Li Peng, Pulugulla Sree H, Das Sonali, Oh Jangsuk, Spolski Rosanne, Lin Jian-Xin, Leonard Warren J
Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
bioRxiv. 2024 Dec 12:2023.05.31.543110. doi: 10.1101/2023.05.31.543110.
Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human gene, which harbors a non-canonical IKZF1 binding site. We confirmed cooperative binding of JUN and IKZF1 and showed that the activity of an -luciferase reporter construct in primary B and T cells depended on both this site and the AP1 binding site within this composite element. Overall, our findings reveal an unappreciated global association of IKZF1 and AP1 and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.
转录因子伙伴可以协同结合到DNA复合元件上以增强基因转录。在此，我们报告了一种新型的蛋白质-DNA结合筛选流程，称为复合元件间距偏好识别（SPICE），它可以系统地预测蛋白质结合伙伴和DNA基序间距偏好。使用SPICE，我们成功鉴定出已知的复合元件，如AP1-IRF复合元件（AICEs）和STAT5四聚体，还发现了几个新的结合伙伴，包括JUN-IKZF1复合元件。在人类基因的上游保守非编码区域CNS9中鉴定出了一种这样的新型相互作用，该区域含有一个非典型的IKZF1结合位点。我们证实了JUN和IKZF1的协同结合，并表明一个荧光素酶报告基因构建体在原代B细胞和T细胞中的活性取决于该位点以及该复合元件内的AP1结合位点。总体而言，我们的发现揭示了IKZF1和AP1之间未被重视的全局关联，并将SPICE确立为预测新型转录结合复合物的有价值的新流程。
