Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data

Martínez de Villarreal, Jaime; Kalisz, Mark; Piedrafita, Gabriel; Graña-Castro, Osvaldo; Chondronasiou, Dafni; Serrano, Manuel; Real, Francisco X.

doi:http://dx.doi.org/10.1093/bioinformatics/btac737

Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data

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Martínez J, Kalisz M, Piedrafita G, Graña-Castro O, Chondronasiou D, Serrano M, et al. Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data. Bioinformatics. 2023 Jan;39(1):btac737. DOI: 10.1093/bioinformatics/btac737

Abstract

Transposable elements (TE) have played a major role in configuring the structures of mammalian genomes through evolution. In normal conditions, the expression of these elements is repressed by different epigenetic regulation mechanisms such as DNA methylation, histone modification and regulation by small RNAs. TE re-activation is associated with stemness potential acquisition, regulation of innate immunity and disease, such as cancer. However, the vast majority of current knowledge in the field is based on bulk expression studies, and very little is known on cell-type- or state-specific expression of TE-derived transcripts. Therefore, cost-efficient single-cell-resolution TE expression analytical approaches are needed. We have implemented an analytical approach based on pseudoalignment to consensus sequences to incorporate TE expression information to scRNAseq data.