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<p>Pseudouridine (Ψ) is an abundant modification in small RNA catalyzed by multiple pseudouridine synthases (PUSs). However, the substrate specificity of human PUSs remains elusive. Here, we adopted PRAISE, a quantitative Ψ detection method, to profile pseudouridylation in small RNA, including cytosolic and mitochondrial tRNAs, snRNA, and snoRNA. We found that snoRNA pseudouridylation is mediated not only by RNA-guided DKC1, but also by the stand-alone enzyme PUS7 at a specific site. Interestingly, several PUS enzymes, including PUS1, RPUSD1, and PUS7, which install nearby Ψ sites within tRNA anticodon stem-loop, can influence pseudouridylation catalyzed by other PUSs, revealing an unrecognized interplay during Ψ formation. For the three RluA family enzymes, RPUSD1 catalyzes the canonical Ψ30 in tRNA-Ile and Ψ72 in tRNA-Arg isoacceptors. RPUSD2 pseudouridylates Ψ31 of mt-tRNA<sup>Leu(CUN)</sup>, Ψ32 of mt-tRNA<sup>Pro</sup> and mt-tRNA<sup>Cys</sup>, whereas RPUSD3 lacks tRNA activity. Together, our quantitative Ψ profiling characterized PUS tRNA substrates and revealed unexpected PUS interplay.</p>

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Quantitative analysis of small RNA pseudouridylation reveals interplay of PUS enzymes in tRNA anticodon stem-loop

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月16日

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  • Wenqing Liu,
  • Yichen Ma,
  • Liping Wang,
  • Bo Lu,
  • Yuyang Dong,
  • Yuan Zhuang,
  • Bo He,
  • Meiling Zhang,
  • Chengqi Yi

摘要

Pseudouridine (Ψ) is an abundant modification in small RNA catalyzed by multiple pseudouridine synthases (PUSs). However, the substrate specificity of human PUSs remains elusive. Here, we adopted PRAISE, a quantitative Ψ detection method, to profile pseudouridylation in small RNA, including cytosolic and mitochondrial tRNAs, snRNA, and snoRNA. We found that snoRNA pseudouridylation is mediated not only by RNA-guided DKC1, but also by the stand-alone enzyme PUS7 at a specific site. Interestingly, several PUS enzymes, including PUS1, RPUSD1, and PUS7, which install nearby Ψ sites within tRNA anticodon stem-loop, can influence pseudouridylation catalyzed by other PUSs, revealing an unrecognized interplay during Ψ formation. For the three RluA family enzymes, RPUSD1 catalyzes the canonical Ψ30 in tRNA-Ile and Ψ72 in tRNA-Arg isoacceptors. RPUSD2 pseudouridylates Ψ31 of mt-tRNALeu(CUN), Ψ32 of mt-tRNAPro and mt-tRNACys, whereas RPUSD3 lacks tRNA activity. Together, our quantitative Ψ profiling characterized PUS tRNA substrates and revealed unexpected PUS interplay.