Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila.
Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila.
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DOI：
10.1186/gb-2007-8-8-r167
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
White R
中科院分区：
文献类型：
--
作者：
Adryan B;Woerfel G;Birch-Machin I;Gao S;Quick M;Meadows L;Russell S;White R
果蝇Su（Hw）结合的分析允许识别新的，孤立的，结合位点，并构建一个新的结合位点的共识。与基因表达数据一起，这支持了Su（Hw）在维持恒定的基因组结构中的作用。绝缘子元件被认为在基因组调控结构的组织中起着关键作用。在果蝇中，最好的研究之一是吉普赛反转录转座子绝缘子，它被毛翅抑制因子（Su [Hw]）转录调节因子结合。免疫定位研究表明，在基因组中有几百个Su（Hw）位点，但这些内源性Su（Hw）结合位点很少被确定。我们使用染色质免疫纯化与基因组微阵列分析，以确定在体内苏（Hw）结合位点的3兆Adh区域。我们找到60个位点，这些位点使得构建一个强大的新的Su（Hw）结合位点共识成为可能。相反，吉普赛绝缘体，其中包含紧密聚集的苏（Hw）结合位点，内源性网站通常发生孤立的网站。这些内源性位点具有三个关键特征。与大多数DNA结合蛋白特异性的分析相反，我们发现与结合一致性的强匹配是结合位点占有率的良好预测因子。在不同的组织和发育阶段的占用检查显示，大多数苏（Hw）网站，如果不是全部，组成性占领，这些孤立的苏（Hw）网站一般是高度保守的。su（Hw）突变体的转录水平分析表明基因表达的广泛和普遍的变化。重要的是，绝大多数表达改变的基因与Su（Hw）结合位点的聚类无关，强调了孤立位点的功能相关性。总之，我们的体内结合和基因表达数据支持Su（Hw）蛋白在维持恒定的基因组结构中的作用。
An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this supports a role for Su(Hw) in maintaining a constant genomic architecture. Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified. We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites. Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture.