Stimulated cells were treated this website with 10 ng/ml of PMA and 1 μg/ml of Ionomycin (P/I). (A) RNA was isolated from cells using Tri-Reagent (Sigma, St. Louis, MO, USA), treated with RNase-free DNase I (Promega, Fitchburg, WI, USA) and converted to cDNA using ImProm-II™ Reverse Transcriptase (Promega) and random nonamer primers. Q-PCR is performed as described in Materials and Methods . (B) Polarized T cells were seeded into 96 well plates (105 cells in 200 μl per well) and incubated for 12 hours with or without stimulation. Supernatants

were analysed by mouse TNF ELISA Ready-SET-Go (eBioscience, San Diego, CA, USA) according to manufacturer’s instructions. (A,B) Data are shown as mean ± SD of two experiments. C, D. TNF expression in subsets of mouse CD4+ T cells. Q-RT-PCR (C) and FACS (D) analysis of CD4+ lymphocytes from FoxP3-IRES-GFP reporter mice . Stimulated cells were treated with 4 μg/ml of anti-CD3 and 1 μg/ml of anti-CD28 antibodies (αCD3/αCD28). (C) RNA was isolated from cells using Tri-Reagent (Sigma), treated with RNase-free DNase I (Promega) and converted to cDNA using ImProm-II™ Reverse Transcriptase (Promega) and random nonamer primers. QPCR is performed as described in Materials and Methods . Data are shown as mean ± SD of two experiments (D) Cells were cultured 4 hours in the presence

of 5 μg/ml of Brefeldin A and fixed for at least 30 min with 2% paraformaldehyde in PBS. Further washing and staining steps were performed in PBS/BSA/EDTA buffer supplemented with 0.5% Saponin. Cells were analyzed on a FACSCalibur, FACS-Canto or Fortessa (BD Biosciences, Franklin Lakes, NJ,

find more USA) flow cytometers using CellQuest (BD Biosciences) and FlowJo 7.6 (Tree Star, Inc., Ashland, OR, USA) software. Data shown are representative of two experiments. Figure S3. Profile of MNase resistance around TNF TSS (-124 +240) in Tregs (FoxP3+) and effector T cells (FoxP3-). Stimulated cells were treated 1 hour with 4 μg/ml of anti-CD3 and 1 μg/ml of anti-CD28 antibodies (αCD3/αCD28). Primary data normalized only to control MNase-digested genomic DNA are representative of two experiments. Figure S4. MNase-ChIP analysis of histone modifications (A) Polarized T cells. Th0s, Th2s and 4��8C Th17s cells are polarized in presence of soluble anti-CD3 antibodies, Th1i – in presence of immobilized anti-CD3 antibodies. Results of two individual experiments are shown. (B) CD4+ T cells from secondary lymphoid organs. Stimulated cells were treated 1 hour with 4 μg/ml of anti- CD3 and 1 μg/ml of anti-CD28 antibodies (αCD3/αCD28). Data are shown as mean ± SD of two experiments. Figure S5. A, B. Analysis of nuclear transcription factors and chromatin conformation at theTNF TSS in primary CD4+ T cells. (A) Western blot analysis of NFAT, NFkB and AP1-related transcription factors in the nuclear fractions of primary CD4+ T cells from secondary lymphoid organs.