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BMC Syst Biol. 2016 Aug 8;10(1):60. doi: 10.1186/s12918-016-0292-1.

Role of plant MicroRNA in cross-species regulatory networks of humans.

Author information

1
Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
2
Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Missouri, USA.
3
Institute of Computational Biomedicine, Weill Cornell Medical College, New York, USA. chz2009@med.cornell.edu.
4
Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China. xudong@missouri.edu.
5
Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Missouri, USA. xudong@missouri.edu.

Abstract

BACKGROUND:

It has been found that microRNAs (miRNAs) can function as a regulatory factor across species. For example, food-derived plant miRNAs may pass through the gastrointestinal (GI) tract, enter into the plasma and serum of mammals, and interact with endogenous RNAs to regulate their expression. Although this new type of regulatory mechanism is not well understood, it provides a fresh look at the relationship between food consumption and physiology. To investigate this new type of mechanism, we conducted a systematic computational study to analyze the potential functions of these dietary miRNAs in the human body.

RESULTS:

In this paper, we predicted human and plant target genes using RNAhybrid and set some criteria to further filter them. Then we built the cross-species regulatory network according to the filtered targets, extracted central nodes by PageRank algorithm and built core modules. We summarized the functions of these modules to three major categories: ion transport, metabolic process and stress response, and especially some target genes are highly related to ion transport, polysaccharides and the lipid metabolic process. Through functional analysis, we found that human and plants have similar functions such as ion transport and stress response, so our study also indicates the existence of a close link between exogenous plant miRNA targets and digestive/urinary organs.

CONCLUSIONS:

According to our analysis results, we suggest that the ingestion of these plant miRNAs may have a functional impact on consuming organisms in a cross-kingdom way, and the dietary habit may affect the physiological condition at a genetic level. Our findings may be useful for discovering cross-species regulatory mechanism in further study.

KEYWORDS:

Core module; Cross-species regulation; Functional analysis; miRNA

PMID:
27502923
PMCID:
PMC4977847
DOI:
10.1186/s12918-016-0292-1
[Indexed for MEDLINE]
Free PMC Article

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