The Molecular Choreography of IRF4 and IRF8 with Immune System Partners HARINDER SINGH, 1,2,4 ELKE GLASMACHER, 1,3 ABRAHAM B. CHANG, 1 AND BRYAN V ANDER LUGT 1 1 Department of Discovery Immunology, Genentech Inc., South San Francisco, California 94080 4 Correspondence: Harinder.Singh@cchmc.org The transcription factors IRF4 and IRF8 represent immune-specific members of the interferon regulatory family. They play major roles in controlling the development and functioning of innate and adaptive cells. Genes encoding these factors appear to have been coopted by the immune system via gene duplication and divergence of regulatory and protein coding sequences to enable the acquisition of unique molecular properties and functions. Unlike other members of the IRF family, IRF4 and IRF8 do not activate transcription of Type 1 interferon genes or positively regulate interferon-induced gene expression. Instead, they bind to unusual composite Ets-IRF or AP-1-IRF elements with specific Ets or AP-1 family transcription factors, respectively, and regulate the expression of diverse sets of immune response genes in innate as well as adaptive cells. The molecular cloning of interferon regulatory factor 8 (IRF8) as interferon consensus sequence-binding pro- tein (ICSBP) led to the realization that it bound inter- feron response sequence elements (ISRE), albeit with low affinity, and antagonized ISRE-mediated gene acti- vation (Driggers et al. 1990). A breakthrough came with the characterization of IRF4 (Pip/ICSAT/LSIRF), which revealed not only its structural relatedness to IRF8 but also its unusual property of cooperatively assembling with the Ets family factor PU.1 on Ets-IRF composite elements (EICEs) (Eisenbeis et al. 1995). IRF8 shared the same distinctive molecular property and this led to the concept that key functions of IRF4 and IRF8 in B lineage and myeloid cells could be executed via complexes with PU.1 assembled on EICE motifs. IRF4 and IRF8 function equivalently in controlling pre-B-cell differentiation (Lu et al. 2003). IRF4, on the other hand, uniquely regulates immunoglobulin gene class switch recombination (CSR) in activated B cells and their differentiation into plasma cells (Sciammas et al. 2006). Conversely, IRF8 has a dom- inant function in regulating the proliferation of myeloid progenitors and their differentiation into macrophages (Tamura et al. 2000). The observations that IRF4 regulates differentiation of T cells into effector states such as Th2 and Th17 raised a molecular conundrum because the aforementioned T help- er cells express very low levels of the interaction partner PU.1 or the related Ets factor Spi-B (Lohoff et al. 2002). These findings suggested the existence of a novel partner for IRF4 and IRF8. ChIP-seq analysis of IRF4-targeted sequences in T cells revealed that IRF4 binds to a novel set of AP-1-IRF composite elements (AICE) (Ciofani et al. 2012; Glasmacher et al. 2012; Li et al. 2012; Tussiwand et al. 2012). Strikingly, this involves cooperative assembly of IRF4 with AP-1 heterodimers containing a basic leucine zipper transcription factor, AFT-like (BATF) subunit. This molecular property is shared by IRF8 but not by other IRF family members, reminiscent of the molecular specif- icity of PU.1-IRF4 or PU.1-IRF8 complexes (Glasmacher et al. 2012). Thus, IRF4 and IRF8 proteins have evolved not only to interact with specific members of the Ets super- family, namely PU.1 and Spi-B, but also with particular members of the AP-1 superfamily, namely, BATF-con- taining heterodimers. Intriguingly, these select members of the Ets and AP-1 family also have their expression largely confined to cells of the immune system. Therefore, considerable protein evolution within the IRF, Ets, and AP-1 families has enabled the establishment of unique immune-specific partnerships. In this perspective, major biological functions of IRF4 and IRF8 within the immune system are discussed in light of these two types of immune- specific transcription factor complexes. ROLES OF IRF4 AND IRF8 IN B-CELL DEVELOPMENT AND ACTIVATION IRF4 was cloned using a cDNA expression library and a DNA probe that corresponded to an EICE present in an immunoglobulin (Ig) l light-chain gene enhancer (Eisen- beis et al. 1995). As anticipated by earlier biochemical analysis, the recombinant protein was shown to coopera- tively bind to EICE sequences present in Ig l as well as Ig k gene enhancers. Based on these biochemical properties, the protein was initially termed Pip for PU.1 interac- tion partner and later redesignated as IRF4 based on its 2 Current address:DivisionofImmunobiologyand the Center for SystemsImmunology, Cincinnati Children’sHospital MedicalCenter, Cincinnati, OH45229. 3 Current address: Helmholtz Zentrum Mu ¨nchen, 85764 Neuherberg, Germany Copyright # 2013 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/sqb.2013.78.020305 Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXVIII 101