DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity, and by systematically mutating 245 HOT loci with a massively parallel mutagenesis assay, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation.

中文翻译：

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剖析具有异常数量的转录因子关联的基因座的调节活性和序列内容。

DNA 相关蛋白 (DAP) 经典地通过与调节基因座（例如增强子或启动子）结合来调节基因表达。随着全基因组 DAP 结合图谱的扩展目录揭示了数千个与大多数传统增强子和启动子不同的位点，这些位点与数十种不同的 DAP 相关联，显然很少考虑基序偏好，了解 DAP 关联和在此类调控位点的协调对于破译这些区域如何促进正常发育和疾病至关重要。在这项研究中，我们汇总了来自在三个细胞系中检测的 469 个人类 DAP 的公开可用的 ChIP-seq 数据，并将这些数据与 352 个非冗余的正交数据集整合在一起，体外衍生的基序映射到 DNase I 超敏足迹内的基因组，以表征具有大量 DAP 关联的区域。我们为高占有率目标 (HOT) 基因座建立了一个通用定义，并确定了 HepG2 细胞中推定的驱动 DAP 基序，包括 HNF4A、SP1、SP5 和 ETV4，它们非常普遍并在 HOT 基因座显示序列保守性。与一个元件相关的不同 DAP 的数量与调节活动的证据呈正相关，通过大规模平行诱变试验系统地突变 245 个 HOT 基因座，我们将调节活动定位到一个中央核心区域，该区域取决于我们之前的基序序列指定的驱动程序 DAP。总共，