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A Nonsequencing Approach for the Rapid Detection of RNA Editing
Published on: April 21, 2022
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Patterns of RNA Editing in Newcastle Disease Virus Infections.
Archana Jadhav1, Lele Zhao2, Alice Ledda3
1Viral Oncogenesis group, The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, UK.
Viruses
|November 5, 2020
Summary
Newcastle disease virus (NDV) accessory protein expression relies on RNA editing. A Markov model accurately describes guanine insertions in viral mRNA, confirming a long-standing hypothesis about polymerase stuttering.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Newcastle disease virus (NDV) non-structural proteins V and W expression is regulated by RNA editing.
- These proteins arise from frameshifts in the P protein sequence due to guanine insertions in mRNA.
Purpose of the Study:
- To investigate mRNA editing patterns in NDV infections using deep RNA sequencing.
- To quantitatively analyze the molecular process of guanine insertions during NDV transcription.
Main Methods:
- Deep RNA sequencing of in vitro and in vivo NDV-infected samples.
- Analysis of guanine insertion patterns using a Markov model.
Main Results:
- The distribution of guanine insertions follows a simple Markov model of polymerase stuttering.
- The initial probability of polymerase stuttering is approximately 0.45, decreasing to 0.3 for subsequent insertions.
- This stuttering probability is largely independent of host cell and viral strain, except for deviations in LaSota infections.
Conclusions:
- The study quantitatively confirms the polymerase stuttering model for NDV RNA editing.
- Deviations in the V/W protein ratio in LaSota infections suggest potential model limitations or additional regulatory mechanisms.
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