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bioRxiv · 10.1101/246900

Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

Allen, R. M.·Zhao, S.·Ramirez-Solano, M. A.·Michell, D. L.·Wang, Y.·Shyr, Y.·Sethupathy, P.·Linton, M. F.·Graf, G. A.·Sheng, Q.·Vickers, K. C.
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Abstract

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 liver samples. A key advance for the TIGER pipeline is the ability to analyze 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. 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.

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Allen, R. M., Zhao, S., Ramirez-Solano, M. A., Michell, D. L., Wang, Y., Shyr, Y., Sethupathy, P., Linton, M. F., Graf, G. A., Sheng, Q., Vickers, K. C.. 2018-01-11. Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins. https://doi.org/10.1101/246900

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