Single-nucleotide variants in human RNA: RNA editing and beyond

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• RNA sequencing (RNA-Seq) is primarily used for gene expression quantification.
• Emerging applications reveal RNA-Seq's utility beyond expression profiling.
• Alternative uses include detecting single-nucleotide variants (SNVs) from RNA editing and genomic variations.

Purpose of the Study:

• To review the history and methodologies for identifying RNA editing events from RNA-Seq data.
• To discuss the challenges and advancements in cataloging RNA editing and genomic variants.
• To highlight the unexpectedly high prevalence of RNA editing events.

Main Methods:

• Analysis of paired high-throughput DNA sequencing (DNA-Seq) and RNA-Seq data.
• Development of methodologies for identifying, predicting, and assessing RNA-editing events.
• Cataloging RNA-editing events and genomic variants.

Main Results:

• RNA-Seq data analysis reveals a high prevalence of RNA-editing events.
• Many observed RNA-editing events are not explained by known mechanisms.
• Significant progress has been made in developing tools to analyze these events over the past 6-7 years.

Conclusions:

• RNA-Seq is a powerful tool for discovering and analyzing RNA editing events and genomic variants.
• Further research is needed to understand the mechanisms behind the high prevalence of unexplained RNA editing.
• Methodologies for RNA-Seq data analysis continue to evolve for variant detection.