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

ORGANISM(S): Oryza sativa

PROVIDER: GSE229958 | 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 [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 [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 [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

2024-07-29 | GSE229960 | GEO

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

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

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

| PRJNA956898 | ENA

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

Project description:MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

2018-04-25 | GSE111440 | GEO

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