Figure 4. TNF selectively controls M2 gene transcription.

(A) Overview of the experimental design. RNA from wild-type BMDMs left untreated (Ctrl), stimulated with IL4/IL13, IL4/IL13 + TNF, or TNF was used for qRT-PCR. TNF was added at the same time like IL4/IL13 (left), 12 h after IL4/IL13 stimulation (middle) or 18 h afterwards (right). The last time point was always 24 h of IL4/IL13 stimulation. qRT-PCR for Retnla was analyzed. Data shown are the mean fold-increase of the Ctrl group. (B) Primary transcript qRT-PCR of the samples shown in (A). Superscripts show statistical significance between IL4/IL13 and IL4/IL13 + TNF. See also Fig S5. (C) Wild-type BMDMs were stimulated with IL4/IL13 or IL4/IL13 + TNF for 24 h or left untreated (Ctrl). Volcano plots of ATACseq data set showing IL4/IL13 versus Ctrl or IL4/IL13 + TNF versus IL4/IL13. Significantly changed sites are colored in blue and a selection of M2 genes are highlighted in orange. (D) Example of successfully identified accessible sites (ACS) in ATACseq data set. Significantly changed transcription sites of the ACS nearby Mgl₂ and Clec10a are highlighted in grey. n = 3 biological replicates.