Rapid and Cost-Effective Digital Quantification of RNA Editing and Maturation in Organelle Transcripts by Oxford Nanopore Target-Indexed-PCR (TIP) Sequencing.

ABSTRACT: RNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted long non-coding (lnc) RNA-seq or targeted amplicon-seq, involve high costs, complex workflows, and limited accessibility. To address these limitations, I developed a rapid and cost-effective long-read sequencing approach, termed Target-Indexed-PCR (TIP) sequencing, for digital quantification of RNA editing and intron retention events in targeted chloroplast transcripts. This method combines multiplexed high-fidelity PCR amplification with Oxford Nanopore sequencing and custom in-house Perl and Python

SUBMITTER: Hua Z 

PROVIDER: S-EPMC12537063 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature