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

Atsutaka Kubosaki, Gabriella Lindgren, Michihira Tagami, Christophe Simon, Yasuhiro Tomaru, Hisashi Miura, Takahiro Suzuki, Erik Arner, Alistair R R Forrest, Katharine Irvine, Kate Schroder, Yuki Hasegawa, Mutsumi Kanamori-Katayama, Michael Rehli, David A Hume, Jun Kawai, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki

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21 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)2295 - 2302
Number of pages8
JournalMolecular Immunology
Volume47
Issue number14
DOIs
Publication statusPublished - 2010
Externally publishedYes

Cite this

Kubosaki, A., Lindgren, G., Tagami, M., Simon, C., Tomaru, Y., Miura, H., Suzuki, T., Arner, E., Forrest, A. R. R., Irvine, K., Schroder, K., Hasegawa, Y., Kanamori-Katayama, M., Rehli, M., Hume, D. A., Kawai, J., Suzuki, M., Suzuki, H., & Hayashizaki, Y. (2010). The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Molecular Immunology, 47(14), 2295 - 2302. https://doi.org/10.1016/j.molimm.2010.05.289