Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons

Area of Science:

• Genomics
• Neuroscience
• Molecular Biology

Background:

• Long-read RNA sequencing (LR-RNA-seq) offers high resolution for transcriptome analysis.
• Understanding transcript diversity is key for modeling brain disorders.

Purpose of the Study:

• To profile transcriptomes of human fibroblasts, induced pluripotent stem cells, and cortical neurons using LR-RNA-seq.
• To identify transcript diversity, differential expression, and differential usage events across cell types.
• To investigate the role of transcript-level variations in neurodevelopmental and neurodegenerative diseases.

Main Methods:

• Nanopore long-read RNA sequencing was performed on three distinct human cell types.
• Bioinformatic analyses were conducted to identify transcript diversity, differential transcript expression, and differential transcript usage.
• Integration of differential transcript expression and usage data provided deeper insights into transcript dynamics.

Main Results:

• Extensive transcript diversity was identified, with over 15,000 transcripts detected in cortical neurons.
• 35,519 differential transcript expression events and 5,135 differential transcript usage events were uncovered.
• Transcript-specific changes in disease-associated genes (e.g., APP, KIF2A, BSCL2) were highlighted by differential transcript usage analysis.

Conclusions:

• LR-RNA-seq provides a comprehensive framework for analyzing transcript diversity in pluripotent and specialized cells.
• Differential transcript usage analysis reveals critical transcript-level variations missed by gene-level analysis.
• This study advances the understanding of transcriptomic regulation in brain disorders and identifies potential transcript-specific therapeutic targets.