Publications by Year: 2026

Somatic variants are increasingly recognized as contributors to diverse non-cancer, developmental, and aging-related disorders. However, most tools for detecting somatic single-nucleotide variants (sSNVs) were designed for DNA sequencing and primarily tailored to cancer datasets, leaving a critical gap in harnessing the rich potential of RNA-seq for sSNV identification, particularly in non-cancer tissues with low mutation rates. Here, we introduce RNA-MosaicHunter, a novel bioinformatic tool for accurate sSNV detection from bulk RNA-seq. In two benchmarking datasets, it demonstrated high precision (94.7% in TCGA and 99.3% in a cell-line mixture) with sensitivities of 53.4% and 38.9%, respectively, in the default mode that maximizes precision. We then applied RNA-MosaicHunter to profile 827 RNA-seq samples in three tissue types from the Genotype Tissue Expression project (GTEx), where it outperformed previous methods in capturing mutational characteristics associated with normal aging. We further utilized RNA-MosaicHunter to analyze RNA-seq data from 382 Alzheimer’s disease (AD) brain samples and 480 age-matched controls and revealed a significantly higher burden of sSNVs in AD cerebral cortex, suggesting the potential contribution of sSNVs to AD pathogenesis. RNA-MosaicHunter enables accurate profiling and characterization of sSNVs from RNA-seq data, advancing the understanding of the role of somatic variants across diverse tissues and diseases.

Background Changes in RNA splicing over the course of evolution have profoundly diversified the functional landscape of the human genome. While DNA sequences proximal to intron-exon junctions are known to be critical for RNA splicing, the impact of distal intronic sequences remains underexplored. Emerging evidence suggests that inverted pairs of intronic Alu elements can promote exon skipping by forming RNA stem-loop structures. However, their prevalence and influence throughout evolution remain unknown.

Results Here, we present a systematic analysis of inverted Alu pairs across the human genome to assess their impact on exon skipping through predicted RNA stem-loop formation and their relevance to hominoid evolution. We found that inverted Alu pairs, particularly pairs of AluY-AluSx1 and AluSz-AluSx, are enriched in the flanking regions of skippable exons genome-wide and are predicted to form stable stem-loop structures. Exons defined by weak 3′ acceptor and strong 5′ donor splice sites appear especially prone to this skipping mechanism. Through comparative genome analysis across nine primate species, we identified 67,126 hominoid-specific Alu insertions, primarily from AluY and AluS subfamilies, which form inverted pairs enriched across skippable exons in genes of ubiquitination-related pathways. Experimental validation of exon skipping among several hominoid-specific inverted Alu pairs further reinforced their potential evolutionary significance.

Conclusion This work extends our current knowledge of the roles of RNA secondary structure formed by inverted Alu pairs and details a newly emerging mechanism through which transposable elements have contributed to genomic innovation across hominoid evolution at the transcriptomic level.