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

ABSTRACT:

Motivation

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.

Results

We have implemented an analytical app

SUBMITTER: de Villarreal JM 

PROVIDER: S-EPMC9825736 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature