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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Oryza sativa

PROVIDER: GSE215857 | 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 [sRNA-Seq]

Project description: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.

2023-10-01 | GSE215854 | GEO

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.

2023-10-01 | GSE215853 | GEO

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

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

2023-10-01 | GSE215855 | GEO

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

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

| PRJNA891036 | ENA

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

Project description:RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

| S-EPMC8325292 | biostudies-literature

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

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

| PRJNA891033 | ENA

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]

| PRJNA891034 | ENA

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

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

| PRJNA891039 | ENA

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.

| S-EPMC8805726 | biostudies-literature

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

Project description:RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long non-coding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development. This SuperSeries is composed of the SubSeries listed below.

2021-07-06 | GSE158711 | GEO

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