DNA-derived short tandem repeats (STRs) are widely used in population and forensic genetics, but their use is largely confined to detecting sequence variations, providing little functional insight. RNA-based STR analysis enables characterization of transcriptional activity, including locus expression, transcript abundance, and potential links between STR variation and gene regulation. However, the properties and genotyping reliability of RNA-derived STRs remain poorly understood, limiting their application. To address this, we conducted the first transcriptome-wide characterization of polymorphic STRs (pSTRs) in human blood using whole-transcriptome sequencing data from 167 individuals and whole-genome sequencing data from a matched subset of 50 individuals from the same cohort. We identified 24,013 pSTRs (genotyping rate ≥ 50% across RNA samples), whose genotypes demonstrated high reliability, with strong consistency across technical replicates and high concordance with matched DNA genotypes. Furthermore, these pSTRs showed region-specific architectures, with coding sequences and 5’ UTR regions enriched for trinucleotide and hexanucleotide motifs that had longer reference alleles and higher polymorphism than those in unconstrained regions. Observed RNA-DNA discordances (RDDs) could be attributed to both biological factors (e.g., RNA editing) and technical artifacts of RNA sequencing. Analysis of disease-associated STRs confirmed low-frequency pathogenic alleles in the population but also underscored the current challenge of short-read RNA-seq for profiling long repeats. Finally, the authenticity of RNA-derived STR genotypes was experimentally validated by capillary electrophoresis. Collectively, this study establishes a foundational atlas and demonstrates the robustness of RNA-STR as genetic markers, highlighting their region-specific evolutionary constraints and providing a critical framework for their application in diverse fields, including population genetics and molecular diagnostics.

Authors

• Jiajun Liu (Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, China)
• Zhiyong Liu (Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, China)