Sun Jingjing, Wu Junzhou, Yuan Yifeng, Fan Leon, Chua Wei Lin Patrina, Ling Yan Han Sharon, Balamkundu Seetharamsing, Priya Dwija, Suen Hazel Chay Suen, de Crécy-Lagard Valérie, Dziergowska Agnieszka, Dedon Peter C
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.
Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore.
bioRxiv. 2024 Jul 2:2024.07.01.601603. doi: 10.1101/2024.07.01.601603.
Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications - the tRNA epitranscriptome - very little is known about how metabolic, signaling, and other networks integrate to regulate tRNA modification levels. Here we took a comprehensive first step at understanding epitranscriptome regulatory networks by developing a high-throughput tRNA isolation and mass spectrometry-based modification profiling platform and applying it to a transposon insertion mutant library comprising 5,746 strains. Analysis of >200,000 tRNA modification data points validated the annotations of predicted tRNA modification genes, uncovered novel tRNA-modifying enzymes, and revealed tRNA modification regulatory networks in . Platform adaptation for RNA-seq library preparation would complement epitranscriptome studies, while application to human cell and mouse tissue demonstrates its utility for biomarker and drug discovery and development.
转运RNA（tRNA）修饰已成为基因表达的关键转录后调节因子，影响多种生物学和疾病过程。虽然人们对安装数十种转录后tRNA修饰（即tRNA表观转录组）的酶有广泛了解，但对于代谢、信号传导和其他网络如何整合以调节tRNA修饰水平却知之甚少。在这里，我们通过开发一个基于高通量tRNA分离和质谱的修饰分析平台，并将其应用于一个包含5746个菌株的转座子插入突变体文库，迈出了理解表观转录组调控网络的全面第一步。对超过200,000个tRNA修饰数据点的分析验证了预测的tRNA修饰基因的注释，发现了新的tRNA修饰酶，并揭示了其中的tRNA修饰调控网络。适用于RNA测序文库制备的平台将补充表观转录组研究，而应用于人类细胞和小鼠组织则证明了其在生物标志物以及药物发现与开发方面的实用性。
