Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation

Jiang Shu, Kevin Chiang, Janos Zempleni, Juan Cui, Ying Xu
2015 PLoS ONE  
MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in
more » ... . Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612 from 194 species, with 1,102 features derived from the micro-RNA sequence and structure. Through in-depth bioinformatics analysis, 8 groups of discriminative features have been used to characterize human circulating microRNAs and infer the likelihood that a microRNA will get transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly transportable candidates where 117 of them have identical sequences with their homologs in human and 73 are known to be associated with exosomes. Through a milk feeding experiment, we have validated 9 cowmilk microRNAs in human plasma using microRNA-sequencing analysis, including the top ranked microRNAs such as bta-miR-487b, miR-181b, and miR-421. The implications in health-related processes have been illustrated in the functional analysis. This work demonstrates the data-driven computational analysis is highly promising to study novel molecular characteristics of transportable microRNAs while bypassing the complex mechanistic details. 1. miRBase [3], which complies the species/kingdom information of 34,612 mature miRNAs included in this study 2. DMD [26], which contains dietary species information of 5,217 miNRAs 3. Weber et al. [25] provides a list of 360 human circulating miRNAs 4. ExoCarta and EVpedia [27, 28] provide 370 exosomal miRNAs in human and mouse. Stems/Pairs 12 %pairAU, %pairGC, %pairGU %A_unpaired, %C_unpaired, %G_unpaired max_stem_length, %G+C_stem, pairs, %pairs, %stems, Base-pairing-propensity Percentage of nucleotides 4 %A+U_P, %A+U_m, %G+C content_P, %G+C content_m, Length/Palindromes 4 Length_m, length_P, palindromes_P, palindromes_seed
doi:10.1371/journal.pone.0140587 pmid:26528912 pmcid:PMC4631372 fatcat:w7ovzvy4wreo7nz54k55isvk6q