Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic
Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic
复制标题
DOI：
10.1371/journal.pgen.1003243
复制
发表时间：
2013-02-01
期刊：
影响因子：
4.5
通讯作者：
Reinitz, John
中科院分区：
文献类型：
--
作者：
Kim, Ah-Ram;Martinez, Carlos;Reinitz, John
位于果蝇偶数跳过基因座转录起始点59的约2.5kb调控DNA的重排导致偶数跳跃条纹2、3和7的表达发生大规模变化。最根本的影响是将最小的条纹增强子MSE2和MSE3并列在具有和不具有长度小于360bp的小“间隔区”片段的条纹2和3上。我们将这些融合构建物置于靶向转化位点，并在细胞分辨率上获得了这些转化子及其控制转录因子的定量表达数据。这些数据表明，重排可以改变条2和2-3条间的表达水平，变化幅度超过10倍。我们推测，这种行为将对基因组顺调控逻辑的可能规则施加严格的限制。为了找到这些约束，我们用计算模型将我们新的表达数据与之前获得的其他结构的数据结合在一起。该模型包含了热力学蛋白质-DNA相互作用的表示，包括空间干扰和协同结合、短程抑制、直接抑制、激活和共激活。该模型受到训练数据的高度约束，它描述的训练数据在实验误差范围内。该模型受到如此严格的限制，能够正确地预测由其他果蝇基因的增强子驱动的表达模式；不包括在训练集中的偶数跳过的增强子；来自各种果蝇和败类物种的条带2、3和7增强子；以及包含多个增强子的偶数跳过的调控DNA的长片段。该模型进一步证明，MSE2和MSE3的融合推动的表达上调是MSE3的一部分被招募成为MSE2的功能成分的结果，表明顺式调节的“元件”不是基本对象。
Rearrangements of about 2.5 kilobases of regulatory DNA located 59 of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small "spacer'' segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2-3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein-DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory "elements'' are not elementary objects.