Cell compartment isoform expression analysis using long-read transcriptomics

Abstract

Motivation: Alternative splicing, a crucial post-transcriptional process, enhances proteomic diversity without increasing gene numbers, playing pivotal roles in gene regulation, specialization, and disease. Short-read sequencing limitations have prompted exploration of long-read sequencing, such as Oxford Nanopore Technologies. Results: This study investigates alternative splicing in the human lymphoblastic leukemia B (BLaER1) cell line’s nucleus and cytosol using second and third-generation sequencing. Long-read Oxford Nanopore data, analyzed with FLAIR, elucidates RNA localization and splicing regulation. Short-read Illumina RNASeq complements this analysis for precise junction validation, employing SQANTI-based filtering for data quality. Adapting ggsashimi for long-read visualization enhances isoform and splicing event assessment. Specific genes (ZDHHC6, MTG1, LAP3) reveal compartmental variations, emphasizing gene regulation’s compartmental importance. Enriched Gene Ontology terms indicate cytosol-nucleus differences in RNA processing, translation, and ribosome biogenesis. These findings provide a comprehensive understanding of alternative splicing, RNA processing, and gene regulation, with implications for splicing-related disease therapeutics.