TY - JOUR TI - Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling AU - Yao, Jun AU - Wu, Douglas C AU - Nottingham, Ryan M AU - Lambowitz, Alan M A2 - Nilsen, Timothy W A2 - Manley, James L A2 - Garcia-Blanco, Mariano A VL - 9 PY - 2020 DA - 2020/09/02 SP - e60743 C1 - eLife 2020;9:e60743 DO - 10.7554/eLife.60743 UR - https://doi.org/10.7554/eLife.60743 AB - Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons. KW - biomarker KW - cell-free RNA KW - diagnostics KW - miRNA KW - RNA-binding protein KW - tRNA fragment JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -