Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements.
The TNF locus on chromosome 6p21 encodes a family of proteins with key roles in the immune response whose dysregulation leads to severe disease. Transcriptional regulation is important, with cell type and stimulus-specific enhancer complexes involving the proximal TNF promoter. We show how quantitative chromatin profiling across a 34 kb region spanning the TNF locus has allowed us to identify a number of novel DNase hypersensitive sites and characterize more distant regulatory elements. We demonstrate DNase hypersensitive sites corresponding to the lymphotoxin alpha (LTA) and tumour necrosis factor (TNF) promoter regions, a CpG island in exon 4 of lymphotoxin beta (LTB), the 3' end of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 (NFKBIL1) and 3.4 kb upstream of LTA. These sites co-localize to highly conserved DNA sequences and show evidence of cell type specificity when lymphoblastoid, Jurkat, U937, HeLa and HEK293T cell lines are analysed using Southern blotting. For Jurkat T cells, we define histone modifications across the locus. Peaks of acetylated histone H3 and H4, together with tri-methyl K4 of histone H3, correspond to hypersensitive sites, notably in exon 4 of LTB. We provide evidence of a functional role for an intergenic DNase I hypersensitive site distal to LTA in Jurkat cells based on reporter gene analysis, with evidence of recruitment of upstream stimulatory factors (USF) transcription factors.
Taylor
Jennifer M
JM
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Wicks
Kate
K
Vandiedonck
Claire
C
Knight
Julian C
JC
D001483:Base Sequence; D015139:Blotting, Southern; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry*; D017124:Conserved Sequence; D018983:DNA Footprinting; D003850:Deoxyribonuclease I; D004742:Enhancer Elements, Genetic; D006657:Histones / Q000378:metabolism; D006801:Humans; D019169:Jurkat Cells; D008233:Lymphotoxin-alpha / Q000235:genetics; D010802:Phylogeny; D050436:Regulatory Elements, Transcriptional; D048069:Tumor Necrosis Factors / Q000235:genetics*
D002843:Chromatin; D006657:Histones; D008233:Lymphotoxin-alpha; D048069:Tumor Necrosis Factors; D003850:Deoxyribonuclease I