Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
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DOI：
10.1073/pnas.1605085113
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发表时间：
2016-06-07
影响因子：
11.1
通讯作者：
Levine, Michael S.
中科院分区：
文献类型：
--
作者：
Farley, Emma K.;Olson, Katrina M.;Levine, Michael S.
转录增强子是短的DNA片段，它能根据多种内在和外在信号开启和关闭基因。尽管30多年前就发现了第一个增强子，但初级DNA序列与增强子活性之间的关系仍然不清楚。特别是，“语法”（结合位点的顺序、方向和间距）的重要性尚不明确。一项高通量筛选鉴定出了在玻璃海鞘胚胎中由ZicL和ETS转录因子组合激活的合成脊索增强子。对这些增强子的操作阐明了脊索特异性表达的序列和语法特征的“调控密码”。这个密码使得能够通过计算机发现真正的脊索增强子，包括那些含有低亲和力结合位点的增强子，这些位点会被标准的基序识别方法排除。新鉴定出的一个增强子位于已知的调控短尾化基因（Ci - Bra）的增强子上游，短尾化基因是脊索特化的关键决定因素。这个新鉴定的Ci - Bra“影子”增强子含有亲和力非常低但语法最佳的结合位点，因此在脊索中介导了令人惊讶的强表达。弱结合位点通过最佳语法得到补偿，而含有高亲和力结合位点的增强子则具有次优的语法。我们认为这种平衡掩盖了调控语法的重要性，因为非规范的结合基序通常被增强子检测方法所忽视。因此，具有低结合亲和力但语法最佳的增强子可能是调控基因组中一个被极大低估的特征。
Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of intrinsic and extrinsic signals. Despite the discovery of the first enhancer more than 30 y ago, the relationship between primary DNA sequence and enhancer activity remains obscure. In particular, the importance of "syntax" (the order, orientation, and spacing of binding sites) is unclear. A high-throughput screen identified synthetic notochord enhancers that are activated by the combination of ZicL and ETS transcription factors in Ciona embryos. Manipulation of these enhancers elucidated a "regulatory code" of sequence and syntax features for notochord-specific expression. This code enabled in silico discovery of bona fide notochord enhancers, including those containing low-affinity binding sites that would be excluded by standard motif identification methods. One of the newly identified enhancers maps upstream of the known enhancer that regulates Brachyury (Ci-Bra), a key determinant of notochord specification. This newly identified Ci-Bra shadow enhancer contains binding sites with very low affinity, but optimal syntax, and therefore mediates surprisingly strong expression in the notochord. Weak binding sites are compensated by optimal syntax, whereas enhancers containing high-affinity binding affinities possess suboptimal syntax. We suggest this balance has obscured the importance of regulatory syntax, as noncanonical binding motifs are typically disregarded by enhancer detection methods. As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome.