TARDIS, a targeted RNA directional sequencing method for rare RNA discovery

Area of Science:

• Molecular Biology
• Genomics
• Transcriptomics

Background:

• High-throughput sequencing reveals numerous novel RNAs.
• Identifying rare transcripts is challenging due to technical limitations in RNA sequencing library preparation and platform performance.

Purpose of the Study:

• To introduce Targeted-RNA Directional Sequencing (TARDIS), a novel hybridization-based method.
• To enable independent interrogation of specific RNA subsets within the transcriptome, irrespective of transcript characteristics.

Main Methods:

• TARDIS is a modular protocol involving DNA trap generation, RNA purification, DNA trap-based RNA capture, and library construction.
• The method utilizes hybridization for targeted RNA capture.
• Coupling RNA capture with strand-specific RNA sequencing.

Main Results:

• TARDIS allows robust identification and reconstruction of novel transcripts.
• It facilitates the definition of sense and antisense RNA pairs.
• Concomitant analysis of long and small RNA pools enables inference of precursor-product relationships.

Conclusions:

• TARDIS is an effective method for interrogating specific RNA subsets.
• The protocol overcomes limitations of standard RNA sequencing for rare and novel transcript discovery.
• TARDIS provides a comprehensive approach to transcriptomic analysis, including novel transcript identification and precursor-product relationship inference.