Long-Read RNA Sequencing Reveals Tissue-Specific Expression and Transcript Boundary Variation of Mouse Prxl2b

Abstract Alternative splicing and transcript boundary variation contribute substantially to transcriptome complexity in mammalian genomes. Prxl2b (Peroxiredoxin-like 2B), also known as prostaglandin F synthase (PGFS), encodes an enzyme with both antioxidant and prostaglandin-metabolizing activities. The protein catalyzes the conversion of prostaglandin H2 (PGH2) to prostaglandin F2α (PGF2α) and prostamide H2 to prostamide F2α, thereby contributing to prostaglandin and prostamide biosynthesis, inflammatory signaling, reproductive processes, and cellular redox homeostasis. Despite its important biological functions, the transcript architecture of Prxl2b across mouse tissues remains incompletely characterized. In this study, publicly available ENCODE long-read RNA-seq datasets generated using PacBio sequencing technology were analyzed to characterize Prxl2b expression patterns and transcript architecture. The reads were aligned to the mouse reference genome (mm10), and transcript models were reconstructed using IsoQuant and validated using FLAIR-based transcript annotation. Gene expression was quantified using transcripts per million (TPM) across multiple mouse tissues and cell types, including cerebral cortex, hippocampus, gastrocnemius muscle, and the C2C12 immortalized mouse myoblast cell line. Genome browser visualization was performed using IGV to evaluate exon connectivity and transcript boundaries. Expression analysis revealed marked tissue-specific variation in Prxl2b, abundance with expression detected predominantly in a subset of tissues and cell types. Transcript reconstruction consistently identified the canonical transcript ENSMUST00000030935.9 across independently analyzed datasets. Comparative analysis with GENCODE annotations demonstrated strong agreement in exon–intron organization and splice junction usage. Long-read evidence additionally suggested variation in transcript boundaries, particularly at the 5′ region, while preserving the overall coding structure of the annotated transcript. These findings demonstrate the utility of long-read RNA sequencing for accurate characterization of Prxl2b transcript architecture and provide a refined view of its expression landscape across mouse tissues.