Analysis of plant-derived miRNAs in animal small RNA datasets

Abstract

BackgroundPlants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA is considered to be unstable within the gastrointestinal tract of many animals, thus limiting potential for any adverse effects from consumption of dietary RNA. A recent paper reported that putative plant miRNAs were detected in animal plasma and serum, presumably acquired through ingestion, and may have a functional impact in the consuming organisms.ResultsTo address the question of how common this phenomenon could be, we searched for plant miRNAs sequences in public sRNA datasets from various tissues of mammals, chicken and insects. Our analyses revealed that plant miRNAs were present in the animal sRNA datasets, and significantly miR168 was extremely over-represented. Furthermore, all or nearly all (>96%) miR168 sequences were monocot derived for most datasets, including datasets for two insects reared on dicot plants in their respective experiments. To investigate if plant-derived miRNAs, including miR168, could accumulate and move systemically in insects, we conducted insect feeding studies for three insects including corn rootworm, which has been shown to be responsive to plant-produced long double-stranded RNAs.ConclusionsOur analyses suggest that the observed plant miRNAs in animal sRNA datasets can originate in the process of sequencing, and that accumulation of plant miRNAs via dietary exposure is not universal in animals.

Negligible uptake and transfer of diet-derived pollen microRNAs in adult honey bees

“…Here, we observed transfer to occur far below the theoretical optimum, which is in line with other studies examining insects. 21 Such a limiting factor may be overcome by a number of scenarios. Evidence in multiple systems, including the honey bee, suggests that selective transport and amplification of small RNA exists.…”

“…19,20 The first description of such a phenomenon, in the report by C-Y Zhang and colleagues, 18 showed that dietary plant miRNAs could enter the mammalian bloodstream and regulate cholesterol metabolism in the ingesting animal. This study stimulated much interest and further investigation [21][22][23][24] since its initial publication. Since then, however, multiple groups have been unable to reproduce these findings.…”

Potential relevance of microRNAs in inter-species epigenetic communication, and implications for disease pathogenesis

“…87 First, the biological relevance was argued, suggesting that the presence of the exogenous miR168a was just an artifact as a result of sequencing methods. 88 On the other hand, the available data are controversial on the efficiency of gastrointestinal absorption for xeno-miRNAs. While the animal-derived miRNAs might be absorbed in significant quantity and might have biological relevance, 63 the amount of absorbed plant-derived miRNAs did not reach meaningful quantity in some investigations.…”

Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture

“…36 In a different study, Zhang et al found no evidence of miRNAs in a number of invertebrates including pea aphid and silkworm and no uptake of miRNAs in feeding experiments with the corn rootworm. 29 By contrast, analysis of uptake of other sRNA types in corn rootworm fed on wild-type plants by another group revealed uptake of plant endogenous long dsRNAs, but not small sRNAs, 37 with no apparent effect on the transcriptome. This same group found uptake in another coleopteran species, the Colorado potato beetle, but no uptake was observed in 2 lepidopteran species.…”

“…25 These studies stimulated much interest, 26,27 and in conjunction with studies showing other sources of exogenous sRNA, 28 particular emphasis was placed on the paradigm-shifting possibility of cross-kingdom communication mediated through the diet. However, a number of subsequent studies provided considerable evidence that systemic uptake of orally ingested foreign miRNAs, as a class of molecules, is negligible in mammals [29][30][31][32] and significantly below levels required to be biologically relevant when acting through canonical sequence-specific RNAimediated mechanisms. With respect to dietary uptake of miRNA or other sRNA in vertebrates, controversy remains, with a number of groups providing data in support or in opposition (reviewed in 33,34 ).…”