Transcriptomics

Dataset Information

413

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana


ABSTRACT: In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). We also examined small RNA abundance at individual CRP genes in the wild type plant, nrpd1, and rdr2 mutant plants.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Marc Schmid   Ueli Grossniklaus  Blake C Meyers  Matthew Spencer  Marjori Matzke  Antonius J Matzke  Lucia Daxinger  Stacey A Simon  Wanhui You  Agata Tyczewska  Blake C. Meyers 

PROVIDER: E-GEOD-34207 | ArrayExpress | 2012-11-22

SECONDARY ACCESSION(S): GSE34207SRP009656PRJNA149671

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana.

You Wanhui W   Tyczewska Agata A   Spencer Matthew M   Daxinger Lucia L   Schmid Marc W MW   Grossniklaus Ueli U   Simon Stacey A SA   Meyers Blake C BC   Matzke Antonius J M AJ   Matzke Marjori M  

BMC Plant Biology 20120419


BACKGROUND: In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the  ...[more]

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