Taylor Jennifer M, Wicks Kate, Vandiedonck Claire, Knight Julian C
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Nucleic Acids Res. 2008 Sep;36(15):4845-62. doi: 10.1093/nar/gkn444. Epub 2008 Jul 24.
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.
位于6号染色体p21区域的肿瘤坏死因子(TNF)基因座编码了一族在免疫反应中起关键作用的蛋白质,其失调会导致严重疾病。转录调控很重要,细胞类型和刺激特异性增强子复合物与TNF近端启动子有关。我们展示了如何通过对跨越TNF基因座的34 kb区域进行定量染色质分析,使我们能够识别出一些新的DNase超敏位点,并对更远距离的调控元件进行表征。我们证明了与淋巴毒素α(LTA)和肿瘤坏死因子(TNF)启动子区域相对应的DNase超敏位点、淋巴毒素β(LTB)第4外显子中的一个CpG岛、B细胞中κ轻链多肽基因增强子的核因子抑制剂样1(NFKBIL1)的3'端以及LTA上游3.4 kb处的位点。当使用Southern印迹法分析淋巴母细胞、Jurkat、U937、HeLa和HEK293T细胞系时,这些位点共定位于高度保守的DNA序列,并显示出细胞类型特异性的证据。对于Jurkat T细胞,我们定义了整个基因座上的组蛋白修饰。乙酰化组蛋白H3和H4的峰值,以及组蛋白H3的三甲基化K4,对应于超敏位点,特别是在LTB的第4外显子中。基于报告基因分析,我们提供了证据表明Jurkat细胞中LTA远端的一个基因间DNase I超敏位点具有功能作用,并证明了上游刺激因子(USF)转录因子的募集。