Transcriptome variation in human tissues revealed by long-read sequencing.

Area of Science:

• Genomics
• Transcriptomics
• Bioinformatics

Background:

• Transcript structure regulation is crucial for human health and disease.
• Long-read sequencing technologies enable deeper investigation of genetic variation's role in transcript structure.

Purpose of the Study:

• To create and analyze a comprehensive human long-read RNA-seq dataset.
• To identify novel transcripts and understand the impact of genetic variants on transcriptome.
• To develop computational tools for analyzing allele-specific expression and transcript structure.

Main Methods:

• Generation of a large human long-read RNA-seq dataset using Oxford Nanopore Technologies from 88 GTEx samples.
• Identification and validation of novel transcripts.
• Development of the LORALS computational package for allele-specific analysis of long reads.
• Perturbation of transcript structure via PTBP1 knockdown.

Main Results:

• Identification of over 70,000 novel transcripts, with protein expression validated for 10%.
• Characterization of allele-specific expression and transcript structure events.
• Demonstration of genetic regulatory effects modified by cellular environment.
• Enhanced variant interpretation for rare variants impacting splicing.

Conclusions:

• Long-read sequencing provides high resolution for studying transcript structure and genetic variation.
• The LORALS package facilitates the analysis of genetic effects on the transcriptome.
• This dataset and methodology advance understanding of transcript diversity, disease, and variant interpretation.