RNA sequencing of Arabidopsis mature seed and germination stages
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE167244 | GEO | 2021/03/23
REPOSITORIES: GEO
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Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels. Illumina sequencing of transcripts from cotyledons of mid-maturation (B1 stage) and late maturation (AA1 stage) seeds, whole dry seeds, and cotyledons of seedlings six days after imbibition.
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Project description:RNA sequencing of Arabidopsis mature seed and germination stages
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Project description:In this study, we sequenced the sRNAs population from embryos of 0, 12, and 24 HAI rice seeds using next-generation deep sequencing technology. A series of miRNAs were identified, including both known and novel miRNAs. We also predicted the potential targets for the miRNAs. RT-PCR and 5’ RACE assay were performed to confirm some deep sequencing and target prediction results. This study provides the unique composition and expressional profiles of miRNAs and their potential regulations in the embryo at the early stages of rice seed germination.
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