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Updated: Oct 18, 2025
mirMachine: A One-Stop Shop for Plant miRNA Annotation
Published on: May 1, 2021
Large-scale identification of extracellular plant miRNAs in mammals implicates their dietary intake
Xi Chen1,2, Lu Liu2,3, Qinjie Chu3
1Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
Abstract:
Extracellular microRNAs (miRNAs) have been proposed to function in cross-kingdom gene regulation. Among these, plant-derived miRNAs of dietary origin have been reported to survive the harsh conditions of the human digestive system, enter the circulatory system, and regulate gene expression and metabolic function. However, definitive evidence supporting the presence of plant-derived miRNAs of dietary origin in mammals has been difficult to obtain due to limited sample sizes. We have developed a bioinformatics pipeline (ePmiRNA_finder) that provides strident miRNA classification and applied it to analyze 421 small RNA sequencing data sets from 10 types of human body fluids and tissues and comparative samples from carnivores and herbivores. A total of 35 miRNAs were identified that map to plants typically found in the human diet and these miRNAs were found in at least one human blood sample and their abundance was significantly different when compared to samples from human microbiome or cow. The plant-derived miRNA profiles were body fluid/tissue-specific and highly abundant in the brain and the breast milk samples, indicating selective absorption and/or the ability to be transported across tissue/organ barriers. Our data provide conclusive evidence for the presence of plant-derived miRNAs as a consequence of dietary intake and their cross-kingdom regulatory function within human circulating system.
Insights
Plant-derived microRNAs (miRNAs) from diet enter human circulation, regulating gene expression. This study confirms their presence and cross-kingdom function in humans using bioinformatics analysis.
Area of Science:
- Molecular Biology
- Genetics
- Nutrition Science
Background:
- Extracellular microRNAs (miRNAs) are implicated in cross-kingdom gene regulation.
- Plant-derived miRNAs are hypothesized to survive digestion and impact mammalian gene expression.
Purpose of the Study:
- To provide conclusive evidence for the presence and cross-kingdom regulatory function of plant-derived miRNAs in the human circulatory system.
- To develop and apply a bioinformatics pipeline for identifying dietary plant miRNAs in human samples.
Main Methods:
- Development of the ePmiRNA_finder bioinformatics pipeline for miRNA classification.
- Analysis of 421 small RNA sequencing datasets from human body fluids/tissues and animal samples.
- Comparative analysis of plant-derived miRNA abundance in human blood versus microbiome and bovine samples.
Main Results:
- Identification of 35 plant-derived miRNAs in human blood samples, originating from common dietary plants.
- Significant differences in plant-derived miRNA abundance compared to human microbiome and cow samples.
- Body fluid/tissue-specific distribution of plant-derived miRNAs, with high abundance in brain and breast milk.
Conclusions:
- Conclusive evidence supports the presence of plant-derived miRNAs in the human circulatory system due to dietary intake.
- Plant-derived miRNAs exhibit cross-kingdom regulatory functions within the human system.
- Selective absorption and inter-organ transport mechanisms are suggested for these dietary miRNAs.
