IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ ouaked-2009-1 Regulation of the foxp3 gene by the Th1 cytokines: the role of IL-27-induced STAT1. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Ouaked N., Mantel P.Y., Bassin C., Burgler S., Siegmund K., Akdis C.A., Schmidt-Weber C.B. IBD - Inflammatory bowel disease Probes are named as in supplementary figure S5; however, numbering in these names does not correlate with the numbering given in supplementary figure S3. Human CD4+ T cells were stimulated with anti-CD3/28, IL-2 and TGF-beta with or without IL-27 for 30 minutes prior to preparation of nuclear extracts. The origin of the STAT1 expression construct (pCMV-STAT1) was confirmed to be human by the corresponding author via e-mail. csweber@tum.de J. Immunol. (0022-1767) 2009 Only protein-protein interactions imex curation ouaked-2009-2 Regulation of the foxp3 gene by the Th1 cytokines: the role of IL-27-induced STAT1. human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Ouaked N., Mantel P.Y., Bassin C., Burgler S., Siegmund K., Akdis C.A., Schmidt-Weber C.B. IBD - Inflammatory bowel disease The authors also show co-immunoprecipitation of untranslated region DNA of the FOXP3 gene with anti-STAT5 antibody; however, as this antibody can detect both STAT5A and STAT5B, the exact identity of the STAT5 participant could not be established, hence this interaction is not captured here. Human CD4+ T cells were stimulated with anti-CD3/28, IL-2, TGF-beta and IL-27 for 30 minutes prior to ChIP analysis. The origin of the STAT1 expression construct (pCMV-STAT1) was confirmed to be human by the corresponding author via e-mail. csweber@tum.de J. Immunol. (0022-1767) 2009 Only protein-protein interactions imex curation ouaked-2009-4 Regulation of the foxp3 gene by the Th1 cytokines: the role of IL-27-induced STAT1. in vitro In vitro elisa enzyme linked immunosorbent assay ELISA ELISA elisa tag perox activity tag visualisation by peroxidase activity tag perox activity Ouaked N., Mantel P.Y., Bassin C., Burgler S., Siegmund K., Akdis C.A., Schmidt-Weber C.B. IBD - Inflammatory bowel disease The origin of the STAT1 expression construct (pCMV-STAT1) was confirmed to be human by the corresponding author via e-mail. csweber@tum.de J. Immunol. (0022-1767) 2009 Only protein-protein interactions imex curation ouaked-2009-3 Regulation of the foxp3 gene by the Th1 cytokines: the role of IL-27-induced STAT1. human-t_reg Homo sapiens regulatory T-lymphocyte t_reg cell regulatory T-lymphocyte ch-ip chromatin immunoprecipitation assay ch-ip q-pcr quantitative pcr q-pcr Ouaked N., Mantel P.Y., Bassin C., Burgler S., Siegmund K., Akdis C.A., Schmidt-Weber C.B. IBD - Inflammatory bowel disease The labels for the bars in the figure are not consistent with the figure legend and the main text; opposite to the labels in the figure, the white bars show results for the isotype control (IC), while black bars show those for anti-acetyl H4. The origin of the STAT1 expression construct (pCMV-STAT1) was confirmed to be human by the corresponding author via e-mail. csweber@tum.de J. Immunol. (0022-1767) 2009 Only protein-protein interactions imex curation stat_consensus-site_dna-probe STAT consensus binding site oligonucleotide DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) CATGTTATGCATATTCCGAGAAGTG stat1_human Signal transducer and activator of transcription 1-alpha/beta STAT1 Transcription factor ISGF-3 components p91/p84 protein protein human Homo sapiens Human MSQWYELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAANDVSFATIRFHDLLSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSFVVERQPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKVKVLFDKDVNERNTVKGFRKFNILGTHTKVMNMEESTNGSLAAEFRHLQLKEQKNAGTRTNEGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVISNVSQLPSGWASILWYNMLVAEPRNLSFFLTPPCARWAQLSEVLSWQFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLIPWTRFCKENINDKNFPFWLWIESILELIKKHLLPLWNDGCIMGFISKERERALLKDQQPGTFLLRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIPENPLKYLYPNIDKDHAFGKYYSRPKEAPEPMELDGPKGTGYIKTELISVSEVHPSRLQTTDNLLPMSPEEFDEVSRIVGSVEFDSMMNTV foxp3_human_-21/+11_dna-probe Human FOXP3 gene promoter region -21 to +11 DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human TGATACGTGACAGTTTCCCACAAGCCAGGC foxp3_human_-111/-81_dna-probe Human FOXP3 gene promoter region -111 to -81 DNA probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human AAAAAATTTGGATTATTAGAAGAGAGAGGT stat3_human Signal transducer and activator of transcription 3 Acute-phase response factor STAT3 APRF protein protein human Homo sapiens Human MAQWNQLQQLDTRYLEQLHQLYSDSFPMELRQFLAPWIESQDWAYAASKESHATLVFHNLLGEIDQQYSRFLQESNVLYQHNLRRIKQFLQSRYLEKPMEIARIVARCLWEESRLLQTAATAAQQGGQANHPTAAVVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSAFVVERQPCMPMHPDRPLVIKTGVQFTTKVRLLVKFPELNYQLKIKVCIDKDSGDVAALRGSRKFNILGTNTKVMNMEESNNGSLSAEFKHLTLREQRCGNGGRANCDASLIVTEELHLITFETEVYHQGLKIDLETHSLPVVVISNICQMPNAWASILWYNMLTNNPKNVNFFTKPPIGTWDQVAEVLSWQFSSTTKRGLSIEQLTTLAEKLLGPGVNYSGCQITWAKFCKENMAGKGFSFWVWLDNIIDLVKKYILALWNEGYIMGFISKERERAILSTKPPGTFLLRFSESSKEGGVTFTWVEKDISGKTQIQSVEPYTKQQLNNMSFAEIIMGYKIMDATNILVSPLVYLYPDIPKEEAFGKYCRPESQEHPEADPGSAAPYLKTKFICVTPTTCSNTIDLPMSPRTLDSLMQFGNNGEGAEPSAGGQFESLTFDMELTSECATSPM 