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

Abstract
Data availability
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Abstract

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

Data availability

Code availability: All scripts used for data processing are deposited in GitHub: https://github.com/wckdouglas/cfNADate deposition: The TGIRT-seq datasets in this manuscript are listed in the Supplementary File and have been deposited in the National Center for Biotechnology Information Sequence Read Archive (accession number: PRJNA640428).

The following data sets were generated

1. Yao J
2. Wu D
3. Nottingham R
4. Lambowitz AM
(2020) Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
SRA, PRJNA640428.

https://www.ncbi.nlm.nih.gov/sra/PRJNA640428

The following previously published data sets were used

(2017) Granzyme A in Human Platelets Regulates Pro-Inflammatory Gene Synthesis by Monocytes in Aging
SRA, PRJNA397446.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA397446
(2015) TGIRT-Seq profiling of human plasma nucleic acids
SRA, PRJNA297566.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA297566

Article and author information

Author details

Jun Yao

Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States

Competing interests
Jun Yao, is an inventors on a patent application filed by the University of Texas at Austin for the use of full-length excised intron RNAs and intron RNA fragments as biomarkers. US patent application 63/014,429.

"This ORCID iD identifies the author of this article:" 0000-0002-1232-1587
Douglas C Wu

Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, United States

Competing interests
Douglas C Wu, is an inventor on a patent application filed by the University of Texas at Austin for the use of full-length excised intron RNAs and intron RNA fragments as biomarkers. US patent application 63/014,429; is currently an employee of QIAGEN..
Ryan M Nottingham

Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-6937-5394
Alan M Lambowitz

Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States

For correspondence
lambowitz@austin.utexas.edu

Competing interests
Alan M Lambowitz, Thermostable group II intron reverse transcriptase (TGIRT) enzymes and methods for their use are the subject of patents and patent applications that have been licensed by the University of Texas and East Tennessee State University to InGex, LLC.Is a minority equity holder in InGex, LLC and receive royalty payments from the sale of TGIRT-enzymes and kits and from the sublicensing of intellectual property by InGex to other companies.Is an inventor on a patent application filed by the University of Texas at Austin for the use of full-length excised intron RNAs and intron RNA fragments as biomarkers. US patent application 63/014,429.

"This ORCID iD identifies the author of this article:" 0000-0001-6036-2423

Funding

National Institute of General Medical Sciences (R01 GM37949)

Alan M Lambowitz

National Institute of General Medical Sciences (R35 GM136216)

Alan M Lambowitz

Welch Foundation (F-1607)

Alan M Lambowitz

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.