Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

• Published in: Nature (London) Vol. 583; no. 7817; pp. 638 - 643
• Main Authors: Sas-Chen, Aldema, Thomas, Justin M., Matzov, Donna, Taoka, Masato, Nance, Kellie D., Nir, Ronit, Bryson, Keri M., Shachar, Ran, Liman, Geraldy L. S., Burkhart, Brett W., Gamage, Supuni Thalalla, Nobe, Yuko, Briney, Chloe A., Levy, Michaella J., Fuchs, Ryan T., Robb, G. Brett, Hartmann, Jesse, Sharma, Sunny, Lin, Qishan, Florens, Laurence, Washburn, Michael P., Isobe, Toshiaki, Santangelo, Thomas J., Shalev-Benami, Moran, Meier, Jordan L., Schwartz, Schraga
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.07.2020; Nature Publishing Group
• Subjects: 101/28; 101/58; 14/1; 38/91; 631/1647/296; 631/208/182; 631/208/514/1949; 631/337/1645/2570; 631/535/1258/1259; Acetylation; Acetyltransferase; Archaea; Archaea - chemistry; Archaea - cytology; Archaea - genetics; Archaea - growth & development; BASIC BIOLOGICAL SCIENCES; Biological evolution; Conserved Sequence; Cryoelectron Microscopy; Cytidine - analogs & derivatives; Cytidine - metabolism; Electron microscopy; Eukaryotic Cells - cytology; Eukaryotic Cells - metabolism; Evolution, Molecular; evolutionary biology; Gene expression; Gene mapping; Genetic research; Genetic transcription; HeLa Cells; Humanities and Social Sciences; Humans; Hyperthermophilic archaea; Mapping; mass spectrometry; Methods; Models, Molecular; multidisciplinary; Mutation; N-Terminal Acetyltransferases - metabolism; Non-coding RNA; Nucleotides; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; Ribosomes - ultrastructure; RNA - chemistry; RNA - metabolism; RNA modification; RNA sequencing; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA-Binding Proteins - metabolism; rRNA; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Science; science & technology; Science (multidisciplinary); Sequence Analysis, DNA; Temperature; Temperature dependence; tRNA; Yeast; Yeasts; United States
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-020-2418-2

N 4 -acetylcytidine (ac 4 C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA 1 – 3 . However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac 4 C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac 4 C at single-nucleotide resolution. In human and yeast mRNAs, ac 4 C sites are not detected but can be induced—at a conserved sequence motif—via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac 4 C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac 4 C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac 4 C and its potential thermoadaptive role. Our studies quantitatively define the ac 4 C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease 4 – 6 . A method termed ac 4 C-seq is introduced for the transcriptome-wide mapping of the RNA modification N 4 -acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.