6C00632211C8012D foxp3_human_gene Forkhead box protein P3 (FOXP3) human gene gene gene human Homo sapiens Human irf1_human_gene Interferon regulatory factor 1 (IRF1) human gene gene gene human Homo sapiens Human h4_human Histone H4 H4-16 H4C1 H4C11 H4C12 H4C13 H4C14 H4C15 H4C2 H4C3 H4C4 H4C5 H4C6 H4C8 H4C9 H4/A H4/B H4/C H4/D H4/E H4/G H4/H H4/I H4/J H4/K H4/M H4/N H4/O H4F2 H4FA H4FB H4FC H4FD H4FE H4FG H4FH H4FI H4FJ H4FK H4FM H4FN H4FO HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4 HIST2H4A HIST2H4B HIST4H4 protein protein human Homo sapiens Human MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG stat-stat1-2 1775841 n/a 1775845 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false t15g_g20c mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1775846 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association false false false Fig. 3c interleukin-27 (IL-27) foxp3-stat1-3 1775841 n/a 1775847 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false t16g mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1775846 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association false false false Fig. 3c interleukin-27 (IL-27) foxp3-stat1-1 1775841 n/a 1775848 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false t14g_a20c mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1775846 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association false false false Fig. 3c interleukin-27 (IL-27) stat-stat3-1 1775841 n/a 1775849 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ n/a 1775845 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false t15g_g20c mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false Suppl. Fig. 4 This interaction was only measured using nuclear extracts from CD4+ T cells stimulated with anti-CD3/28, IL-2, TGF-beta and IL-27. foxp3-stat3-2 1775841 n/a 1775849 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ n/a 1775847 unspecified role unspecified role bait bait t16g mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false Suppl. Fig. 4 This interaction was only measured using nuclear extracts from CD4+ T cells stimulated with anti-CD3/28, IL-2, TGF-beta and IL-27. stat1-foxp3-1 1775842 n/a 1775846 unspecified role unspecified role bait bait n/a 1775850 unspecified role unspecified role prey prey promoter region -86/-3 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false promoter region -501/-416 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false promoter region -204/-114 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 4 P42224 increases expression at RNA level of ENSG00000049768 stat1-irf1-1 1775842 n/a 1775846 unspecified role unspecified role bait bait n/a 1775851 unspecified role unspecified role prey prey promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 4 stat3-foxp3-3 1775842 n/a 1775849 unspecified role unspecified role bait bait n/a 1775850 unspecified role unspecified role prey prey untranslated region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 4 stat-stat1-1 1775843 n/a 1775846 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ n/a 1775845 unspecified role unspecified role bait bait region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false t15g_g20c mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false Fig. 3b stimulation with anti-CD3, anti-CD28, IL-2, TGF-beta and IL-27 foxp3-stat1-2 1775843 n/a 1775850 unspecified role unspecified role bait bait promoter region -59/+177 sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro n/a 1775846 unspecified role unspecified role prey prey human-t cells cd 4+ Homo sapiens t-cell_cd4+ t cell cd4+ physical association physical association false false false Fig. 3b stimulation with anti-CD3, anti-CD28, IL-2, TGF-beta and IL-27 hist1h4a-foxp3-1 1775844 n/a 1775852 unspecified role unspecified role bait bait possible acetylated residue ac1res monoacetylated residue Acetyl Acetylation (N terminus, N epsilon of Lysine, O of Serine) (Ac) Acetylation Ac1Res undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1775850 unspecified role unspecified role prey prey promoter region -86/-3 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false promoter region -501/-416 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false promoter region -204/-114 binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 6 interleukin-27 (IL-27) In conditions without IL-27, acetylated Histone H4 was already detected at the -501/-416 FOXP3 promoter region, while no binding was detected at the other regions; addition of IL-27 induced binding to the -204/-114 and -86/-3 regions, and increased binding to the -501/-416 region.