Zhao Dongyan, Hamilton John P, Hardigan Michael, Yin Dongmei, He Tao, Vaillancourt Brieanne, Reynoso Mauricio, Pauluzzi Germain, Funkhouser Scott, Cui Yuehua, Bailey-Serres Julia, Jiang Jiming, Buell C Robin, Jiang Ning
Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
G3 (Bethesda). 2017 Jan 5;7(1):203-219. doi: 10.1534/g3.116.036020.
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5' untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
基因表达在转录和转录后水平受到调控，包括通过核糖体介导的翻译将信使核糖核酸（mRNA）解码为多肽。在双子叶模式植物拟南芥中，翻译调控已得到深入研究。在本研究中，我们通过翻译核糖体亲和纯化结合mRNA测序（TRAP-seq），评估了单子叶模式植物及最重要粮食作物水稻（稻属）中mRNA的翻译状态[与核糖体相关的稳态mRNA比例]。对三个组织的调查发现，大多数转录的水稻基因都能被翻译，而很少有转座元件与核糖体相关。编码区短且富含GC的基因在与核糖体相关的mRNA中占比过高，这表明禾本科植物编码序列的富含GC特性可能是一种有利于高效翻译的适应性特征。内含子保留和5'非翻译区延长的转录本在核糖体上的占比过低，属于不同进化谱系的水稻基因在核糖体上表现出与GC含量相关的差异富集。参与光合作用和应激反应的基因优先与核糖体相关，而表观遗传调控途径中的基因在核糖体上的富集程度最低。这种差异在水稻中比在拟南芥中更为显著，并且与水稻转录本GC含量的广泛差异相关。综上所述，单个转录本翻译状态的差异反映了重要的基因调控机制，这可能在进化和多样化过程中发挥作用。
