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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [sRNA-Seq]

ABSTRACT: To investigate the function of FEM2 in regulation of 24-nt siRNA accumulation, 18-day-old seedlings wer used for RNA-seq, BS-seq and sRNA-seq.

ORGANISM(S): Oryza sativa

PROVIDER: GSE215854 | GEO | 2023/10/01

REPOSITORIES: GEO

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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [RNA-Seq]

Project description:To investigate the function of FEM2 in regulation of gene expression, 18-day-old seedlings wer used for RNA-seq, BS-seq and sRNA-seq.

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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [Bisulfite-Seq]

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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [sRNA-Seq]

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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice

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FVE affects 24-nt siRNA accumulation downstream of RdDM pathway

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Resetting of the 24-nt siRNA landscape in rice zygotes.

Project description:The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells-the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Owing to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epigenome, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation is accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ∼70% of the zygote siRNA loci do not overlap any egg cell siRNA loci. Newly detected siRNA loci in zygote are gene-proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci that are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci are associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that, in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.

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Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development.

Project description:Endogenous 24 nt short interfering RNAs (siRNAs), derived mostly from intergenic and repetitive genomic regions, constitute a major class of endogenous small RNAs in flowering plants. Accumulation of Arabidopsis thaliana 24 nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24 nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21 nt microRNAs (miRNAs) and 21-22 nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci that consistently produced a mixture of 21-24 nt siRNAs with a peak at 23 nt. These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5 mC) DNA modification. Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22-24 nt siRNAs, but not 21 nt siRNAs, at Pp23SR loci. The 21 nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6. Transcriptome-wide, Ppdcl3 mutants failed to accumulate 22-24 nt small RNAs from repetitive regions while transcripts from two abundant families of long terminal repeat (LTR) retrotransposon-associated reverse transcriptases were up-regulated. Ppdcl3 mutants also displayed an acceleration of leafy gametophore production, suggesting that repetitive siRNAs may play a role in the development of P. patens. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants.

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The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice.

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FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [RNA-Seq]

Project description:FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [RNA-Seq]

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Project description:FEM2 regulates the whole genome 24-nt siRNA accumulation and CHH DNA methylation in rice [Bisulfite-Seq]

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