Ko Bokang, Van Raamsdonk Jeremy M
Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada.
Metabolic Disorders and Complications Program (MeDiC), Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada.
Biology (Basel). 2023 Jun 2;12(6):812. doi: 10.3390/biology12060812.
Analysis of gene expression changes across the genome provides a powerful, unbiased tool for gaining insight into molecular mechanisms. We have effectively used RNA sequencing to identify differentially expressed genes in long-lived genetic mutants in to advance our understanding of the genetic pathways that control longevity. Although RNA sequencing costs have come down, cost remains a barrier to examining multiple strains and time points with a sufficient number of biological replicates. To circumvent this, we have examined the efficacy of identifying differentially expressed genes by sequencing a pooled RNA sample from long-lived mitochondrial mutant worms. We found that sequencing a pooled RNA sample could effectively identify genes that were found to be significantly upregulated in the two individually sequenced RNA-seq experiments. Finally, we compared the genes significantly upregulated in the two individually sequenced RNA-seq experiments to two previous microarray experiments to come up with a high-confidence list of modulated genes in long-lived mutant worms. Overall, this work demonstrates that RNA sequencing of pooled RNA samples can be used to identify differentially expressed genes.
对全基因组基因表达变化的分析为深入了解分子机制提供了一个强大且无偏倚的工具。我们已有效地利用RNA测序来鉴定长寿基因变异体中的差异表达基因，以增进我们对控制寿命的遗传途径的理解。尽管RNA测序成本已经下降，但成本仍然是在有足够数量生物学重复的情况下检测多个品系和时间点的一个障碍。为了规避这一问题，我们通过对来自长寿线粒体突变蠕虫的混合RNA样本进行测序，研究了鉴定差异表达基因的功效。我们发现，对混合RNA样本进行测序能够有效地鉴定出在两个单独测序的RNA测序实验中被发现显著上调的基因。最后，我们将在两个单独测序的RNA测序实验中显著上调的基因与之前的两个微阵列实验进行比较，以得出长寿突变蠕虫中经调控基因的高可信度列表。总体而言，这项工作表明，混合RNA样本的RNA测序可用于鉴定差异表达基因。
