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Deep sequencing of small RNAs from Tribolium castaneum

ABSTRACT: Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries.

ORGANISM(S): Tribolium castaneum

PROVIDER: GSE26036 | GEO | 2010/12/29

SECONDARY ACCESSION(S): PRJNA135507

REPOSITORIES: GEO

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Deep sequencing of small RNAs from Tribolium castaneum

Project description:Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries. Sequencing of Tribolium small RNAs from adults and embryos.

2010-12-29 | E-GEOD-26036 | biostudies-arrayexpress

Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle

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Project description:Genome-wide survey of transcriptional differences between males and females of Tribolium castaneum, the red flour beetle Four biological replicates for male and female beetles with 20 individuals per replicate. Two technical replicates, one replicate per sex. 16,434 genes/expressed non-coding regions represented twice on each array. Three 60 mer probes for most exons/expressed non-coding regions. 167,538 unique genomic probes replicated twice per array.

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Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

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Survey of methylomes of two beetles, Nicrophorus vespilloides and Tribolium castaneum

Project description:The presence of DNA methylation in beetles (Coleoptera) has only been investigated with bisulfite sequencing of Tribolium castaneum, which produced no evidence of DNA methylation. Here, we used whole genome bisulfite sequencing to assay if DNA methylation was present in another beetle, Nicrophorus vespilloides. We used T. castaneum as a negative control.

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Project description:Genome sequencing of Tribolium castaneum GA2 (red flour beetle) adult male alternate pseudohaplotype

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Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum

Project description:Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set of Dnmts. But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle, Tribolium castaneum, lacks Dnmt3 but possesses Dnmt1 and it has been controversial whether it has a functional DNA methylation system. Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we found Dnmt1 expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown of Dnmt1 caused a developmental arrest in offspring embryos. We show that Dnmt1 plays an essential role in T. castaneum embryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.

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