Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Genome Res. 2012 Dec;22(12):2409-17. doi: 10.1101/gr.139378.112. Epub 2012 Jul 20.
Gene expression depends on the frequency of transcription events (burst frequency) and on the number of mRNA molecules made per event (burst size). Both processes are encoded in promoter sequence, yet their dependence on mutations is poorly understood. Theory suggests that burst size and frequency can be distinguished by monitoring the stochastic variation (noise) in gene expression: Increasing burst size will increase mean expression without changing noise, while increasing burst frequency will increase mean expression and decrease noise. To reveal principles by which promoter sequence regulates burst size and frequency, we randomly mutated 22 yeast promoters chosen to span a range of expression and noise levels, generating libraries of hundreds of sequence variants. In each library, mean expression (m) and noise (coefficient of variation, η) varied together, defining a scaling curve: η(2) = b/m + η(ext)(2). This relation is expected if sequence mutations modulate burst frequency primarily. The estimated burst size (b) differed between promoters, being higher in promoter containing a TATA box and lacking a nucleosome-free region. The rare variants that significantly decreased b were explained by mutations in TATA, or by an insertion of an out-of-frame translation start site. The decrease in burst size due to mutations in TATA was promoter-dependent, but independent of other mutations. These TATA box mutations also modulated the responsiveness of gene expression to changing conditions. Our results suggest that burst size is a promoter-specific property that is relatively robust to sequence mutations but is strongly dependent on the interaction between the TATA box and promoter nucleosomes.
基因表达取决于转录事件的频率（爆发频率）和每个事件产生的 mRNA 分子数量（爆发大小）。这两个过程都编码在启动子序列中，但它们对突变的依赖性还知之甚少。理论表明，可以通过监测基因表达的随机变化（噪声）来区分爆发大小和频率：增加爆发大小将在不改变噪声的情况下增加平均表达，而增加爆发频率将增加平均表达并降低噪声。为了揭示启动子序列调节爆发大小和频率的原则，我们随机突变了 22 个酵母启动子，这些启动子选择跨越表达和噪声水平的范围，生成了数百个序列变体的文库。在每个文库中，平均表达（m）和噪声（变异系数，η）一起变化，定义了一个缩放曲线：η(2) = b/m + η(ext)(2)。如果序列突变主要调节爆发频率，则可以预期这种关系。估计的爆发大小（b）因启动子而异，含有 TATA 盒且没有无核小体区的启动子较大。显著降低 b 的稀有变体可以用 TATA 突变或无义翻译起始位点的插入来解释。由于 TATA 突变导致的爆发大小的降低是启动子依赖性的，但与其他突变无关。这些 TATA 盒突变还调节了基因表达对变化条件的响应性。我们的结果表明，爆发大小是一个启动子特异性的特性，对序列突变相对稳健，但强烈依赖于 TATA 盒和启动子核小体之间的相互作用。
