Figure 3: ICE chromatin structure and interaction with the Ifnb1 promoter during activation of macrophages.
From: TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation
(a) ChIP-qPCR analysis of c-jun or p65 binding at ICE in WT and Trim33−/− BMDM treated for the indicated times with LPS. Mean±s.e.m., n=2 to 4. (b) ChIP-qPCR analysis of RNA Pol II (upper left panel) and H3K4me3 (lower left panel) at ICE in WT and Trim33−/− BMDM treated for the indicated times with LPS. Mean±s.e.m., n=3 to 5. (Right panel) UCSC genome browser images showing H3K4me3 ChIP-seq profiles at ICE in WT and Trim33−/− BMDM treated for the indicated times with LPS. (c) ChIP-qPCR analysis of acetylated histone H3 (left panel) and CBP/p300 (right panel) at ICE in WT and Trim33−/− BMDM treated for the indicated times with LPS. Mean±s.e.m., n=4. **P<0.01, Mann–Whitney test. (d) DNA looping at the Ifnb1 locus was determined by 3C-seq performed before or 24 h after LPS activation of WT and Trim33−/− BMDM using either ICE (upper panel) or Ifnb1 gene (lower panel) as viewpoints (shown by an eye and a yellow band). Data represent normalized reads per million (r.p.m.) per restriction fragment. The x axis shows the genomic coordinates of the Ifnb1 locus. The positions of the EcoRI restriction sites and the TRIM33 ChIP-seq profile in BMDM are indicated on the top.
