Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers.
Here we provide a mechanism for specific, efficient transcription of the TNF gene and, potentially, other genes residing within multigene loci. We identify and characterize highly conserved noncoding elements flanking the TNF gene, which undergo activation-dependent intrachromosomal interactions. These elements, hypersensitive site (HSS)-9 and HSS+3 (9 kb upstream and 3 kb downstream of the TNF gene, respectively), contain DNase I hypersensitive sites in naive, T helper 1, and T helper 2 primary T cells. Both HSS-9 and HSS+3 inducibly associate with acetylated histones, indicative of chromatin remodeling, bind the transcription factor nuclear factor of activated T cells (NFAT)p in vitro and in vivo, and function as enhancers of NFAT-dependent transactivation mediated by the TNF promoter. Using the chromosome conformation capture assay, we demonstrate that upon T cell activation intrachromosomal looping occurs in the TNF locus. HSS-9 and HSS+3 each associate with the TNF promoter and with each other, circularizing the TNF gene and bringing NFAT-containing nucleoprotein complexes into close proximity. TNF gene regulation thus reveals a mode of intrachromosomal interaction that combines a looped gene topology with interactions between enhancers and a gene promoter.
Tsytsykova
Alla V
AV
Immune Disease Institute, Harvard Medical School, 800 Huntington Avenue, Boston, MA 02115, USA.
Rajsbaum
Ricardo
R
Falvo
James V
JV
Ligeiro
Filipa
F
Neely
Simon R
SR
Goldfeld
Anne E
AE
D000107:Acetylation; D000818:Animals; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism; D002478:Cells, Cultured; D033481:Chromosomes, Mammalian / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D006657:Histones / Q000378:metabolism; D008233:Lymphotoxin-alpha / Q000235:genetics; D051379:Mice; D008957:Models, Genetic; D050778:NFATC Transcription Factors / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D051996:Transcription Factor RelA / Q000378:metabolism; D014158:Transcription, Genetic; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*
D006657:Histones; D008233:Lymphotoxin-alpha; D050778:NFATC Transcription Factors; D051996:Transcription Factor RelA; D014409:Tumor Necrosis Factor-alpha; D003850:Deoxyribonuclease I