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Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

Authors :
Ryan M. Nottingham
Alan M. Lambowitz
Douglas C. Wu
Jun Yao
Source :
eLife, Vol 9 (2020), eLife
Publication Year :
2020
Publisher :
Cold Spring Harbor Laboratory, 2020.

Abstract

SummaryHuman 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 introns RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.

Details

Database :
OpenAIRE
Journal :
eLife, Vol 9 (2020), eLife
Accession number :
edsair.doi.dedup.....933fa180f5fc56d32235a2ca2f3a9e54
Full Text :
https://doi.org/10.1101/2020.06.25.171439