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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ChIP_seq]

ABSTRACT: Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

ORGANISM(S): Oryza sativa

PROVIDER: GSE260649 | GEO | 2024/07/29

REPOSITORIES: GEO

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [Bisulfite_seq]

Project description:Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [bisulfite_PCR]

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [PCR_product_deep_sequencing]

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [targeted bisulfite PCR]

Project description:Knock down of CLSY3 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY3 in rice endosperm by profiling sRNA, targeted bisulfite PCR and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

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Imprinted expression of genes and small RNA is triggered by localized demethylation of the maternal genome in rice endosperm

Project description:We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small Class II (cut and paste) transposable elements, those in endosperm are much more uniformly derived, including sequences from other TE classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that demethylation of maternal endosperm DNA is conserved in flowering plants.

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Imprinted expression of genes and small RNA is triggered by localized demethylation of the maternal genome in rice endosperm

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ChIP_seq]

Project description:Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ChIP_seq]

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