HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Ivana Cavallin
- Marek Bartosovic
- Tomas Skalicky
- Praveenkumar Rengaraj
- Martin Demko
- Martina Christina Schmidt-Dengler
- Aleksej Drino
- Mark Helm
- Stepanka Vanacova
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000886671000002&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1261/rna.079421.122
- eISSN
- 1469-9001
- Externe Identifier
- Clarivate Analytics Document Solution ID: 6J2QB
- PubMed Identifier: 36192131
- ISSN
- 1355-8382
- Ausgabe der Veröffentlichung
- 12
- Zeitschrift
- RNA
- Schlüsselwörter
- ALKBH8
- Trm9
- wobble uridine modification
- mcm(5)U
- mcm(5)s(2)U
- HITS-CLIP
- Paginierung
- 1568 - 1581
- Datum der Veröffentlichung
- 2022
- Status
- Published
- Titel
- HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
- Sub types
- Article
- Ausgabe der Zeitschrift
- 28
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Abstract
- <jats:p>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.</jats:p>
- Autoren
- Ivana Cavallin
- Marek Bartosovic
- Tomas Skalicky
- Praveenkumar Rengaraj
- Martin Demko
- Martina Christina Schmidt-Dengler
- Aleksej Drino
- Mark Helm
- Stepanka Vanacova
- DOI
- 10.1261/rna.079421.122
- eISSN
- 1469-9001
- ISSN
- 1355-8382
- Zeitschrift
- RNA
- Sprache
- en
- Online publication date
- 2022
- Paginierung
- rna.079421.122 - rna.079421.122
- Status
- Published online
- Herausgeber
- Cold Spring Harbor Laboratory
- Herausgeber URL
- http://dx.doi.org/10.1261/rna.079421.122
- Datum der Datenerfassung
- 2022
- Titel
- HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs
Datenquelle: Crossref
- 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 (mcm<sup>5</sup>U<sub>34</sub>) or 5-methoxycarbonylmethyl-2-thiouridine (mcm<sup>5</sup>s<sup>2</sup>U<sub>34</sub>), 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.
- Addresses
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
- Autoren
- Ivana Cavallin
- Marek Bartosovic
- Tomas Skalicky
- Praveenkumar Rengaraj
- Martin Demko
- Martina Christina Schmidt-Dengler
- Aleksej Drino
- Mark Helm
- Stepanka Vanacova
- DOI
- 10.1261/rna.079421.122
- eISSN
- 1469-9001
- Externe Identifier
- PubMed Identifier: 36192131
- PubMed Central ID: PMC9670814
- Open access
- true
- ISSN
- 1355-8382
- Ausgabe der Veröffentlichung
- 12
- Zeitschrift
- RNA (New York, N.Y.)
- Schlüsselwörter
- Humans
- RNA, Transfer
- Anticodon
- RNA, Untranslated
- AlkB Homolog 8, tRNA Methyltransferase
- Chromatin Immunoprecipitation Sequencing
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2022
- Open access status
- Open Access
- Paginierung
- 1568 - 1581
- Datum der Veröffentlichung
- 2022
- Status
- Published
- Publisher licence
- CC BY-NC
- Datum der Datenerfassung
- 2022
- Titel
- HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs.
- Sub types
- Research Support, Non-U.S. Gov't
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 28
Files
https://europepmc.org/articles/PMC9670814?pdf=render
Datenquelle: Europe PubMed Central
- 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, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
- Date of acceptance
- 2022
- Autoren
- Ivana Cavallin
- Marek Bartosovic
- Tomas Skalicky
- Praveenkumar Rengaraj
- Martin Demko
- Martina Christina Schmidt-Dengler
- Aleksej Drino
- Mark Helm
- Stepanka Vanacova
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/36192131
- DOI
- 10.1261/rna.079421.122
- eISSN
- 1469-9001
- Externe Identifier
- PubMed Central ID: PMC9670814
- Ausgabe der Veröffentlichung
- 12
- Zeitschrift
- RNA
- Schlüsselwörter
- ALKBH8
- HITS-CLIP
- Trm9
- mcm5U
- mcm5s2U
- wobble uridine modification
- Humans
- Chromatin Immunoprecipitation Sequencing
- RNA, Transfer
- Anticodon
- RNA, Untranslated
- AlkB Homolog 8, tRNA Methyltransferase
- Sprache
- eng
- Country
- United States
- Paginierung
- 1568 - 1581
- PII
- rna.079421.122
- Datum der Veröffentlichung
- 2022
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2022
- Titel
- HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 28
Datenquelle: PubMed
- Beziehungen:
- Eigentum von