Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome.
Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome.
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DOI：
10.1093/nar/gkp1195
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发表时间：
2010-04
影响因子：
14.9
通讯作者：
Landsman D
中科院分区：
文献类型：
--
作者：
Hansen L;Mariño-Ramírez L;Landsman D
基因表达的启动和调控在很大程度上依赖于转录调控因子的结合，而转录调控因子的结合往往是时间和位置特异的。许多转录调控因子识别并结合特定的DNA基序。这些基序的长度和简并性导致它们经常出现在基因组中，只有一小部分作为实际的结合位点。通过占据潜在的结合位点，核小体放置可以指定哪个序列基序可用于DNA结合调节因子。因此，核小体放置的规范以允许随时随地访问转录调控因子是至关重要的。我们发现酿酒酵母中的许多DNA结合基序显示出强烈的位置偏好，只出现在潜在的调节区。此外，利用基因本体丰富工具，我们证明了具有最强位置偏好的结合基序的蛋白质也有具有染色质修饰属性和功能的趋势。这表明，一些DNA结合蛋白可能依赖于它们的结合基序在整个基因组中的分布来帮助确定特异性。由于许多这些DNA结合蛋白具有染色质重塑特性，它们可以将局部核小体结构改变为更允许和/或更受限的状态，从而帮助确定DNA结合蛋白的特异性。
Initiation and regulation of gene expression is critically dependent on the binding of transcriptional regulators, which is often temporal and position specific. Many transcriptional regulators recognize and bind specific DNA motifs. The length and degeneracy of these motifs results in their frequent occurrence within the genome, with only a small subset serving as actual binding sites. By occupying potential binding sites, nucleosome placement can specify which sequence motif is available for DNA-binding regulatory factors. Therefore, the specification of nucleosome placement to allow access to transcriptional regulators whenever and wherever required is critical. We show that many DNA-binding motifs in Saccharomyces cerevisiae show a strong positional preference to occur only in potential regulatory regions. Furthermore, using gene ontology enrichment tools, we demonstrate that proteins with binding motifs that show the strongest positional preference also have a tendency to have chromatin-modifying properties and functions. This suggests that some DNA-binding proteins may depend on the distribution of their binding motifs across the genome to assist in the determination of specificity. Since many of these DNA-binding proteins have chromatin remodeling properties, they can alter the local nucleosome structure to a more permissive and/or restrictive state, thereby assisting in determining DNA-binding protein specificity.