Ikaros regulates chromatin landscape in mature B cells, and is critical for B cell tolerance

Abstract

Abstract The zinc finger transcription factor Ikaros plays central roles in the gene regulatory programs associated with proper B cell development. While mutations in the IKZF1 gene have been implicated in autoimmune disease and various B cell malignancies, the resultant epigenetic and transcriptional alterations in Ikzf1-mutated B cells remain largely unknown. We recently found in mouse models that deletion of the fourth zinc finger domain in the Ikzf1 gene (Ikzf1ΔF4/ΔF4) results in a B cell hyper-reactive (HR) phenotype. We hypothesized that Ikaros is required to establish and maintain an epigenetic program for co-stimulatory activation of B cells. To test this hypothesis, we have generated genome-wide transcriptome and chromatin-accessibility profiles of wildtype and Ikzf1ΔF4/ΔF4naïve splenic B cells following ex vivo co-stimulatory activation. We found that Ikaros mutant B cells have an overall similar accessible chromatin landscape as wildtype, but Ikzf1ΔF4/ΔF4B cells exhibit deregulated chromatin structure at inflammatory gene pathways linked to B cell growth and survival. To then explore the direct Ikaros targets we determined the Ikaros chromatin binding sites by Cleavage Under Targets & Release Using Nuclease (CUT&RUN) in wildtype B cells. Integration of gene expression and chromatin binding data indicates that Ikaros has a role in the repression of gene targets associated with cell proliferation and inflammation. Our data supports the model that Ikaros antagonizes NFkB actions at inflammatory gene pathways. Overall, our results reveal distinct mechanisms of Ikaros in the regulation of inflammatory genes in mature B cells and defines altered pathways that may be responsible for the HR phenotype of Ikaros-mutated B cells.