Rodríguez-Martínez José A, Reinke Aaron W, Bhimsaria Devesh, Keating Amy E, Ansari Aseem Z
Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.
Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.
Elife. 2017 Feb 10;6:e19272. doi: 10.7554/eLife.19272.
How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers. These binding sites were biochemically validated by EMSA-FRET analysis and validated in vivo by ChIP-seq data from human cell lines. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome-wide binding of ATF3 is best explained by considering many dimers in which it participates. Importantly, our compendium of bZIP-DNA interactomes predicted bZIP binding to 156 disease associated SNPs, of which only 20 were previously annotated with known bZIP motifs.
转录因子二聚化如何影响DNA结合特异性，目前尚不清楚。根据蛋白质二聚化特性，我们研究了270个人类bZIP对的DNA结合特异性。80个异源二聚体和22个同源二聚体的DNA相互作用组显示，72%的异源二聚体基序对应于配对单体偏好的相连半位点。值得注意的是，其余的基序由间隔可变的半位点（12%）或“新出现”的位点（16%）组成，这些位点无法从配对单体的半位点偏好中轻易推断出来。这些结合位点通过EMSA-FRET分析进行了生化验证，并通过来自人类细胞系的ChIP-seq数据在体内得到验证。以ATF3为重点，我们观察到不同的bZIP伙伴赋予了不同的同源位点偏好，并证明通过考虑ATF3参与的许多二聚体，能最好地解释其在全基因组范围内的结合。重要的是，我们的bZIP-DNA相互作用组汇编预测bZIP与156个疾病相关单核苷酸多态性结合，其中只有20个先前被注释有已知的bZIP基序。
