Long-read sequencing disentangles isoform complexity at allele-specific loci.

Area of Science:

• Genomics
• Transcriptomics
• Molecular Biology

Background:

• Long-read sequencing offers high accuracy for detecting transcript isoforms.
• Disentangling complex allele-specific loci, arising from genetic or epigenetic variations, remains a challenge.

Purpose of the Study:

• To assess the capability of long-read sequencing to resolve allele-specific transcript isoforms.
• To develop and validate a workflow for analyzing complex allele-specific loci using long-read transcriptomics.

Main Methods:

• Combined PacBio Iso-Seq workflow with WhatsHap phasing.
• Applied the workflow to polymorphic F1 mouse hybrids.
• Compared long-read data with matched short-read sequencing data.

Main Results:

• Demonstrated consistency between long-read sequencing and allele-specific information from short reads.
• Confirmed imprinting status of known imprinted genes.
• Characterized allele-specific isoforms at the complex Gnas locus and identified isoforms from active and inactive X chromosomes for X-inactivation escape genes.

Conclusions:

• The developed workflow effectively disentangles complex allele-specific transcriptomes.
• Long-read transcriptomic data provides powerful mechanistic insights into allele-specific gene regulation.