1. Chromosomes and Gene Expression

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

  1. Jun Yao
  2. Douglas C Wu
  3. Ryan M Nottingham
  4. Alan M Lambowitz  Is a corresponding author
  1. University of Texas at Austin, United States
https://doi.org/10.7554/eLife.60743
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  1. Jun Yao
  2. Douglas C Wu
  3. Ryan M Nottingham
  4. Alan M Lambowitz
(2020)
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
eLife 9:e60743.
https://doi.org/10.7554/eLife.60743
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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
The following previously published data sets were used

Article and author information

Author details

  1. 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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1232-1587

  2. 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..

  3. Ryan M Nottingham

    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6937-5394

  4. 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.
    ORCID icon "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.

Reviewing Editor

  1. Timothy W Nilsen, Case Western Reserve University, United States

Version history

  1. Received: July 6, 2020
  2. Accepted: September 1, 2020
  3. Accepted Manuscript published: September 2, 2020 (version 1)
  4. Accepted Manuscript updated: September 3, 2020 (version 2)
  5. Version of Record published: September 25, 2020 (version 3)

Copyright

© 2020, Yao et al.

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.

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  1. Jun Yao
  2. Douglas C Wu
  3. Ryan M Nottingham
  4. Alan M Lambowitz
(2020)
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
eLife 9:e60743.
https://doi.org/10.7554/eLife.60743

Share this article

https://doi.org/10.7554/eLife.60743

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