A new pipeline denoted SPICE identifies novel JUN-IKZF1 composite elements

Abstract

Abstract DNA composite elements allow combinatorial transcription factor binding, which is important for fine tuning gene expression in response to physiological stimuli and in pathological conditions. Moreover, composite elements may contribute to epigenetic regulation. Accordingly, developing screening algorithms to identify novel composite elements and their compositions is crucial. Here we report a pipeline termed Spacing Preference Identification of Composite Elements (SPICE), that systematically predicts novel protein binding partners along with their DNA motifs and spacing preferences in a genome wide fashion. Besides predicting known composite elements like AP1-IRF composite elements (AICE) and STAT5 tetramers, SPICE de novo predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We validated JUN-IKZF1 association by co-immunoprecipitation and showed cooperative binding of these factors to an upstream conserved noncoding region, CNS9, in the human IL10 gene based on electrophoretic mobility shift assays. Furthermore, the activity of an IL10 luciferase reporter depended on both AP1 and IKZF1 binding sites within this composite element in mouse B and T cells, confirming its transcriptional relevance. These data establish SPICE as a valuable pipeline for predicting novel transcription factor complexes that regulate gene transcription and provide insights into the biological cooperation of IKZF1 and AP1. Division of Intramural Research, NHLBI.