Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.
Nature. 2010 Apr 22;464(7292):1187-91. doi: 10.1038/nature08934. Epub 2010 Mar 17.
Variation in transcriptional regulation is thought to be a major cause of phenotypic diversity. Although widespread differences in gene expression among individuals of a species have been observed, studies to examine the variability of transcription factor binding on a global scale have not been performed, and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. By mapping differences in transcription factor binding among individuals, here we present the genetic basis of such variation on a genome-wide scale. Whole-genome Ste12-binding profiles were determined using chromatin immunoprecipitation coupled with DNA sequencing in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains and their parental lines. We identified extensive Ste12-binding variation among individuals, and mapped underlying cis- and trans-acting loci responsible for such variation. We showed that most transcription factor binding variation is cis-linked, and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several proposed Ste12 cofactors. We also identified two trans-factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than ten genes under alpha-factor treatment. Neither of these two genes was previously known to regulate Ste12, and we suggest that they may be mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable-bound genes are involved in cell wall organization and biogenesis. Overall, these studies identified genetic regulators of molecular diversity among individuals and provide new insights into mechanisms of gene regulation.
转录调控的变异性被认为是表型多样性的主要原因。尽管已经观察到同一物种个体之间的基因表达存在广泛差异，但尚未进行研究以检查转录因子结合的可变性在全球范围内，因此转录因子结合多样性的程度和潜在遗传基础尚不清楚。通过比较个体之间转录因子结合的差异，我们在此在全基因组范围内展示了这种变异的遗传基础。使用染色质免疫沉淀结合 DNA 测序，在来自两个高度分化酵母菌株及其亲本的交配的 43 个分离子的受激素处理的细胞中，确定了 Ste12 结合的全基因组图谱。我们发现个体之间存在广泛的 Ste12 结合变异性，并绘制了导致这种变异性的顺式和反式作用基因座图。我们表明，大多数转录因子结合变异性是顺式的，并且许多变异性与位于 Ste12 结合基序中的多态性以及几个提议的 Ste12 共因子的多态性有关。我们还鉴定了两个反式因子 AMN1 和 FLO8，它们在α因子处理下调节 Ste12 结合到十个以上基因的启动子。这两个基因以前都不调控 Ste12，我们认为它们可能是基因活性和表型多样性的介导者。Ste12 结合与 200 多个基因的基因表达高度相关，表明结合变异性是功能性的。许多可变结合的基因参与细胞壁组织和生物发生。总体而言，这些研究确定了个体之间分子多样性的遗传调节剂，并为基因调控机制提供了新的见解。
