Chim SSC, Shing TKF, Hung ECW, Leung TY, Lau TK, Chiu RWK, et al. Detection and characterization of placental microRNAs in maternal plasma. Clin Chem. 2008;54:482–90.
Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, et al. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 2008;105:10513–8.
Ratajczak J, Miekus K, Kucia M, Zhang J, Reca R, Dvorak P, et al. Embryonic stem cell-derived microvesicles reprogram hematopoietic progenitors: evidence for horizontal transfer of mRNA and protein delivery. Leukemia. 2006;20:847–56.
Ratajczak J, Wysoczynski M, Hayek F, Janowska-Wieczorek A, Ratajczak MZ. Membrane-derived microvesicles: important and underappreciated mediators of cell-to-cell communication. Leukemia. 2006;20:1487–95.
Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, Lötvall JO. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007;9:654–9.
Zernecke A, Bidzhekov K, Noels H, Shagdarsuren E, Gan L, Denecke B, et al. Delivery of microRNA-126 by apoptotic bodies induces CXCL12-dependent vascular protection. Sci Signal. 2009;2:ra81.
Pegtel DM, Cosmopoulos K, Thorley-Lawson DA, van Eijndhoven MAJ, Hopmans ES, Lindenberg JL, et al. Functional delivery of viral miRNAs via exosomes. Proc Natl Acad Sci U S A. 2010;107:6328–33.
Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science. 2010;328:872–5.
Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A. 2011;108:5003–8.
Turchinovich A, Weiz L, Langheinz A, Burwinkel B. Characterization of extracellular circulating microRNA. Nucleic Acids Res. 2011;39:7223–33.
Tomilov AA, Tomilova NB, Wroblewski T, Michelmore R, Yoder JI. Trans-specific gene silencing between host and parasitic plants. Plant J. 2008;56:389–97.
Kosaka N, Izumi H, Sekine K, Ochiya T. microRNA as a new immune-regulatory agent in breast milk. Silence. 2010;1:7.
Knip M, Constantin ME, Thordal-Christensen H. Trans-kingdom cross-talk: small RNAs on the move. PLoS Genet. 2014;10:e1004602.
Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, et al. Sources and functions of extracellular small RNAs in human circulation. Annu Rev Nutr. 2016;36:301–36.
Koeppen K, Hampton TH, Jarek M, Scharfe M, Gerber SA, Mielcarz DW, et al. A novel mechanism of host-pathogen interaction through sRNA in bacterial outer membrane vesicles. PLoS Pathog. 2016;12:e1005672.
LaMonte G, Philip N, Reardon J, Lacsina JR, Majoros W, Chapman L, et al. Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance. Cell Host Microbe. 2012;12:187–99.
Liu S, da Cunha AP, Rezende RM, Cialic R, Wei Z, Bry L, et al. The host shapes the gut microbiota via fecal microRNA. Cell Host Microbe. 2016;19:32–43.
Weiberg A, Wang M, Lin F-M, Zhao H, Zhang Z, Kaloshian I, et al. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science. 2013;342:118–23.
Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, et al. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat Commun. 2014;5:5488.
Wang K, Li H, Yuan Y, Etheridge A, Zhou Y, Huang D, et al. The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS One. 2012;7:e51009.
Zhang Y, Wiggins BE, Lawrence C, Petrick J, Ivashuta S, Heck G. Analysis of plant-derived miRNAs in animal small RNA datasets. BMC Genomics. 2012;13:381.
Tosar JP, Rovira C, Naya H, Cayota A. Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS. RNA. 2014;20:754–7.
Witwer KW. Contamination or artifacts may explain reports of plant miRNAs in humans. J Nutr Biochem. 2015;26:1685.
Kang W, Bang-Berthelsen CH, Holm A, Houben AJS, Müller AH, Thymann T, et al. Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts. RNA. 2017;23:433–45.
Witwer KW, Zhang C-Y. Diet-derived microRNAs: unicorn or silver bullet? Genes Nutr. 2017;12:15.
Ghosal A, Upadhyaya BB, Fritz JV, Heintz-Buschart A, Desai MS, Yusuf D, et al. The extracellular RNA complement of Escherichia coli. Microbiology Open. 2015;4:252–66.
Celluzzi A, Masotti A. How our other genome controls our epi-genome. Trends Microbiol. 2016;24:777–87.
Blenkiron C, Simonov D, Muthukaruppan A, Tsai P, Dauros P, Green S, et al. Uropathogenic Escherichia coli releases extracellular vesicles that are associated with RNA. PLoS One. 2016;11:e0160440–16.
Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, et al. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2012;22:107–26.
Zhou Z, Li X, Liu J, Dong L, Chen Q, Liu J, et al. Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses. Cell Res. 2015;25:39–49.
Liang G, Zhu Y, Sun B, Shao Y, Jing A, Wang J, et al. Assessing the survival of exogenous plant microRNA in mice. Food Sci Nutr. 2014;2:380–8.
Baier SR, Nguyen C, Xie F, Wood JR, Zempleni J. microRNAs are absorbed in biologically meaningful amounts from nutritionally relevant doses of cow milk and affect gene expression in peripheral blood mononuclear cells, HEK-293 kidney cell cultures, and mouse livers. J Nutri. 2014;144:1495–500.
Snow JW, Hale AE, Isaacs SK, Baggish AL, Chan SY. Ineffective delivery of diet-derived microRNAs to recipient animal organisms. RNA Biol. 2014;10:1107–16.
