School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
PLoS Genet. 2019 Oct 25;15(10):e1008466. doi: 10.1371/journal.pgen.1008466. eCollection 2019 Oct.
What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other's loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background. Here, using gene essentiality profiles of 558 genetically heterogeneous tumor cell lines, we analyze the contribution of paralogy to variable essentiality. We find that, compared to singleton genes, paralogs are less frequently essential and that this is more evident when considering genes with multiple paralogs or with highly sequence-similar paralogs. In addition, we find that paralogs derived from whole genome duplication exhibit more variable essentiality than those derived from small-scale duplications. We provide evidence that in 13-17% of cases the variable essentiality of paralogs can be attributed to buffering relationships between paralog pairs, as evidenced by synthetic lethality. Paralog pairs derived from whole genome duplication and pairs that function in protein complexes are significantly more likely to display such synthetic lethal relationships. Overall we find that many of the observations made using a single strain of budding yeast can be extended to understand patterns of essentiality in genetically heterogeneous cancer cell lines.
是什么使一个基因对细胞生存至关重要?在模式生物,如 budding yeast 中,系统的基因敲除研究表明,旁系同源基因比单基因更不容易成为必需基因,这部分归因于旁系同源基因相互缓冲缺失的能力。然而,基因的必需性不是固定的特性,在不同的遗传背景下可能会有很大的变化。目前尚不清楚旁系同源基因在多大程度上促成了这种变化,因为大多数研究分析的都是在单一遗传背景下被鉴定为必需的基因。在这里,我们使用 558 种遗传异质肿瘤细胞系的基因必需性谱,分析了旁系同源基因对可变必需性的贡献。我们发现,与单基因相比,旁系同源基因不太容易成为必需基因,而当考虑具有多个旁系同源基因或具有高度序列相似性的旁系同源基因时,这种情况更为明显。此外,我们发现,来自全基因组复制的旁系同源基因比来自小规模复制的旁系同源基因表现出更可变的必需性。我们提供的证据表明,在 13-17%的情况下,旁系同源基因的可变必需性可以归因于旁系同源基因对之间的缓冲关系,这可以通过合成致死性来证明。来自全基因组复制的旁系同源基因对和在蛋白质复合物中起作用的旁系同源基因对更有可能显示出这种合成致死关系。总的来说,我们发现,在使用单一 budding yeast 菌株进行的许多观察可以扩展到理解遗传异质癌细胞系中必需性模式。