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Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [Bisulfite-Seq]

ABSTRACT: We performed whole genome bisulfite sequencing in se-2 and the related triple mutants. se-2 mutant did not display obvious changes in genome wide methylation in CG, CHG and CHH contexts. Thus, the H3K27me1 hypomethylation and suppression of atxr5/6-reactivated loci in se-2 mutant was not through DNA methylation defect.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE111742 | GEO | 2018/06/26

REPOSITORIES: GEO

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Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [ChIP-Seq]

Project description:We performed ChIP-seq of SE and selected histone modifications. ATXR5/6 deposit histone3 lysine27 monomethylation (H3K27me1) to promote heterochromatin formation and repress transposable elements (TEs) in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions.

2018-06-26 | GSE111811 | GEO

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [RNA-Seq]

Project description:We performed Illumina sequencing of ribosome depletion RNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is required for transposon reactivation in atxr5 atxr6 mutant.

2018-06-26 | GSE111812 | GEO

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [sRNA-Seq]

Project description:We performed Illumina sequencing of sRNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is a key component in miRNA processing and pre-mRNA splicing, whereas ATXR5/6 is engaged in epigenetic silencing. Genome-wide sRNA sequencing revealed that ATXR5/6 did not participate in SE-mediated miRNA biogenesis.

2018-06-26 | GSE111813 | GEO

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression

Project description:Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression

| PRJNA438235 | ENA

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [Bisulfite-Seq]

Project description:Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [Bisulfite-Seq]

| PRJNA438055 | ENA

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [RNA-Seq]

Project description:Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [RNA-Seq]

| PRJNA438240 | ENA

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [ChIP-Seq]

Project description:Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [ChIP-Seq]

| PRJNA438239 | ENA

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [sRNA-Seq]

Project description:Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression [sRNA-Seq]

| PRJNA438241 | ENA

Arabidopsis SE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-26 | GSE111814 | GEO

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_11]

Project description:ARABIDOPSIS THRITHORAX-RELATED PROTEINS 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements, chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, upregulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6 null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.

2021-11-23 | GSE166886 | GEO

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