HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
| Authors | |
|---|---|
| Year of publication | 2022 |
| Type | Article in Periodical |
| Magazine / Source | RNA |
| MU Faculty or unit | |
| 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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