Detecting short full length excised introns using TGIRT-seq

We used a method (TGIRT-seq) that gives end-to-end sequence reads of highly structured RNAs to identify thousands of short (300 nt and shorter) full-length excised intron (FLEXI) RNAs in human cells and plasma. Many FLEXI RNAs are predicted to have stable secondary structures, and some correspond to mirtron pre-miRNAs or agotrons. FLEXI RNA profiles are cell-type specific, and comparisons of matched tumor and healthy tissues from breast cancer patients and cell lines revealed hundreds of diseases-specific differences. FLEXI RNAs could function in gene regulatory pathways directly or as precursors of short regulatory RNAs. As FLEXI RNAs are linked to the expression of thousands of protein-coding and lincRNA genes, they potentially constitute a new class of broadly applicable, highly discriminatory RNA biomarkers for human diseases.