HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs

Ivana Cavallin, Marek Bartosovic, Tomas Skalicky, Praveenkumar Rengaraj, Martin Demko, Martina Christina Schmidt-Dengler, Aleksej Drino, Mark Helm, Stepanka Vanacova

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U–containing tRNAs obtain 5-methoxycar-bonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U–containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.

Original languageEnglish
Pages (from-to)1568-1581
Number of pages14
JournalRNA
Volume28
Issue number12
DOIs
StatePublished - Dec 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 Cold Spring Harbor Laboratory Press. All rights reserved.

Keywords

  • ALKBH8
  • HITS-CLIP
  • Trm9
  • mcmU
  • mcmsU
  • wobble uridine modification

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