Phylogenetic and Functional Analyses Identify Ets‐1 as an Important Regulator of the Th2 Cytokine Gene Locus

Abstract

The Th2 cytokine gene locus has emerged as a remarkable example of coordinated gene expression, the regulation of which appears to be rooted in an extensive array of cis‐regulatory regions. Using a computational approach that integrated multi‐species (n=11) sequence comparisons with algorithm‐based transcription factor (TF) binding site predictions, we sought to identify evolutionarily conserved non‐coding regions (ECRs), and motifs shared among them, which may underlie coregulation. Twenty‐two TF families were predicted to have binding sites in at least two Th2 ECRs. The ranking of these shared binding motifs according to their distribution and relative frequency pointed to a regulatory hierarchy among the TF families. Indeed, GATA sites were the most prevalent and widely distributed, consistent with the known role of GATA3 as a Th2 master switch. Sites for ETS‐domain proteins were also predicted within several Th2 ECRs, and the majority of these sites supported Ets‐1 binding in vitro. Analysis of Ets‐1 binding in vivo is ongoing. Interestingly, the expression of IL5, IL13 and IL4, but not IL10, was significantly decreased in Th2 cells generated from Ets‐1‐deficient mice. Collectively, our data suggest that Ets‐1 binding to motifs throughout the Th2 locus may contribute to the regulation of Th2 cytokine genes.