The Use of Transcriptomics to Unveil the Role of Nutrients in Mammalian Liver

Liver is the organ primarily responding to diet, and it is crucial in determining plasma carbohydrate, protein, and lipid levels. In addition, it is mainly responsible for transformation of xenobiotics. For these reasons, it has been a target of transcriptomic analyses. In this review, we have covered the works dealing with the response of mammalian liver to different nutritional stimuli such as fasting/feeding, caloric restriction, dietary carbohydrate, cholesterol, fat, protein, bile acid, salt, vitamin, and oligoelement contents. Quality of fats or proteins has been equally addressed, and has the influence of minor dietary components. Other compounds, not purely nutritional as those represented by alcohol and food additives, have been included due to their relevance in processed food. The influence has been studied not only on mRNA but also on miRNA. The wide scope of the technology clearly reflects that any simple intervention has profound changes in many metabolic parameters and that there is a synergy in response when more compounds are included in the intervention. Standardized arrays to systematically test the same genes in all studies and analyzing data to establish patterns of response are required, particularly for RNA sequencing. Moreover, RNA is a valuable, easy-screening ally but always requires further confirmation. 1. Introduction The postgenomic era poses a new challenge: to use genomic structural information, to display and analyze biological processes on a genome-wide scale, to assign gene function, and to know its response to different environmental stimuli. All functional genomic approaches such as genome-wide association studies, whole-genome and whole-exome sequencing, array-based comparative genomic hybridization, global DNA methylome mapping, and gene or noncoding RNA expression profiling [1] and other systems biology tools will be required to achieve such endeavor. Transcriptomic analyses cover the step of passing information from DNA to RNA. In contrast to DNA, there is not a single transcriptome but one for each cell. In addition, it may change in different circumstances. DNA microarrays are a miniaturized, ordered arrangement of nucleic acid fragments from individual genes located at defined positions on a solid support. They are powerful tools to detect changes in the expression of thousands of genes simultaneously by specific hybridization in multiple samples in parallel and identify the effect of different nutrients. Recently, whole genome sequencing technologies have emerged as new high-throughput methods to quantify