Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.
Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125.
Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):E2930-E2939. doi: 10.1073/pnas.1712387115. Epub 2018 Mar 12.
RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1-dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.
RNA 测序（RNA-seq）常用于鉴定对干扰有反应的遗传模块。在单细胞中，转录组已被用作表型，但这一概念尚未应用于全生物体 RNA-seq。此外，使用表达谱量化和解释上位性效应仍然是一个挑战。我们开发了一个单一的系数来量化转录组范围的上位性，它反映了潜在的相互作用，可以直观地解释。为了演示我们的方法，我们对四个单突变体和两个双突变体进行了测序。从这些突变体中，我们重建了已知的缺氧途径。此外，我们还发现了一类 56 个基因，它们的表达依赖于 HIF-1，在两个基因的突变体中，它们的表达有相反的变化，这两个基因合作负调控 HIF-1 的丰度；然而，这两个基因的双突变体表现出抑制上位性。这一类违反了 HIF-1 调节的经典模型，但可以通过假设羟化 HIF-1 在转录控制中的作用来解释。
