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

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Authors

CAVALLIN Ivana BARTOŠOVIČ Marek SKALICKÝ Tomáš RENGARAJ Praveenkumar DEMKO Martin SCHMIDT-DENGLER Martina Christina DRINO Aleksej HELM Mark VAŇÁČOVÁ Štěpánka

Year of publication 2022
Type Article in Periodical
Magazine / Source RNA
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://rnajournal.cshlp.org/content/28/12/1568
Doi http://dx.doi.org/10.1261/rna.079421.122
Keywords ALKBH8; Trm9; wobble uridine modification; mcm(5)U; mcm(5)s(2)U; HITS-CLIP
Attached files
Description 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 (mcm(5)U(34)) or 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 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.
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