Nakano Yuko, Gamper Howard, McGuigan Henri, Maharjan Sunita, Li Jiatong, Sun Zhiyi, Yigit Erbay, Grünberg Sebastian, Krishnan Keerthana, Li Nan-Sheng, Piccirilli Joseph A, Kleiner Ralph, Nichols Nicole, Gregory Brian D, Hou Ya-Ming
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
Department of Biology, University of Pennsylvania, Pennsylvania, PA, USA.
Nat Commun. 2025 Jan 26;16(1):1047. doi: 10.1038/s41467-025-56348-1.
While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro-a new group-II intron-encoded RT-to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and three mouse tissues and show that, while the landscape of modifications is highly variable throughout the tRNA sequence framework, it is stabilized for modifications that are required for reading of the genetic code. The coordinated changes have fundamental importance for development of tRNA modifications in protein homeostasis.
虽然所有天然转运RNA（tRNA）都会经历广泛的转录后修饰，作为调节基因表达的一种机制，但对这些修饰进行定位仍然具有挑战性。关键障碍在于逆转录酶（RT）难以通读这些修饰。在这里，我们使用Induro（一种新的II类内含子编码的RT）在Induro-tRNAseq中对全基因组的tRNA修饰进行定位和定量。我们表明，Induro通过选择性地克服RT终止而不改变错误掺入频率，随着时间的推移逐渐增加通读率。在对Induro与一种相关RT的平行分析中，我们提供了比较数据集，以促进对每种修饰的预测。我们评估了五种人类细胞系和三种小鼠组织中的tRNA修饰，结果表明，虽然修饰格局在整个tRNA序列框架中高度可变，但对于遗传密码读取所需的修饰而言，它是稳定的。这些协同变化对于蛋白质稳态中tRNA修饰的发展具有至关重要的意义。
