Whole-genome cartography of estrogen receptor alpha binding sites.
Whole-genome cartography of estrogen receptor alpha binding sites.
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DOI：
10.1371/journal.pgen.0030087
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发表时间：
2007-06
期刊：
影响因子：
4.5
通讯作者：
Liu ET
中科院分区：
文献类型：
--
作者：
Lin CY;Vega VB;Thomsen JS;Zhang T;Kong SL;Xie M;Chiu KP;Lipovich L;Barnett DH;Stossi F;Yeo A;George J;Kuznetsov VA;Lee YK;Charn TH;Palanisamy N;Miller LD;Cheung E;Katzenellenbogen BS;Ruan Y;Bourque G;Wei CL;Liu ET
采用染色质免疫沉淀配对末端双标签克隆和测序策略，我们在MCF-7乳腺癌细胞中定位了雌激素受体α（ERα）结合位点。我们鉴定了1，234个高置信度结合簇，其中94%预计是真正的ERα结合区域。只有5%的雌激素受体结合位点位于相邻基因转录起始位点上游5 kb内，包含近端启动子的区域，而绝大多数位点位于内含子或远端位置（距离相邻转录本的5′和3′端>5 kb），表明转录调控机制跨越显著的物理距离。在所有已鉴定的位点中，71%的位点具有推定的完整雌激素反应元件（ERE），25%的位点具有ERE半位点，只有4%的位点没有可识别的ERE序列。在MCF-7细胞中，ERα结合位点附近的基因被雌二醇富集以进行调节，并且它们在患者样本中的表达谱将ERα阳性乳腺肿瘤与ERα阴性乳腺肿瘤分开。ERα结合位点附近基因的表达动力学表明，通过与ERE样序列结合直接诱导基因表达，而ERα的转录抑制似乎是通过间接机制。我们的分析还表明，许多候选转录因子结合位点邻近被占据的ER，其频率远高于偶然，包括先前报道的FOXA 1位点，并证明了一个这样的推定邻近因子Sp1在ERα靶基因的全局调节中的潜在参与。出乎意料的是，我们发现只有22%-24%的真正的人类ERα结合位点与全基因组脊椎动物比对中的保守区域重叠，这表明功能结合位点的保守性有限。总之，这种基因组规模的分析表明，复杂的，但可定义的规则，ERα结合和基因调控。雌激素受体（ER）在促进靶组织中激素功能的转录效应中起关键作用。为了获得ERα结合位点的全基因组视图，我们应用染色质免疫沉淀结合使用染色质免疫沉淀对末端标记技术的克隆和测序策略来定位MCF-7人乳腺癌细胞中的ERα结合位点。我们在人类基因组中鉴定了1，234个高质量的ERα结合位点，并证明这些结合位点通常与乳腺癌疾病状态和结果显著相关的基因相邻。定位结果还显示，ERα可以影响基因表达的距离高达100个酶或更多，被诱导或抑制的基因利用相对于转录本不同区域的位点（表明不同的作用机制），ERα结合位点在进化中仅适度保守。使用计算方法，我们确定了与ERα结合元件附近的其他转录因子结合位点的潜在相互作用。总之，这些发现表明了控制ERα结合和基因调控的复杂但可定义的规则，并为乳腺癌生物学中最重要的核激素受体之一的精确控制节点的映射提供了有价值的数据集。
Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor α (ERα) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERα binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5′ and 3′ ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERα binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERα-positive from ERα-negative breast tumors. The expression dynamics of the genes adjacent to ERα binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERα appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERα target genes. Unexpectedly, we found that only 22%–24% of the bona fide human ERα binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERα binding and gene regulation. Estrogen receptors (ERs) play key roles in facilitating the transcriptional effects of hormone functions in target tissues. To obtain a genome-wide view of ERα binding sites, we applied chromatin immunoprecipitation coupled with a cloning and sequencing strategy using chromatin immunoprecipitation pair end-tagging technology to map ERα binding sites in MCF-7 human breast cancer cells. We identified 1,234 high quality ERα binding sites in the human genome and demonstrated that the binding sites are frequently adjacent to genes significantly associated with breast cancer disease status and outcome. The mapping results also revealed that ERα can influence gene expression across distances of up to 100 kilobases or more, that genes that are induced or repressed utilize sites in different regions relative to the transcript (suggesting different mechanisms of action), and that ERα binding sites are only modestly conserved in evolution. Using computational approaches, we identified potential interactions with other transcription factor binding sites adjacent to the ERα binding elements. Taken together, these findings suggest complex but definable rules governing ERα binding and gene regulation and provide a valuable dataset for mapping the precise control nodes for one of the most important nuclear hormone receptors in breast cancer biology.
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影响因子：
12.3
作者：
Lin CY;Ström A;Vega VB;Kong SL;Yeo AL;Thomsen JS;Chan WC;Doray B;Bangarusamy DK;Ramasamy A;Vergara LA;Tang S;Chong A;Bajic VB;Miller LD;Gustafsson JA;Liu ET
通讯作者：
Liu ET
影响因子：
30.8
作者：
Carroll, Jason S.;Meyer, Clifford A.;Brown, Myles
通讯作者：
Brown, Myles
影响因子：
4.8
作者：
Dong, LA;Wang, WL;Safe, S
通讯作者：
Safe, S
影响因子：
3.5
作者：
Inoue, A;Yoshida, N;Hayashi, S
通讯作者：
Hayashi, S
影响因子：
64.5
作者：
Métivier, R;Penot, G;Gannon, F
通讯作者：
Gannon, F