HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
- Ivana Cavallin1,
- Marek Bartosovic2,
- Tomas Skalicky2,
- Praveenkumar Rengaraj1,
- Martin Demko1,
- Martina Christina Schmidt-Dengler3,
- Aleksej Drino4,
- Mark Helm5 and
- Stepanka Vanacova1,6
- 1 Masaryk University, Central European Institute of Technology;
- 2 Masaryk University, CEITEC;
- 3 Johannes Gutenberg-University Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS);
- 4 Medical University of Vienna, Center for Anatomy & Cell Biology;
- 5 Johannes Gutenberg-University
- ↵* Corresponding author; email: stepanka.vanacova{at}ceitec.muni.cz
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-methoxycarbonylmethyluridine (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, our both approaches revealed ALKBH8 binding to several other types of non-coding RNAs, in particular C/D box snoRNAs.
Keywords
- Received August 16, 2022.
- Accepted September 9, 2022.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
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