The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells

Gene regulatory networks in living cells are controlled by the interaction of multiple cell type-specific transcription regulators with DNA binding sites in target genes Interferon regulatory factor 8 (IRF8) also known as Interferon consensus sequence binding protein (ICSBP) is a transcription factor expressed predominantly in myeloid and lymphoid cell lineages To find the functional direct target genes of IRF8 the gene expression profiles of siRNA knockdown samples and genome-wide binding locations by ChIP-chip were analyzed in THP-1 myelomonocytic leukemia cells Consequently 84 genes were identified as functional direct targets The ETS family transcription factor PU 1 also known as SPI1 binds to IRF8 and regulates basal transcription in macrophages Using the same approach we identified 53 direct target genes of PU 1 these overlapped with 19 IRF8 targets These 19 genes included key molecules of IFN signaling such as OAS1 and IRF9 but excluded other IFN-related genes amongst the IRF8 functional direct target genes We suggest that IRF8 and PU 1 can have both combined and independent actions on different promoters in myeloid cells (C) 2010 Elsevier Ltd All rights reserved