Molecular basis of RNA-dependent RNA polymerase II activity

@article{Lehmann2007MolecularBO,
  title={Molecular basis of RNA-dependent RNA polymerase II activity},
  author={Elisabeth Lehmann and Florian Brueckner and Patrick Cramer},
  journal={Nature},
  year={2007},
  volume={450},
  pages={445-449}
}
RNA polymerase (Pol) II catalyses DNA-dependent RNA synthesis during gene transcription. There is, however, evidence that Pol II also possesses RNA-dependent RNA polymerase (RdRP) activity. Pol II can use a homopolymeric RNA template, can extend RNA by several nucleotides in the absence of DNA, and has been implicated in the replication of the RNA genomes of hepatitis delta virus (HDV) and plant viroids. Here we show the intrinsic RdRP activity of Pol II with only pure polymerase, an RNA… 
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References

SHOWING 1-10 OF 38 REFERENCES
Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity
TLDR
This work proposes a model in which HDAg interacts with and loosens the clamp, and thereby accelerates forward translocation of Pol II at the cost of fidelity, which may facilitate the unusual RNA‐dependent RNA synthesis by Pol II.
Structure of an RNA polymerase II–RNA inhibitor complex elucidates transcription regulation by noncoding RNAs
TLDR
The crystal structure of FC*, the central part of FC RNA, bound to Pol II indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.
Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase
TLDR
It is reported that the mechanism of 6S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding.
Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity.
TLDR
The data suggest that the overextended RNA:DNA hybrid formed in the absence of the non-template DNA acts as a negative regulator of EC stability, which provides a mechanism for the control of a correct nucleic acid architecture in the EC and of RNA polymerase II processivity.
Role of deoxyribonucleic acid-ribonucleic acid hybrids in eukaryotes. Study of the template requirements of yeast ribonucleic acid polymerases and nature of the ribonucleic acid product.
TLDR
An excellent template is produced by successive treatment of T7 DNA by pancreatic DNase and exonuclease II, indicating that RNA polymerases A (or I) and B (or II) can transcribe a duplex structure containing unpaired gaps and is very labile and release of RNA chains occurs continuously during transcription.
The Structure of an RNAi Polymerase Links RNA Silencing and Transcription
TLDR
The 2.3-Å resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, is reported and it is found that it forms a relatively compact dimeric molecule, each subunit with a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription.
Transcription Termination: Primary Intermediates and Secondary Adducts*
TLDR
Analysis of complexes formed between DNA template, nascent RNA, and Escherichia coli RNA polymerase during transcription through the tR2 terminator of bacteriophage λ shows no termination intermediates that withstand dissociation in the time scale appropriate for biochemical studies.
Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts
TLDR
It is shown for the first time that 6S RNA acts as a template for the transcription of defined RNA molecules in the absence of DNA and does not generally distinguish between exponential- and stationary-phase-specific promoters.
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