Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

Ryan M. Allen, Shilin Zhao, Marisol A. Ramirez Solano, Wanying Zhu, Danielle L. Michell, Yuhuan Wang, Yu Shyr, Praveen Sethupathy, MacRae F. Linton, Gregory A. Graf, Quanhu Sheng, Kasey C. Vickers

Research output: Contribution to journalArticlepeer-review

46 Scopus citations


To comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), we developed a novel pipeline to overcome current limitations in analysis entitled, “Tools for Integrative Genome analysis of Extracellular sRNAs (TIGER)”. To demonstrate the power of this tool, sRNA-seq was performed on mouse lipoproteins, bile, urine and livers. A key advance for the TIGER pipeline is the ability to analyse both host and non-host sRNAs at genomic, parent RNA and individual fragment levels. TIGER was able to identify approximately 60% of sRNAs on lipoproteins and >85% of sRNAs in liver, bile and urine, a significant advance compared to existing software. Moreover, TIGER facilitated the comparison of lipoprotein sRNA signatures to disparate sample types at each level using hierarchical clustering, correlations, beta-dispersions, principal coordinate analysis and permutational multivariate analysis of variance. TIGER analysis was also used to quantify distinct features of exRNAs, including 5ʹ miRNA variants, 3ʹ miRNA non-templated additions and parent RNA positional coverage. Results suggest that the majority of sRNAs on lipoproteins are non-host sRNAs derived from bacterial sources in the microbiome and environment, specifically rRNA-derived sRNAs from Proteobacteria. Collectively, TIGER facilitated novel discoveries of lipoprotein and biofluid sRNAs and has tremendous applicability for the field of extracellular RNA.

Original languageEnglish
Article number1506198
JournalJournal of Extracellular Vesicles
Issue number1
StatePublished - Jan 1 2018

Bibliographical note

Funding Information:
This work was supported by the National Institutes of Health [HL128996 to K.C.V., HL113039 to K.C.V., HL127173 to K. C.V. and M.F.L., HL116263 to M.F.L., DK113625 to G.A.G., RR021954 to G.A.G., GM103527 to G.A.G., TR000117 to G. A.G., CA179514 to K.C.V.]; and the American Heart Association [CSA2066001 to K.C.V. and P.S., POST25710170 to R.M.A., POST26630003 to D.L.M.].

Publisher Copyright:
© 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group on behalf of The International Society for Extracellular Vesicles.


  • APOB
  • HDL
  • MicroRNA
  • bile
  • exogenous RNA
  • extracellular RNA
  • high-throughput sequencing
  • lipoprotein
  • small RNA
  • urine

ASJC Scopus subject areas

  • Histology
  • Cell Biology


Dive into the research topics of 'Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins'. Together they form a unique fingerprint.

Cite this