Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts.
Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts.
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DOI：
10.1074/jbc.m901790200
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发表时间：
2009-06-19
期刊：
影响因子：
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通讯作者：
Ratcliffe PJ
中科院分区：
文献类型：
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作者：
Mole DR;Blancher C;Copley RR;Pollard PJ;Gleadle JM;Ragoussis J;Ratcliffe PJ
缺氧诱导因子（HIF）控制着对缺氧的广泛适应性反应。为了更好地理解这种转录级联反应，我们使用针对两种主要HIF-α亚基的抗体进行了全基因组染色质免疫沉淀，并将结果与全基因组转录谱相关联。在平铺的启动子阵列中，我们分别鉴定了546和143个以高严格性与HIF-1α或HIF-2α结合的序列。对这些序列的分析证实了HIF-1α和HIF-2α（RCGTG）具有相同的核心结合基序，但表明与该基序的结合具有高度选择性，在转录起始点的上游和下游的不同区域富集结合。HIF-启动子结合数据与转录本表达中的双向HIF依赖性变化的比较表明，尽管相当大比例的阳性应答（在所有显著调节的基因中>20%）是直接的，但HIF依赖性基因抑制几乎完全是间接的。比较HIF-1α与HIF-2α结合位点发现，尽管一些位点单独结合HIF-1α，但许多位点以相似的亲和力结合两种亚型。尽管HIF-2α与多个启动子有高亲和力结合，但在这些位点对急性缺氧的转录反应很少（如果有的话）。鉴于HIF-1α与HIF-2α生物学功能不同的新证据，理解限制HIF-2α活性的机制将是有意义的。
Hypoxia-inducible factor (HIF) controls an extensive range of adaptive responses to hypoxia. To better understand this transcriptional cascade we performed genome-wide chromatin immunoprecipitation using antibodies to two major HIF-α subunits, and correlated the results with genome-wide transcript profiling. Within a tiled promoter array we identified 546 and 143 sequences that bound, respectively, to HIF-1α or HIF-2α at high stringency. Analysis of these sequences confirmed an identical core binding motif for HIF-1α and HIF-2α (RCGTG) but demonstrated that binding to this motif was highly selective, with binding enriched at distinct regions both upstream and downstream of the transcriptional start. Comparison of HIF-promoter binding data with bidirectional HIF-dependent changes in transcript expression indicated that whereas a substantial proportion of positive responses (>20% across all significantly regulated genes) are direct, HIF-dependent gene suppression is almost entirely indirect. Comparison of HIF-1α- versus HIF-2α-binding sites revealed that whereas some loci bound HIF-1α in isolation, many bound both isoforms with similar affinity. Despite high-affinity binding to multiple promoters, HIF-2α contributed to few, if any, of the transcriptional responses to acute hypoxia at these loci. Given emerging evidence for biologically distinct functions of HIF-1α versus HIF-2α understanding the mechanisms restricting HIF-2α activity will be of interest.