoan organisms requires precise spatiotemporal regulation of gene expression during development. To identify different modes of developmental gene regulation we measured the transcriptome throughout development of the nematode Caenorhabditis elegans by mRNA sequencing with high temporal resolution. We find that approximately 2,000 transcripts undergo expression oscillations synchronized with larval transitions while thousands of genes are expressed in temporal gradients, similar to known timing regulators. By counting transcripts in individual animals, we show that the pulsatile expression of the microRNA (miRNA) lin-4 maintains the temporal gradient of its target lin-14 by dampening its expression oscillations. Our results demonstrate that this insulation is optimal when pulsatile expression of the miRNA and its target is synchronous. We propose that such a miRNA-mediated incoherent feed-forward loop is a potent filter that prevents propagation of potentially deleterious gene expression fluctuations during the development of an organism. We analyzed RNA-seq data of wild-type worms at two different temperatures, 20C and 25C, from samples picked every 2hrs and 1.5 hrs, resspectively, spanning all larval stages (L1,L2,L3,L4). At 20C we picked samples for L1-L3 (sample DH2: 0 hrs to 38 hrs) and for L4 (sample DH5: 38 hrs to 48 hrs) from independent populations. At 25C, all samples were picked from the same worm population (sample DH3: 0 hrs to 28.5 hrs). This time course ends at 28.5 hrs since at higher temperature nematode development is accelarated. Finally, we measured mRNA expression at 20C in a lin-4 knockout mutant worm (lin-4(e912)), again spanning all larval stages (sample DH4: 0 hrs to 48 hrs). Each sequencing sample consisted of a mixture of all time points with mRNA from different time points barcoded with Illumina barcodes and was sequenced on one or more lanes (DH2: 3 lanes; DH3: 3 lanes; DH4: 4 lanes; DH5: 1 lane) of an Illumina HiSeq2000.
2013-09-15 | E-GEOD-49043 | biostudies-arrayexpress
Project description:The double-stranded RNA-binding protein Staufen has been implicated in various posttranscriptional gene regulatory processes. Here, we demonstrate that the Caenorhabditis elegans homolog of Staufen, STAU-1, functionally interacts with microRNAs. Loss-of-function mutations of stau-1 significantly suppress phenotypes of let-7 family microRNA mutants, a hypomorphic allele of dicer and a lsy-6 microRNA partial loss-of-function mutant. Furthermore, STAU-1 modulates the activity of lin-14, a target of lin-4 and let-7 family microRNAs, and this modulation is abolished when the 3' untranslated region of lin-14 is removed. Deep sequencing of small RNA cDNA libraries reveals no dramatic change in the levels of microRNAs, or other small RNA populations between wild-type and stau-1 mutants, with the exception of certain endogenous siRNAs in the WAGO pathway. The modulation of microRNA activity by STAU-1 does not seem to be associated with the previously reported enhanced exogenous RNAi (Eri) phenotype of stau-1 mutants, since eri-1 exhibits the opposite effect on microRNA activity. Altogether, our results suggest that STAU-1 negatively modulates microRNA activity downstream of biogenesis, possibly by competing with microRNAs for binding on the 3' untranslated region of target mRNAs
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Project description:Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans [miRNA-Seq]
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Project description:Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41 [Ribosome footprinting]
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