PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues

Abstract

Peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most extensively studied ligand-inducible transcription factors (TFs), able to modulate its transcriptional activity through conformational changes. It is of particular interest because of its pleiotropic functions: it plays a crucial role in the expression of key genes involved in adipogenesis, lipid and glucid metabolism, atherosclerosis, inflammation, and cancer. Its protein isoforms, the wide number of PPARγ target genes, ligands, and coregulators contribute to determine the complexity of its function. In addition, the presence of genetic variants is likely to affect expression levels of target genes although the impact of PPARG gene variations on the expression of target genes is not fully understood. The introduction of massively parallel sequencing platforms-in the Next Generation Sequencing (NGS) era-has revolutionized the way of investigating the genetic causes of inherited diseases. In this context, DNA-Seq for identifying-within both coding and regulatory regions of PPARG gene-novel nucleotide variations and haplotypes associated to human diseases, ChIP-Seq for defining a PPARγ binding map, and RNA-Seq for unraveling the wide and intricate gene pathways regulated by PPARG, represent incredible steps toward the understanding of PPARγ in health and disease.

Figure 1

Novel insight into PPARG world trough new approaches. In the presence of ligands (upper), PPARγ binds to its PPRE as heterodimer with RXR to activate or repress target genes' expression. The figure summarizes novel molecular mechanisms of PPARγ obtained through ChIP-seq. PPARγ- and RXR-binding sites detected by ChIP-seq reveal different spatial and temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis (right panel, study from [28]). P P A R γ in Adipocytes and Macrophages: tissue-specific regulatory regions employ cell-type-specific coregulators, C/EBPβ in adipocytes and PU.1 in macrophages (lower panel; ChIP-Seq study from [31]).

Figure 2

Innovative approaches by using next generation sequencing technologies. Next generation sequencing can be applied to many scientific contexts: targeted resequencing for the identification of disease-causing nucleotide variations for both coding and unexplored regulatory regions of genes (CNV-Seq and DNA-Seq); ChIP-Seq, for DNA-protein interaction studies coupling chromatin immuno-precipitation (ChIP) and massively parallel sequencing; RNA-Seq, for whole transcriptome studies, including expression levels of known and yet unknown transcripts (both coding and non-coding), differential splicing, allele-specific expression, RNA editing, and fusion transcripts (see review [121]).