Fazlollahi Mina, Lee Eunjee, Muroff Ivor, Lu Xiang-Jun, Gomez-Alcala Pilar, Causton Helen C, Bussemaker Harmen J
Department of Biological Sciences, Columbia University, New York, New York 10027 Department of Systems Biology, Columbia University, New York, New York 10032.
Department of Biological Sciences, Columbia University, New York, New York 10027.
G3 (Bethesda). 2014 Jun 17;4(8):1539-53. doi: 10.1534/g3.114.012039.
Understanding how genomic variation influences phenotypic variation through the molecular networks of the cell is one of the central challenges of biology. Transcriptional regulation has received much attention, but equally important is the posttranscriptional regulation of mRNA stability. Here we applied a systems genetics approach to dissect posttranscriptional regulatory networks in the budding yeast Saccharomyces cerevisiae. Quantitative sequence-to-affinity models were built from high-throughput in vivo RNA binding protein (RBP) binding data for 15 yeast RBPs. Integration of these models with genome-wide mRNA expression data allowed us to estimate protein-level RBP regulatory activity for individual segregants from a genetic cross between two yeast strains. Treating these activities as a quantitative trait, we mapped trans-acting loci (activity quantitative trait loci, or aQTLs) that act via posttranscriptional regulation of transcript stability. We predicted and experimentally confirmed that a coding polymorphism at the IRA2 locus modulates Puf4p activity. Our results also indicate that Puf3p activity is modulated by distinct loci, depending on whether it acts via the 5' or the 3' untranslated region of its target mRNAs. Together, our results validate a general strategy for dissecting the connectivity between posttranscriptional [corrected] regulators and their upstream signaling pathways.
理解基因组变异如何通过细胞分子网络影响表型变异是生物学的核心挑战之一。转录调控备受关注，但mRNA稳定性的转录后调控同样重要。在这里，我们应用系统遗传学方法剖析了芽殖酵母酿酒酵母中的转录后调控网络。基于15种酵母RNA结合蛋白（RBP）的高通量体内RNA结合蛋白结合数据构建了定量序列与亲和力模型。将这些模型与全基因组mRNA表达数据整合，使我们能够估计来自两个酵母菌株之间遗传杂交的单个分离株的蛋白质水平RBP调控活性。将这些活性视为数量性状，我们绘制了通过转录本稳定性的转录后调控起作用的反式作用位点（活性数量性状位点，或aQTL）。我们预测并通过实验证实IRA2位点的编码多态性调节Puf4p活性。我们的结果还表明，Puf3p活性受不同位点调节，这取决于它是通过其靶mRNA的5'还是3'非翻译区起作用。总之，我们的结果验证了一种剖析转录后[校正后]调节因子与其上游信号通路之间连接性的通用策略。
