GSE125978
The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [BiSulfite-seq]
Although much research has been done on the diversity of gut microbiome, little is known about the way it influences intestinal homeostasis under normal and pathogenic conditions. Epigenetic mechanisms have recently been suggested as operating at the interface between the microbiota and the intestinal epithelium cells (IECs). Using genome-wide analyses, we discovered that exposure to microbiota induced both global DNA hypomethylation and localized changes at regulatory elements, which culminates in activation of a set of “early sentinel” response genes that play a role in maintaining gut homeostasis. Furthermore, we demonstrated that exposure to microbiota in acute inflammation results in profound DNA methylation and chromatin accessibility changes at regulatory elements leading to alterations in the gene expression program in colitis and colon cancer. Our studies add a new dimension to our understanding of the cross talk between the microbiota and IECs, and provide the foundation for how microbiota impact epigenetic programming. Overall design: Whole genome methylation analysis of M. musculus. Four conditions were sequenced and analyzed, the first is an untreated control, the second corresponds to inflammation, the third mice with a germ-free condition and the fourth to a germ-free condition in combination with inflammation