Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

ABSTRACT: Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. To define the function of this new pathway, we have focused on the RDR6 protein, which plays a central role in the pathway we refer to as RDR6-dependent RNA-directed DNA Methylation (RDR6-RdDM). Methods: We have sequenced total small RNAs from wild-type and three mutant genotypes: ddm1, ddm1/rdr6, and rdr6. Conclusions: We demonstrate that RDR6-RdDM utilizes 21 and 22 nucleotide siRNAs to de novo methylate actively transcribing TEs. In addition, we find that the RDR6-RdDM pathway functions in the efficient initiation and re-establishment of TE transcriptional silencing, while it is not necessary to maintain trans-generational epigenetic silencing. Examination of flower bud small RNAs from wild-type and 3 mutant genotypes

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Richard Slotkin 

PROVIDER: E-GEOD-41755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.

Nuthikattu Saivageethi S   McCue Andrea D AD   Panda Kaushik K   Fultz Dalen D   DeFraia Christopher C   Thomas Erica N EN   Slotkin R Keith RK  

Plant physiology 20130329 1

Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE  ...[more]

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