Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America ; Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.
PLoS Genet. 2013;9(9):e1003753. doi: 10.1371/journal.pgen.1003753. Epub 2013 Sep 5.
The Yorkie/Yap transcriptional coactivator is a well-known regulator of cellular proliferation in both invertebrates and mammals. As a coactivator, Yorkie (Yki) lacks a DNA binding domain and must partner with sequence-specific DNA binding proteins in the nucleus to regulate gene expression; in Drosophila, the developmental regulators Scalloped (Sd) and Homothorax (Hth) are two such partners. To determine the range of target genes regulated by these three transcription factors, we performed genome-wide chromatin immunoprecipitation experiments for each factor in both the wing and eye-antenna imaginal discs. Strong, tissue-specific binding patterns are observed for Sd and Hth, while Yki binding is remarkably similar across both tissues. Binding events common to the eye and wing are also present for Sd and Hth; these are associated with genes regulating cell proliferation and "housekeeping" functions, and account for the majority of Yki binding. In contrast, tissue-specific binding events for Sd and Hth significantly overlap enhancers that are active in the given tissue, are enriched in Sd and Hth DNA binding sites, respectively, and are associated with genes that are consistent with each factor's previously established tissue-specific functions. Tissue-specific binding events are also significantly associated with Polycomb targeted chromatin domains. To provide mechanistic insights into tissue-specific regulation, we identify and characterize eye and wing enhancers of the Yki-targeted bantam microRNA gene and demonstrate that they are dependent on direct binding by Hth and Sd, respectively. Overall these results suggest that both Sd and Hth use distinct strategies - one shared between tissues and associated with Yki, the other tissue-specific, generally Yki-independent and associated with developmental patterning - to regulate distinct gene sets during development.
约克夏/Yap 转录共激活因子是一种在无脊椎动物和哺乳动物中都熟知的细胞增殖调控因子。作为一个共激活因子，约克夏（Yki）缺乏 DNA 结合结构域，必须与核内的序列特异性 DNA 结合蛋白相互作用，以调节基因表达；在果蝇中，发育调控因子 Scalloped（Sd）和 Homothorax（Hth）就是两个这样的伙伴。为了确定这三个转录因子调控的靶基因范围，我们对每个因子在翅膀和眼-触角成虫盘的全基因组染色质免疫沉淀实验进行了研究。Sd 和 Hth 表现出强烈的组织特异性结合模式，而 Yki 的结合在两种组织中非常相似。Sd 和 Hth 也存在与眼睛和翅膀共有的结合事件；这些事件与调节细胞增殖和“管家”功能的基因相关，占 Yki 结合的大部分。相比之下，Sd 和 Hth 的组织特异性结合事件与在特定组织中活跃的增强子显著重叠，分别富集在 Sd 和 Hth 的 DNA 结合位点上，并且与与每个因子先前建立的组织特异性功能一致的基因相关。组织特异性结合事件也与 Polycomb 靶向染色质域显著相关。为了深入了解组织特异性调控的机制，我们鉴定并表征了 Yki 靶向 bantam 微 RNA 基因的眼睛和翅膀增强子，并证明它们分别依赖于 Hth 和 Sd 的直接结合。总的来说，这些结果表明，Sd 和 Hth 都使用了不同的策略——一种在组织之间共享并与 Yki 相关，另一种组织特异性，通常与 Yki 无关，与发育模式相关——来在发育过程中调控不同的基因集。
