Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America.
PLoS Genet. 2009 Dec;5(12):e1000778. doi: 10.1371/journal.pgen.1000778. Epub 2009 Dec 18.
To elucidate how genomic sequences build transcriptional control networks, we need to understand the connection between DNA sequence and transcription factor binding and function. Binding predictions based solely on consensus predictions are limited, because a single factor can use degenerate sequence motifs and because related transcription factors often prefer identical sequences. The ETS family transcription factor, ETS1, exemplifies these challenges. Unexpected, redundant occupancy of ETS1 and other ETS proteins is observed at promoters of housekeeping genes in T cells due to common sequence preferences and the presence of strong consensus motifs. However, ETS1 exhibits a specific function in T cell activation; thus, unique transcriptional targets are predicted. To uncover the sequence motifs that mediate specific functions of ETS1, a genome-wide approach, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), identified both promoter and enhancer binding events in Jurkat T cells. A comparison with DNase I sensitivity both validated the dataset and also improved accuracy. Redundant occupancy of ETS1 with the ETS protein GABPA occurred primarily in promoters of housekeeping genes, whereas ETS1 specific occupancy occurred in the enhancers of T cell-specific genes. Two routes to ETS1 specificity were identified: an intrinsic preference of ETS1 for a variant of the ETS family consensus sequence and the presence of a composite sequence that can support cooperative binding with a RUNX transcription factor. Genome-wide occupancy of RUNX factors corroborated the importance of this partnership. Furthermore, genome-wide occupancy of co-activator CBP indicated tight co-localization with ETS1 at specific enhancers, but not redundant promoters. The distinct sequences associated with redundant versus specific ETS1 occupancy were predictive of promoter or enhancer location and the ontology of nearby genes. These findings demonstrate that diversity of DNA binding motifs may enable variable transcription factor function at different genomic sites.
为了阐明基因组序列如何构建转录调控网络，我们需要了解 DNA 序列与转录因子结合和功能之间的联系。仅基于共识预测的结合预测是有限的，因为单个因子可以使用简并序列基序，并且相关的转录因子通常更喜欢相同的序列。ETS 家族转录因子 ETS1 就是一个很好的例子。由于共同的序列偏好和强共有序列基序的存在，在 T 细胞的管家基因启动子中观察到 ETS1 和其他 ETS 蛋白的意外、冗余占据。然而，ETS1 在 T 细胞激活中表现出特定的功能；因此，预测了独特的转录靶标。为了揭示介导 ETS1 特定功能的序列基序，我们采用了一种全基因组方法，即染色质免疫沉淀结合高通量测序（ChIP-seq），在 Jurkat T 细胞中鉴定了启动子和增强子结合事件。与 DNase I 敏感性的比较不仅验证了数据集，而且还提高了准确性。ETS1 与 ETS 蛋白 GABPA 的冗余占据主要发生在管家基因的启动子中，而 ETS1 特异性占据则发生在 T 细胞特异性基因的增强子中。确定了两种 ETS1 特异性的途径：ETS1 对 ETS 家族共有序列变体的固有偏好，以及可以支持与 RUNX 转录因子协同结合的复合序列的存在。全基因组 RUNX 因子占据证实了这种伙伴关系的重要性。此外，辅激活因子 CBP 的全基因组占据表明其与 ETS1 在特定增强子上紧密共定位，但不在冗余启动子上。与冗余和特定 ETS1 占据相关的不同序列可预测启动子或增强子的位置以及附近基因的本体论。这些发现表明，DNA 结合基序的多样性可能使不同的转录因子在不同的基因组位点具有可变的功能。
