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

Publication type:
Journal article
Metadata:
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

Data source: Web of Science (Lite)

Other metadata sources:
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

Data source: 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

Data source: 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

Data source: PubMed

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