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

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 and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

ORGANISM(S): Oryza sativa

PROVIDER: GSE229960 | GEO | 2024/07/29

REPOSITORIES: GEO

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Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [RNA-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 and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm development.

2024-07-29 | GSE229959 | GEO

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

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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

2024-07-29 | GSE260651 | GEO

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

2024-07-29 | GSE260649 | GEO

Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [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,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY3 in Endosperm

2024-07-29 | GSE260648 | GEO

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

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

2024-07-29 | GSE260647 | GEO

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

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

| PRJNA956899 | ENA

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.

2013-05-01 | GSE44898 | GEO

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

2013-05-01 | E-GEOD-44898 | biostudies-arrayexpress

Application of microdroplet PCR for large-scale targeted bisulfite sequencing.

Project description:Cytosine methylation of DNA CpG dinucleotides in gene promoters is an epigenetic modification that regulates gene transcription. While many methods exist to interrogate methylation states, few current methods offer large-scale, targeted, single CpG resolution. We report an approach combining bisulfite treatment followed by microdroplet PCR with next-generation sequencing to assay the methylation state of 50 genes in the regions 1 kb upstream of and downstream from their transcription start sites. This method yielded 96% coverage of the targeted CpGs and demonstrated high correlation between CpG island (CGI) DNA methylation and transcriptional regulation. The method was scaled to interrogate the methylation status of 77,674 CpGs in the promoter regions of 2100 genes in primary CD4 T cells. The 2100 gene library yielded 97% coverage of all targeted CpGs and 99% of the target amplicons.

| S-EPMC3202290 | biostudies-literature

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