Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms

Here, we applied Oxford Nanopore native RNA sequencing to generate an isoform-level transcriptome of primary human monocytes before and after activation with lipopolysaccharide (LPS). We identify over 24,000 expressed isoforms, including thousands of previously unannotated variants.

Activation with LPS induced widespread isoform-specific expression changes, leading to extensive isoform switching events, which were validated using matched short-read RNA-Seq. These activation-induced shifts enhanced transcript immune-regulatory functions: activated monocytes preferentially express longer, coding-competent isoforms with complete open reading frames, fewer retained introns, and increased domain complexity.