Dickinson B, Zhang Y, Petrick JS, Heck G, Ivashuta S, Marshall WS. Lack of detectable oral bioavailability of plant microRNAs after feeding in mice. Nat Biotechnol. 2013;31:965–7.
Witwer KW, Hirschi KD. Transfer and functional consequences of dietary microRNAs in vertebrates: concepts in search of corroboration. BioEssays. 2014;36:394–406.
Title AC, Denzler R, Stoffel M. Uptake and function studies of maternal milk-derived microRNAs. J Biol Chem. 2015;290:23680–91.
Auerbach A, Vyas G, Li A, Halushka M, Witwer K. Uptake of dietary milk miRNAs by adult humans: a validation study. F1000Res. 2016;5:721.
Lusk RW. Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. PLoS One. 2014;9:e110808.
Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, et al. Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system. Neurol Neuroimmunol Neuroinflamm. 2016;3:e251.
Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, et al. The perils of pathogen discovery: origin of a novel Parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J Virol. 2013;87:11966–77.
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
Huang X, Yuan T, Tschannen M, Sun Z, Jacob H, Du M, et al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics. 2013;14:319.
Spornraft M, Kirchner B, Haase B, Benes V, Pfaffl MW, Riedmaier I. Optimization of extraction of circulating RNAs from plasma – enabling small RNA sequencing. PLoS One. 2014;9:e107259.
Beatty M, Guduric-Fuchs J, Brown E, Bridgett S, Chakravarthy U, Hogg RE, et al. Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma. BMC Genomics. 2014;15:933.
Santa-Maria I, Alaniz ME, Renwick N, Cela C, Fulga TA, Van Vactor D, et al. Dysregulation of microRNA-219 promotes neurodegeneration through post-transcriptional regulation of tau. J Clin Invest. 2015;125:681–6.
Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol. 2010;17:1030–4.
Chen C, Ai H, Ren J, Li W, Li P, Qiao R, et al. A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing. BMC Genomics. 2011;12:448.
Liu J-L, Liang X-H, Su R-W, Lei W, Jia B, Feng X-H, et al. Combined analysis of microRNome and 3′-UTRome reveals a species-specific regulation of progesterone receptor expression in the endometrium of Rhesus monkey. J Biol Chem. 2012;287:13899–910.
Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, Landthaler M, et al. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell. 2011;43:340–52.
Kuchen S, Resch W, Yamane A, Kuo N, Li Z, Chakraborty T, et al. Regulation of microRNA expression and abundance during lymphopoiesis. Immunity. 2010;32:828–39.
Wei Y, Chen S, Yang P, Ma Z, Kang L. Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol. 2009;10:R6.
Mayr C, Bartel DP. Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell. 2009;138:673–84.
Su R-W, Lei W, Liu J-L, Zhang Z-R, Jia B, Feng X-H, et al. The integrative analysis of microRNA and mRNA expression in mouse uterus under delayed implantation and activation. PLoS One. 2010;5:e15513–8.
Chen X, Yu X, Cai Y, Zheng H, Yu D, Liu G, et al. Next-generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera. Insect Mol Biol. 2010;19:799–805.
Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, et al. Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics. 2010;11:281.
Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, Kulshreshtha R, et al. Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics. 2010;11:288.
Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q. MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics. 2010;11:148.
Lian L, Qu L, Chen Y, Lamont SJ, Yang N. A systematic analysis of miRNA transcriptome in Marek’s disease virus-induced lymphoma reveals novel and differentially expressed miRNAs. PLoS One. 2012;7:e51003–13.
Nolte-'t Hoen ENM, Buermans HPJ, Waasdorp M, Stoorvogel W, MHM W, PAC t’ H. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 2012;40:9272–85.
Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, et al. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome. 2016;4:29.
Glassing A, Dowd SE, Galandiuk S, Davis B, Chiodini RJ. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog. 2016;8:24.
Li Y, Kowdley KV. Method for microRNA isolation from clinical serum samples. Anal Biochem. 2012;431:69–75.
Burgos KL, Javaherian A, Bomprezzi R, Ghaffari L, Rhodes S, Courtright A, et al. Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing. RNA. 2013;19:712–22.
Moret I, Sánchez-Izquierdo D, Iborra M, Tortosa L, Navarro-Puche A, Nos P, et al. Assessing an improved protocol for plasma microRNA extraction. PLoS One. 2013;8:e82753.
Meerson A, Ploug T. Assessment of six commercial plasma small RNA isolation kits using qRT-PCR and electrophoretic separation: higher recovery of microRNA following ultracentrifugation. Biol Methods Protoc. 2016;1(1):bpw003.
Yeri A, Courtright A, Reiman R, Carlson E, Beecroft T, Janss A, et al. Total extracellular small RNA profiles from plasma, saliva, and urine of healthy subjects. Sci Rep. 2017;7:44061.
FASTX toolkit. http://hannonlab.cshl.edu/fastx_toolkit.
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res. 2012;41:D36–42.
The NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH Human Microbiome Project. Genome Res. 2009;19:2317–23.
de Hoon MJL, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, et al. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res. 2010;20:257–64.
McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, et al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001;413:852–6.
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. Database indexing for production MegaBLAST searches. Bioinformatics. 2008;24:1757–64.
NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2016;44:D7–D19.
Varrette S, Bouvry P, Cartiaux H, Georgatos F. Management of an academic HPC cluster: The UL experience. Proc. of the 2014 Intl. Conf. on High Performance Computing & Simulation (HPCS 2014) Bologna: IEEE;2014 p.959–67.