Year: 2018
Type: article
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 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 5' miRNA variants, 3' 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.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,410
Awards: Circulating microRNAs Control Cholesterol Homeostasis through hepatic mechanisms, Center of Research in Obesity and Cardiovascular Disease (1P20 RR021954-01A1), G2898209822, G3097919878, Center of Research on Obesity and Cardiovascular Diseases, G4636502544, Secreted RNA during CRC progression biogenesis function and clinical markers, G6013349954, HDL-microRNA Intercellular Communication in Atherosclerosis, Macrophage SR-BI Regulates Autophagy, Angiogenin and tRNA-derived small RNAs, G9000044366, G9000085001, G9000242039, G9000253430, G9000309481, G9000334498, Contributions of Hepatic and Intestinal Pathways to Cholesterol Excretion, Molecular and Cellular Basis for Digestive Diseases, HDL Function in Human Disease
OpenAlex ID: W2952595797