Targeted sequencing of mutations via RNA-templated gap filling of oligonucleotides for single-cell RNA-seq

Saurty-Seerunghen, M. S.; Lee, H.; Holdar, M.; Roach, M.; Moein, S.; Kang, T.; Hu, T.; Nilsson, M.; Martelotto, L. G.; Nam, A. S.; Grillo, M.

doi:10.64898/2026.04.10.717677

bioRxiv · 10.64898/2026.04.10.717677

Targeted sequencing of mutations via RNA-templated gap filling of oligonucleotides for single-cell RNA-seq

Saurty-Seerunghen, M. S.·Lee, H.·Holdar, M.·Roach, M.·Moein, S.·Kang, T.·Hu, T.·Nilsson, M.·Martelotto, L. G.·Nam, A. S.·Grillo, M.

View original source ↗Export metadata ↓

Abstract

We describe a method for targeted sequencing of expressed mutations in single cells. The approach exploits the reverse transcriptase and nick translation activities of the Bst DNA polymerase (Full Length) from Bacillus stearothermophilus (BstFL) to perform an RNA-templated gap filling and ligation between flanking probes. Integrated with probe-based single cell RNAseq workflows, it enables simultaneous whole transcriptomic and multiplexed mutation profiling from the same cell, overcoming key limitations of mutation detection in existing scRNA-seq approaches.

Explore related subjects

molecular biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Saurty-Seerunghen, M. S., Lee, H., Holdar, M., Roach, M., Moein, S., Kang, T., Hu, T., Nilsson, M., Martelotto, L. G., Nam, A. S., Grillo, M.. 2026-04-11. Targeted sequencing of mutations via RNA-templated gap filling of oligonucleotides for single-cell RNA-seq. https://doi.org/10.64898/2026.04.10.717677

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Dietary selenium deficiency drives sex-specific circadian disturbance through redox imbalance and causes early systolic dysfunction in mice

Background: Selenium is a vital trace element involved in antioxidant defence and cardiovascular health. Although selenium deficiency is implicated in cardiomyopathies, its early cardiac effects and underlying mechanisms remain poorly defined. Methods: C57BL6/Njr mice were fed either a selenium deficient or control diet for 12 weeks. Systemic selenium status, cardiac function by echocardiography, left ventricular (LV) transcriptomic profiles, redox balance, and circadian pathway markers were assessed, including sex-specific analyses. Results: Selenium deficiency reduced plasma selenium levels without inducing overt cardiac hypertrophy or fibrosis. Echocardiography showed preserved ejection fraction and fractional shortening but reduced global longitudinal strain, indicating early systolic dysfunction. Cardiac stress markers were increased predominantly in male mice. Left ventricular RNA sequencing revealed enrichment of pathways related to cardiac remodelling, redox regulation, mitochondrial function, and circadian rhythm. Additional protein and metabolic analyses supported sex-specific redox circadian alterations, with males showing a more pronounced stress response profile. Conclusions: Dietary selenium deficiency induces early myocardial dysfunction and molecular remodelling before overt cardiac failure. These changes are associated with redox and circadian pathway disruption and show sex specific features, suggesting that selenium contributes to cardiac homeostasis through sex dependent redox circadian regulation.

molecular biology↗

bioRxiv2026

Dysregulation of FMR1 Splicing in Human Fragile X Syndrome

Fragile X Syndrome (FXS) is a neuro-developmental disorder caused by a CGG expansion in FMR1, leading to transcriptional silencing and loss of the encoded protein FMRP. Surprisingly, ~70% of FXS individuals express FMR1, but the RNA is mis-spliced to isoform FMR1-217, composed of exon 1 spliced to a pseudo-exon in intron 1 and cannot produce FMRP. Splice-switching ASOs rescue proper FMR1 splicing and restore FMRP. FMR1-217 mis-splicing increases with CGG repeat length and is negatively correlated with patient IQ. FMR1-217 is associated with ribosome footprints, indicating it is translated into a polypeptide that may impair cognition. R-loops form at the FMR1 locus and extend into the pseudo-exon, but splice-switching ASOs reduce FMR1-217 and elevate FMRP independently of R-loop formation. DRB-based transcription analysis identified impaired Pol II elongation at the 5 prime region of FMR1 in FXS cells, indicated by accumulation of hypophosphorylated Pol II at the transcription start site. Consistent with this, camptothecin-induced Pol II stalling increased FMR1-217 pseudo-exon inclusion. The splicing factors PTBP1 and PTBP2 regulate FMR1-217 splicing in a differentiation stage-dependent manner. Together, these findings indicate that FMR1-217 mis-splicing in FXS is associated with CGG repeat expansion, R-loop formation, impaired co-transcriptional Pol II elongation and context-dependent regulation by PTBP1/PTBP2.

molecular biology↗

bioRxiv2026

Hidden Biodiversity in Wildlife Trade Networks: DNA Barcoding Reveals Fish and Crocodilian Species in Commercialized Swim Bladders

International wildlife trade represents one of the major drivers of biodiversity exploitation worldwide. However, the true taxonomic diversity embedded within commercial wildlife products often remains unknown because processing removes diagnostic morphological characteristics, preventing reliable species identification. Consequently, biodiversity assessments based solely on product labels may substantially underestimate the diversity of species involved in trade networks. To investigate hidden biodiversity within wildlife trade products, we applied DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene to 77 products commercialized as fish swim bladders and seized at Guarulhos International Airport, Brazil. Molecular analyses successfully identified all samples and revealed the presence of four species: Plagioscion auratus (n = 38), Cynoscion acoupa (n = 7), Melanosuchus niger (n = 17), and Caiman crocodilus (n = 15). Fish species accounted for 71.4% of all samples, whereas crocodilians represented 28.6%, demonstrating that products marketed under a single commercial category may conceal substantial taxonomic diversity. Notably, the occurrence of two Amazonian crocodilian species within a trade chain traditionally associated with fish products reveals a previously undocumented component of the international wildlife trade. Our findings demonstrate that DNA barcoding is an effective tool for uncovering hidden biodiversity within processed wildlife products and provide evidence that wildlife trade networks may involve a broader spectrum of species than suggested by commercial labels. These results highlight the importance of molecular surveillance for biodiversity monitoring, wildlife trade regulation, and conservation planning.

molecular biology↗