背景:近年来,RNA核苷酸上的共价修饰已成为影响结构的关键部分,函数,和RNA聚合酶II转录物的调节过程,如mRNA和lncRNA。然而,我们对它们的生物学作用以及这些作用在真核生物中是否保守的理解仍然有限.
结果:在这项研究中,我们利用标准的聚腺苷酸化富集RNA测序数据来鉴定和表征在cDNA读段中引入碱基配对错误的RNA修饰.我们的调查结合了来自三个禾本科(玉米,双色高粱,和Setariaitalica),以及来自高粱和拟南芥一系列压力和遗传环境的公开数据。我们发现了RNA共价修饰(RCM)的强烈富集,其沉积在涉及这些物种的光合作用和翻译的保守核心核核mRNAs上。然而,修改后的转录本队列根据环境背景和发展计划而改变,一种在开花植物中也保守的模式。我们确定RCM可以部分解释高粱耐旱性的加入水平差异,与胁迫相关的基因在耐旱性中接受更高水平的RCM。要寻址函数,我们确定RCM在编码区内外显子连接附近显著富集,暗示与剪接有关。有趣的是,我们发现这些破坏RCM的碱基对与稳定的mRNA相关,与蛋白质丰度高度相关,因此可能与促进翻译有关。
结论:我们的数据表明RCM在开花植物谱系的mRNA稳定性和翻译中的保守作用。
BACKGROUND: In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our understanding of their biological roles and whether these roles are conserved across eukaryotes remains limited.
RESULTS: In this study, we leveraged standard polyadenylation-enriched RNA-sequencing data to identify and characterize RNA modifications that introduce base-pairing errors into cDNA reads. Our investigation incorporated data from three Poaceae (Zea mays, Sorghum bicolor, and Setaria italica), as well as publicly available data from a range of stress and genetic contexts in Sorghum and Arabidopsis thaliana. We uncovered a strong enrichment of RNA covalent modifications (RCMs) deposited on a conserved core set of nuclear mRNAs involved in photosynthesis and translation across these species. However, the cohort of modified transcripts changed based on environmental context and developmental program, a pattern that was also conserved across flowering plants. We determined that RCMs can partly explain accession-level differences in drought tolerance in Sorghum, with stress-associated genes receiving a higher level of RCMs in a drought tolerant accession. To address function, we determined that RCMs are significantly enriched near exon junctions within coding regions, suggesting an association with splicing. Intriguingly, we found that these base-pair disrupting RCMs are associated with stable mRNAs, are highly correlated with protein abundance, and thus likely associated with facilitating translation.
CONCLUSIONS: Our data point to a conserved role for RCMs in mRNA stability and translation across the flowering plant lineage.