Identification of Transcriptional Targets of IRF8 in Germinal Center B Cells.

The development and function of cells of the innate and adaptive immune systems are governed by a series of hierarchical regulatory networks. The components of these networks are particularly well understood for the very early as well as the terminal stages of B cell differentiation; however, information regarding the set of regulatory factors governing B cell fate from the pro-B through the germinal center (GC) stage of differentiation is less well developed. A previous study identified IRF8 as an important component of the network as it contributes to the direct transcriptional activation of BCL6 and AID, key elements of the GC reaction. To identify additional targets of IRF8, we used the chromatin immunoprecipitation (ChIP)-on-Chip approach to study three human cell lines of GC origin - Ly1, Odh1 and Val - and the multiple myeloma cell line, MMS1. By coupling this study with ChIP-on-chip analysis for POLII using the same cell lines, we identified 248 transcriptionally active IRF8 targets. They comprised both known targets, such as B2M and ISGF3G, and a spectrum of novel targets that included important elements of innate immune responses such as RIG-1 and MDA-5. A functional classification of IRF8 targets by GO and a comparison of the GO term frequency with the global frequency in the human genome showed that IRF8 targets were significantly enriched in genes regulating the immune response, effecting DNA repair, and governing transcription. These results significantly enhance our understanding of the roles played by IRF8 in the transcriptional regulation of GC B cells, and identify innate immune mechanisms that contribute to their adaptive immune functions.