biostudies-literatureStuart CJHHS | NIH | National Institute of General Medical SciencesNIGMS NIH HHSHHS | NIH | National Institute of General Medical Sciences (NIGMS)e2502364122https://www.ebi.ac.uk/biostudies/studies/S-EPMC12168002biostudies-literatureUnknown122(23)tRNA introns are a universally conserved feature of eukaryotic genomes, but the reason for their conservation has remained obscure. We have previously shown that a defect in the essential tRNA splicing endonuclease of yeast results in transcriptome remodeling, resembling that of the integrated stress response (ISR). In this study, we show that ISR activation in this mutant requires the canonical ISR components, including the collided ribosome sensor Gcn1. We further show that splicing of tyrosine tRNA, but not splicing of any of the other intron-containing tRNAs, controls the ISR. Using nanopore direct RNA sequencing, we show that the intron of tyrosine tRNA affects ^m1A58 modification in the T arm loop of the mature tRNA. In support of these results, we show that deletion of eitProceedings of the National Academy of Sciences of the United States of AmericaThe highly conserved intron of tyrosine tRNA is critical for <sup>m1</sup>A58 modification and controls the integrated stress response.PMC12168002R35GM141710R35 GM141710van Hoof AHurtig JEThomas NKJain MStuart CJTzadikario TfalseThe highly conserved intron of tyrosine tRNA is critical for <sup>m1</sup>A58 modification and controls the integrated stress response.tRNA introns are a universally conserved feature of eukaryotic genomes, but the reason for their conservation has remained obscure. We have previously shown that a defect in the essential tRNA splicing endonuclease of yeast results in transcriptome remodeling, resembling that of the integrated stress response (ISR). In this study, we show that ISR activation in this mutant requires the canonical ISR components, including the collided ribosome sensor Gcn1. We further show that splicing of tyrosine tRNA, but not splicing of any of the other intron-containing tRNAs, controls the ISR. Using nanopore direct RNA sequencing, we show that the intron of tyrosine tRNA affects ^m1A58 modification in the T arm loop of the mature tRNA. In support of these results, we show that deletion of eit2025-01-01T00:00:00Z2025 Jun2026-06-10T05:19:13.228Z2026-06-10T03:07:51.195ZS-EPMC121680024047887510.1073/pnas.2502364122