A new pipeline SPICE identifies novel JUN-IKZF1 composite elements

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. SPICE de novo predicted known composite elements, including AP1-IRF composite elements (AICE) and STAT5 tetramers, and also predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We confirmed cooperative binding of JUN and IKZF1 to an upstream conserved noncoding region, CNS9, in the human IL10 gene, that contains a non-canonical IKZF1 site, and the activity of an IL10-luciferase reporter construct depended on both this site and the AP1 binding site within this composite element in primary B and T cells. Our findings reveal an unappreciated global association of IKZF1 and AP1, and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes. ChIP-Seq experiments with antibodies to IKZF1 and JUN in primary mouse B cells that were either untreated or treated with LPS or LPS + IL-21 for 3 hours.