Figure 1: Microarray analyses reveal a role of IRF8 in autophagy.

(a) The Venn diagrams depict the number of genes positively and negatively regulated by IRF8 in UT DCs and those treated with TLR ligands for 6 h identified by microarray analysis. Overlapped regions represent the number of genes positively or negatively regulated both in UT and TLR-stimulated DCs. See GO classification in Supplementary Fig. 1a,b. (b) IRF8-dependent autophagy genes identified by microarray analysis. Differentially expressed genes were identified by one-way analysis of variance (P≤0.05 and fold change ≥2). Colour gradients indicate average signal intensities of genes in log2 scale. Normalization was performed by GeneChip Operating Software (GCOS) and Expression Console software’s relative to the UT. (c) qRT–PCR analysis of IRF8-dependent autophagy genes in DCs. WT and Irf8^−/− DCs were stimulated with the TLR ligands for 6 h. The numbers represent transcript levels normalized by gapdh levels. Data represent the average of three independent assays. P≤0.01, Student’s t-test. (d) qRT–PCR analysis of IRF8-dependent autophagy genes in MΦs. WT and Irf8^−/− MΦs were treated overnight with IFNγ and stimulated with TLR ligands for the indicated times. The number in each box represents transcript levels normalized by the value of UT WT cells. Values are the average of three independent assays. P≤0.01 (Student’s t-test). See autophagy genes not affected by IRF8 in Supplementary Fig. 2. (e) Irf8^−/− MФs were transduced with pMSCV retroviral vector containing WT Irf8 or mutant Irf8 (K79E), and stimulated with IFNγ/TLR for 8 h. Relative expression of indicated autophagy genes was detected by qRT–PCR. The numbers represent transcript levels normalized by those of cells transduced with empty vector. Irf8 expression was normalized by gapdh. Values are the average of three experiments. P≤0.05 (Student’s t-test). Il12b and Hprt were tested as controls.