RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting...

Area of Science:

• Molecular Biology
• Genomics
• Pharmacogenomics

Background:

• RNA targeting drugs are crucial for various therapies.
• Accurate mapping of RNA 5' ends is essential for understanding drug mechanisms.
• Identifying RNA variants is key for personalized medicine and drug resistance prediction.

Purpose of the Study:

• To present a high-throughput sequencing method for mapping RNA 5' ends.
• To detail a bioinformatics pipeline for analyzing sequencing data.
• To adapt the method for predicting drug susceptibility in RNA viruses and replicons.

Main Methods:

• High-throughput sequencing of 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) products.
• Preparation of sequencing libraries for Illumina and Ion Torrent platforms.
• Development of a bioinformatics pipeline for target site activity definition and enumeration.

Main Results:

• The RACE-SEQ method enables precise mapping and digital enumeration of RNA 5' ends.
• The bioinformatics pipeline effectively defines target site activity.
• The modified pipeline (RACE-SEQ-MM) can assess drug susceptibility of known and unknown RNA polymorphisms.

Conclusions:

• RACE-SEQ is a powerful tool for documenting RNA-targeting drug action and precision.
• The method facilitates patient selection, stratification, and resistance prediction.
• RACE-SEQ-MM offers a patient-free approach to evaluate drug susceptibility across diverse RNA variants.