Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500, USA.
J Mol Biol. 2011 Sep 30;412(4):634-46. doi: 10.1016/j.jmb.2011.07.032. Epub 2011 Jul 29.
Cooperativity in transcription factor (TF) binding is essential in eukaryotic gene regulation and arises through diverse mechanisms. Here, we focus on one mechanism, collaborative competition, which is of interest because it arises both automatically (with no requirement for TF coevolution) and spontaneously (with no requirement for ATP-dependent nucleosome remodeling factors). Previous experimental studies of collaborative competition analyzed cases in which target sites for pairs of cooperating TFs were contained within the same side of the nucleosome. Here, we utilize new assays to measure cooperativity in protein binding to pairs of nucleosomal DNA target sites. We focus on the cases that are of greatest in vivo relevance, in which one binding site is located close to the end of a nucleosome and the other binding site is located at diverse positions throughout the nucleosome. Our results reveal energetically significant positive (favorable) cooperativity for pairs of sites on the same side of the nucleosome but, for the cases examined, energetically insignificant cooperativity between sites on opposite sides of the nucleosome. These findings imply a special significance for TF binding sites that are spaced within one-half nucleosome length (74 bp) or less along the genome and may prove useful for prediction of cooperatively acting TFs genome wide.
协同作用在转录因子（TF）结合中对真核基因调控至关重要，其产生机制多种多样。在这里，我们重点关注一种机制，即协同竞争，它之所以引起人们的兴趣，是因为它既可以自动产生（不需要 TF 共同进化），也可以自发产生（不需要依赖 ATP 的核小体重塑因子）。以前对协同竞争的实验研究分析了两对协同 TF 的靶位点位于核小体同一侧的情况。在这里，我们利用新的测定法来测量蛋白质与核小体 DNA 靶位点对的结合的协同性。我们关注的是与体内相关性最大的情况，其中一个结合位点位于核小体末端附近，而另一个结合位点位于核小体内部的不同位置。我们的结果揭示了位于核小体同一侧的两个位点之间具有显著的能量正（有利）协同作用，但对于所检查的情况，位于核小体相对侧的两个位点之间的协同作用能量上并不显著。这些发现意味着对于在基因组上相隔半个核小体长度（74bp）或更短距离内的 TF 结合位点具有特殊意义，并且可能有助于预测全基因组中协同作用的 TF。
