Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

@article{Jia2009LossOR,
  title={Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs},
  author={Yi Jia and D. Lisch and K. Ohtsu and M. Scanlon and D. Nettleton and P. Schnable},
  journal={PLoS Genetics},
  year={2009},
  volume={5}
}
Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA… Expand

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References

SHOWING 1-10 OF 61 REFERENCES
Production and Processing of siRNA Precursor Transcripts from the Highly Repetitive Maize Genome
TLDR
It is shown that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR) retrotransposons, the most common repetitive feature in the maize genome. Expand
Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant
TLDR
Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size, and the enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced. Expand
Genetic and Functional Diversification of Small RNA Pathways in Plants
TLDR
It is concluded that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense. Expand
An RNA-dependent RNA polymerase is required for paramutation in maize
TLDR
It is proposed that the mop1 RDRP is required to maintain a threshold level of repeat RNA, which functions in trans to establish and maintain the heritable chromatin states associated with paramutation. Expand
Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
TLDR
It is concluded that the widespread accumulation patterns for RDR2- and DCL3-dependent siRNAs throughout the Arabidopsis genome largely reflect mechanisms to silence highly repeated sequences. Expand
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.
TLDR
Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs. Expand
RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production.
TLDR
It is shown that a point mutation within the catalytic domain of Rdp1 abolished its RNA-dependent RNA polymerase activity and resulted in the loss of transcriptional silencing and heterochromatin at centromeres, together with defects in mitotic chromosome segregation and telomere clustering. Expand
Distinct Mechanisms Determine Transposon Inheritance and Methylation via Small Interfering RNA and Histone Modification
TLDR
According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposons silencing. Expand
RNA silencing systems and their relevance to plant development.
TLDR
Plant RNA silencing systems are organized into a network with shared components and overlapping functions, and microRNAs, and probably trans-acting small RNAs, help regulate development at the posttranscriptional level. Expand
Initiation, Establishment, and Maintenance of Heritable MuDR Transposon Silencing in Maize Are Mediated by Distinct Factors
TLDR
It is shown that this gene, Mop1 (Mediator of paramutation1) codes for a putative RNA-dependent RNA polymerase, whose activity is required for the production of small RNAs that correspond to the MuDR transposon sequence, suggesting that the establishment and maintenance of MuDR silencing have distinct requirements. Expand
...
1
2
3
4
5
...