The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications
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DOI：
10.1073/pnas.0605343103
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发表时间：
2006-08-15
影响因子：
11.1
通讯作者：
Dekker, Job
中科院分区：
文献类型：
--
作者：
Gheldof, Nele;Tabuchi, Tornoko M.;Dekker, Job
我们已经分析了基因激活对染色质构象的影响，整个约170 kb的区域，包括人类脆性X基因座，其中包括一个单一的表达基因，FMR 1（脆性X智力低下1）。我们已经应用了三种方法：（t）染色体构象捕获，其评估染色质片段的相对相互作用频率;（h）这种方法的扩展，其识别构象不同于平均值的结构域，我们开发并命名为染色体构象分析;和（M）组蛋白修饰的ChIP分析。我们发现，在FMR 1有活性的正常细胞中，FMR 1启动子位于片段间相互作用减少的大（~ 50 kb）结构域的中心。相反，在FMR 1不活跃的脆性X细胞中，染色质构象在整个区域是均匀的。我们还发现，组蛋白修饰是活性基因的特征，在正常细胞中紧密定位在FMR 1启动子周围，而在脆性X细胞中不存在。因此，表达相关的构象变化影响一个显着更大的域比组蛋白修饰标记。全域的相互作用概率的变化可能反映了增加的染色质扩张，也可能与改变的空间配置，导致增加与无关基因座的混合。所描述的方法广泛适用于任何感兴趣基因座的构象变化的研究。
We have analyzed the effects of gene activation on chromatin conformation throughout an approximate to 170-kb region comprising the human fragile X locus, which includes a single expressed gene, FMR1 (fragile X mental retardation 1). We have applied three approaches: (t) chromosome conformation capture, which assesses relative interaction frequencies of chromatin segments; (h) an extension of this approach that identifies domains whose conformation differs from the average, which we developed and named chromosome conformation profiling; and (M) ChIP analysis of histone modifications. We find that, in normal cells where FMR1 is active, the FMR1 promoter is at the center of a large (-50 kb) domain of reduced intersegment interactions. In contrast, in fragile X cells where FMR1 is inactive, chromatin conformation is uniform across the entire region. We also find that histone modifications that are characteristic of active genes occur tightly localized around the FMR1 promoter in normal cells and are absent in fragile X cells. Therefore, the expression-correlated change in conformation affects a significantly larger domain than that marked by histone modifications. Domain-wide changes in interaction probability could reflect increased chromatin expansion and may also be related to an altered spatial disposition that results in increased intermingling with unrelated loci. The described approaches are widely applicable to the study of conformational changes of any locus of interest.