Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements
Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements
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DOI：
10.1016/j.bbrc.2005.10.188
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发表时间：
2006-01-06
影响因子：
3.1
通讯作者：
Inoue, S
中科院分区：
文献类型：
--
作者：
Horie-Inoue, K;Takayama, K;Inoue, S
类固醇激素受体包括雄激素受体（AR）、糖皮质激素受体（GR）、孕激素受体（PR）和盐皮质激素受体（MR）识别并结合相同的共有激素反应元件（HRE），其由两个六聚体半位点（5 '-AGAACA-3'）组成，所述六聚体半位点以反向重复序列与3-bp间隔区排列。虽然在已知的类固醇靶基因的转录调控区中仅鉴定出少数接近共有的HRE序列，但确切的共有序列是否在体内作为真正的HRE起作用还不清楚。回文HRE的全基因组计算机筛选鉴定了人类基因组中的565个精确共有序列（NCBI 35组装）。在这项研究中，在565个精确的共有元件中，通过染色质免疫沉淀（ChIP）试验，使用内源性表达类固醇激素受体的细胞，对位于注释基因5'端上游10 kb内的26个序列进行了体内受体结合功能评价。通过定量RT-PCR检测近端基因表达的激素反应性。就进行AR、GR和PR的ChIP测定而言，26种元素中的14种通过激素处理显著募集至少一种受体（相对于载体>2倍富集）。在上述14个功能完善的HRE附近的基因表达方面，激素处理使4个基因上调>2倍。目前的数据表明，生物信息学分析和定量实验评价的结合是有用的，以确定新的功能HRE，可能有助于类固醇靶基因的转录调控。(c)2005年爱思唯尔公司All rights reserved.
Steroid hormone receptors including androgen receptor (AR), glucocorticoid receptor (GR), progesterone receptor (PR), and mineralocorticoid receptor (MR) recognize and bind to identical consensus hormone response elements (HREs), which consist of two hexameric half-sites (5'-AGAACA-3') arranged as inverted repeats with a 3-bp spacer. Although only a few near-consensus HRE sequences have been identified in the transcriptional regulatory regions of known steroid target genes, it has been Unclear whether the exact consensus sequences function as bona fide HREs in vivo. A genome-wide in silico screening of palindromic HREs identified 565 exact consensus sequences in human genome (NCBI 35 assembly). In this study, of 565 exact consensus elements, functional in vivo receptor binding was evaluated regarding 26 sequences located within 10 kb upstream to the 5' end of annotated genes through chromatin immunoprecipitation (ChIP) assay using cells endogenously expressing steroid hormone receptors. Hormone responsiveness of proximal gene expression was examined through quantitative RT-PCR. As far as performing ChIP assay for AR, GR, and PR, 14 of 26 elements significantly recruited at least one of the receptors by hormone treatment (>2-fold enrichment versus vehicle). In terms of gene expression in the vicinity of the above 14 functional perfect HREs, four genes were upregulated by >2-fold with hormone treatment. The present data suggest that the combination of bioinformatics analysis and quantitative experimental evaluation is useful to identify novel functional HREs that may contribute to the transcriptional regulation of steroid target genes. (c) 2005 Elsevier Inc. All rights reserved.