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A model for rearrangements in RNA genomes
E V Pilipenko1, A P Gmyl, V I Agol
1M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy Sciences, Moscow Region.
Nucleic Acids Research
|June 11, 1995
Summary
Engineered viral RNA rearrangements, including deletions and insertions, often utilize short direct repeats as preferred sites. This process involves nascent strand pausing, polymerase dissociation, and re-annealing for synthesis resumption.
Area of Science:
- Molecular Biology
- Virology
- Genetics
Background:
- Engineered viral mutants of Theiler's murine encephalomyelitis virus (TMEV) and poliovirus exhibit altered spacing in translational control elements.
- These mutants generate pseudorevertants with deletions or insertions that restore wild-type structure.
Purpose of the Study:
- To investigate the mechanisms underlying RNA rearrangements in viral pseudorevertants.
- To identify preferred sites for strand jumps during RNA synthesis.
Main Methods:
- Analysis of the primary structure of rearranged regions in pseudorevertant viral genomes.
- Comparative genomics of engineered viral mutants and their pseudorevertants.
Main Results:
- Short direct repeats are strongly preferred as parting and anchoring sites for nascent strand 3' end jumps.
- Longer RNA segments between sites can be brought together by template strand folding.
- A model for RNA rearrangement is proposed involving pausing, polymerase dissociation, and re-annealing.
Conclusions:
- RNA rearrangements in viruses like TMEV and poliovirus are mechanistically guided by specific sequence features.
- The proposed model elucidates a pathway for deletions, insertions, and some recombinations during viral RNA synthesis.