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 Technologie ...»»»»
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.^^^^
