How Ikaros and Aiolos homo- and heterodimers drive gene expression to ensure B cell development

Ikaros family transcription factors (TF) are major regulators of cell differentiation and function. They function as homo- and heterodimers, but the contribution of specific dimers to gene regulation is unknown. We investigated the function of Ikaros-Ikaros, Ikaros-Aiolos and Aiolos-Aiolos in B cell development, and show that the dimers are not equivalent. Ikaros homodimers are required in proB and large preB cells where they bind and regulate the expression of a surprisingly small number of genes related to cell adhesion and migration, predominantly as transcriptional repressors. In contrast, Ikaros-Aiolos heterodimers and Aiolos homodimers are required in small preB and immature IgM+ B cells to regulate 10-fold larger target gene repertoires involved in B cell receptor signaling and immune functions. Aiolos-containing dimers act mainly as repressors in small preB cells but activators in immature B cells, where Aiolos-Aiolos antagonizes Ikaros-Ikaros. Mechanistically, Aiolos binds more GGAA motifs with different flanking nucleotides than Ikaros, which depends on a single amino acid difference in zinc finger 3 of its DNA binding domain. These results illustrate how homo- and heterodimerization of homologous TF proteins can markedly impact binding specificity, target gene response and pathway modulation in cells of the same lineage.