Nano3P-seq

Nano3P-seq enables transcriptome-wide measurement of RNA abundance, 3' end composition, and polyadenylation tail length dynamics using nanopore cDNA 3' end-capture sequencing.

Key Features:

• Simultaneous quantification: Quantifies RNA abundance, 3' tail composition, and polyA tail length at per-read resolution across transcripts.
• Template-switching protocol: Uses a template-switching-based sequencing protocol to sequence RNA molecules from their 3' ends without PCR amplification or RNA adapter ligation, enabling analysis regardless of polyadenylation status.
• Minimal library preparation bias: Exhibits minimal biases during library preparation, supporting accurate measurements across coding and non-coding transcripts.
• Diverse RNA biotype detection: Captures a wide range of RNA biotypes including mRNA, long non-coding RNA, and polyA tails on 16S mitochondrial rRNA in mouse and zebrafish.
• Isoform-specific tail regulation: Reveals isoform-specific regulation of mRNA tail lengths during vertebrate embryogenesis and correlates tail dynamics with mRNA decay.
• Non-A base detection in tails: Identifies non-A bases within polyA tails across varied lengths and reports their distribution during vertebrate embryogenesis.

Scientific Applications:

• RNA maturation and stability studies: Quantifies RNA abundance and tail length/composition to investigate RNA maturation, fate, and stability.
• Developmental biology and embryogenesis: Analyzes isoform-specific polyadenylation dynamics and non-A base incorporation during vertebrate embryogenesis.
• Mitochondrial RNA research: Detects polyA tails on 16S mitochondrial rRNA in model organisms such as mouse and zebrafish to study mitochondrial RNA processing.
• Coding and non-coding transcriptome analysis: Enables comparative analysis of polyadenylation and tail composition across coding and long non-coding RNAs.

Methodology:

Computational analysis operates at per-read resolution on nanopore cDNA 3' end-capture sequencing data to quantify RNA abundance, 3' tail composition, and polyA tail length.