Laboratory of Developmental Systems Biology, Genetics and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Development. 2012 Mar;139(6):1164-74. doi: 10.1242/dev.077362. Epub 2012 Feb 1.
A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein-binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs that have mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To understand better the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou-binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity.
果蝇同源结构域(HD)转录因子(TFs)的一个亚家族控制着单个肌肉创始细胞(FCs)的身份。然而,这些 TF 产生独特的 FC 遗传程序的分子机制尚不清楚。为了解决这个问题,我们首先应用全基因组 mRNA 表达谱分析来鉴定受肌肉 HD TFs Slouch(Slou)和肌肉节同源盒(Msh)激活或抑制的基因。接下来,我们使用蛋白质结合微阵列来定义 Slou、Msh 和其他具有中胚层表达的 HD TFs 结合的序列。这些研究表明,一大类 HDs,包括 Slou 和 Msh,主要识别 TAAT 核心序列,但每个 HD 也结合到偏离这个典型基序的独特位点。为了更好地理解单个 FC 身份 HD 的调节特异性,我们评估了在由该 TF 激活或抑制的肌肉增强子中,Slou 相对于其他 HD 优先结合的非典型结合位点的功能。这些研究表明,Slou 通过 Slou 优先结合的序列调节特定成肌细胞增强子的活性,而将这些序列替换为能够结合多个 HD 家族成员的位点并不能支持 Slou 的正常调节功能。此外,在与额外的 Slou 反应性 FC 基因相关的假定增强子中,非典型的 Slou 结合位点过度表达。总之,这些研究为单个 HD TFs 在确定细胞身份中的作用提供了新的见解,并表明 HD 结合偏好的多样性可以赋予调节特异性。