Dr. Weeks’ Comment: You are what you eat – even at the genetic level. So eat the seeds – as long as they are organic and non-GMO!
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs
Kevin Chiang, Jiang Shu, Janos Zempleni, Juan Cui
Published: June 1, 2015http://dx.doi.org/10.1371/journal.pone.0128089
SOURCE http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128089
With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental pre-microRNAs, cross-species sequence comparison, disease relevance, and the experimentally validated gene targets. Furthermore, a few functional analyses including target prediction, pathway enrichment and gene network construction have been integrated into the system, which enable users to generate functional insights through viewing the functional pathways and building protein-protein interaction networks associated with each microRNA. Another unique feature of DMD is that it provides a feature generator where a total of 411 descriptive attributes can be calculated for any given microRNAs based on their sequences and structures. DMD would be particularly useful for research groups studying microRNA regulation from a nutrition point of view. The database can be accessed at http://sbbi.unl.edu/dmd/.
Introduction
Empowered by revolutionary sequencing technology, microRNAs have been extensively discovered in various dietary resources including plants (e.g. rice and tomato) and animals (e.g. milk and meats). Given the broad implications of microRNA in health and disease [1-8], research enthusiasm for functional impacts of exogenous food microRNA in human cellular phenotypes has soared, which warrants the efforts to build related bioinformatics tools and databases. The Dietary MicroRNA Database (DMD) represents the first repository in this domain for archiving and distributing the published food-borne microRNAs in literatures and public databases.
There are several public databases focused on microRNA identification and targets prediction that archive validated microRNAs with sequence, structure and interaction information. For example, miRBase (http://www.mirbase.org) records 64,473 microRNAs from 223 species [9] and MiRecords [10] hosts 2,705 records of interactions between 644 microRNAs and 1,901 target genes in 9 animal species. Databases such as TargetScan [11], Miranda [12] and MirTarBase [13] provide information of the validated gene targets as well as the computationally predicted targets. For example, 60% of human genes are regulated by microRNAs, participating in many major cellular processes such as cell growth, differentiation and apoptosis [14, 15]. In addition, microRNA expression data, although limited, are archived in public databases such as GEO databases [16] and TCGA [17]. However, none of the aforementioned databases cover dietary information that may represent new horizon in microRNA research. For example, miRBase has reported 808 microRNAs in bovine, whereas only 243 of them have been found in cow milk [18] and 213 in the fat of cow beef [19]. Likewise, human breast milk only contains 434 microRNAs, out of the total of 2,588 microRNAs in human [20].