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.
Kubosaki
Atsutaka
A
RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Lindgren
Gabriella
G
Tagami
Michihira
M
Simon
Christophe
C
Tomaru
Yasuhiro
Y
Miura
Hisashi
H
Suzuki
Takahiro
T
Arner
Erik
E
Forrest
Alistair R R
AR
Irvine
Katharine M
KM
Schroder
Kate
K
Hasegawa
Yuki
Y
Kanamori-Katayama
Mutsumi
M
Rehli
Michael
M
Hume
David A
DA
Kawai
Jun
J
Suzuki
Masanori
M
Suzuki
Harukazu
H
Hayashizaki
Yoshihide
Y
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D053263:Gene Regulatory Networks; D005821:Genetic Techniques; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics* / Q000378:metabolism*; D008954:Models, Biological; D022423:Myeloid Cells / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics; D015398:Signal Transduction; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D000099185:Interferon Regulatory Factor-8; D000099232:Proto-Oncogene Protein Spi-1
D050835:Interferon Regulatory Factors; D011518:Proto-Oncogene Proteins; D034741:RNA, Small Interfering; D015534:Trans-Activators; D000099185:Interferon Regulatory Factor-8; D000099232:Proto-Oncogene Protein Spi-1