T cell-specific expression of the human TNF-alpha gene involves a functional and highly conserved chromatin signature in intron 3.
Using a phylogenetic approach, we identified highly conserved sequences within intron 3 of the human TNF-alpha gene. These sequences form cell type-specific DNase I hypersensitivity sites and display cell type-specific DNA-protein contacts in in vivo genomic footprints. Consistent with these results, intron 3 confers specific activity upon a TNF-alpha reporter gene in Jurkat T cells, but not THP-1 monocytic cells. Thus, using a combinatorial approach of phylogenetic analysis, DNase I hypersensitivity analysis, in vivo footprinting, and transfection analysis, we demonstrate that intronic regulatory elements are involved in the cell type-specific regulation of TNF-alpha gene expression.
D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics / Q000502:physiology*; D017124:Conserved Sequence / Q000235:genetics*; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000235:genetics; D003850:Deoxyribonuclease I / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000032:analysis / Q000096:biosynthesis / Q000235:genetics*; D019143:Evolution, Molecular; D015972:Gene Expression Regulation, Neoplastic / Q000276:immunology*; D017930:Genes, Reporter / Q000276:immunology; D000882:Haplorhini; D006367:HeLa Cells; D006801:Humans; D007438:Introns / Q000276:immunology; D019169:Jurkat Cells; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000276:immunology; D015183:Restriction Mapping; D013601:T-Lymphocytes / Q000276:immunology / Q000378:metabolism*; D024363:Transcription Initiation Site; D014409:Tumor Necrosis Factor-alpha / Q000032:analysis / Q000096:biosynthesis / Q000235:genetics* / Q000502:physiology
D002843:Chromatin; D004268:DNA-Binding Proteins; D018984:Epitopes, T-Lymphocyte; D014409:Tumor Necrosis Factor-alpha; D003850:Deoxyribonuclease I