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Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
- 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.
- Subjects :
- 0301 basic medicine
QH301-705.5
RNA-binding protein
Science
cell-free RNA
Biology
General Biochemistry, Genetics and Molecular Biology
03 medical and health sciences
0302 clinical medicine
Mirtron
microRNA
diagnostics
Humans
RNA, Messenger
Biology (General)
Gene
miRNA
tRNA fragment
Genetics
Messenger RNA
Binding Sites
General Immunology and Microbiology
Sequence Analysis, RNA
General Neuroscience
Intron
RNA
RNA-Directed DNA Polymerase
General Medicine
DNA
Group II intron
Chromosomes and Gene Expression
Introns
030104 developmental biology
030220 oncology & carcinogenesis
Transfer RNA
biomarker
Medicine
Peak calling
Research Article
Human
Protein Binding
Subjects
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