RNA-seq of liver tissue and liver cancer cell lines

This dataset has been designed to test whether codons in mRNAs and anticodons in tRNAs vary in order to maximize translation in specific cellular conditions in mammals. Prokaryotes and simple unicellular eukaryotes optimize their translational rates by adjusting the codons in the protein-coding transcriptome to the available pool of anticodons in the tRNA transcriptome. We found no evidence supporting this mechanism in mammals, even when subsets of genes were considered, such as those found in Gene Ontology functional categories or in tissue-specific transcriptional signatures. The simplest explanation accounting for the observed codon distributions in mammals is the variation in GC content of gene categories. GC variation across the mammalian genome is most likely to result from the interplay of genome repair and gene duplication mechanisms, rather than selective pressures caused by codon-driven translational rates. This work is part of experiment series: ChIP-Seq E-MTAB-23282326.本数据集旨在检验哺乳动物体内信使RNA（mRNA）中的密码子与转运RNA（tRNA）中的反密码子是否会发生变异，以在特定细胞条件下最大化翻译效率。原核生物与简单单细胞真核生物会通过调整蛋白质编码转录组中的密码子，使其匹配tRNA转录组中可用的反密码子库，以此优化翻译速率。本研究未在哺乳动物中发现支持该机制的证据，即便针对特定基因子集进行分析时亦是如此——例如隶属于基因本体（Gene Ontology, GO）功能类别或具有组织特异性转录特征的基因。解释哺乳动物中观测到的密码子分布的最简假说，与各类基因的鸟嘌呤-胞嘧啶（GC）含量变异相关。哺乳动物全基因组范围内的GC含量变异，最可能源于基因组修复与基因复制机制的相互作用，而非密码子驱动的翻译速率所带来的选择压力。本研究隶属于系列实验：染色质免疫共沉淀测序（ChIP-Seq）E-MTAB-23282326。