Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2-O-Methylation
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Virginie Marchand
- Florian Pichot
- Kathrin Thuering
- Lilia Ayadi
- Isabel Freund
- Alexander Dalpke
- Mark Helm
- Yuri Motorin
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000398687100012&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.3390/biom7010013
- Externe Identifier
- Clarivate Analytics Document Solution ID: ER3HI
- PubMed Identifier: 28208788
- ISSN
- 2218-273X
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- BIOMOLECULES
- Schlüsselwörter
- tRNA
- 2-O-methylation
- RiboMethSeq
- high-throughput sequencing
- deleted strain
- TrmH
- TRM3
- Artikelnummer
- ARTN 13
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Titel
- Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2-<i>O</i>-Methylation
- Sub types
- Article
- Ausgabe der Zeitschrift
- 7
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Virginie Marchand
- Florian Pichot
- Kathrin Thüring
- Lilia Ayadi
- Isabel Freund
- Alexander Dalpke
- Mark Helm
- Yuri Motorin
- DOI
- 10.3390/biom7010013
- eISSN
- 2218-273X
- Ausgabe der Veröffentlichung
- 4
- Zeitschrift
- Biomolecules
- Sprache
- en
- Online publication date
- 2017
- Paginierung
- 13 - 13
- Status
- Published online
- Herausgeber
- MDPI AG
- Herausgeber URL
- http://dx.doi.org/10.3390/biom7010013
- Datum der Datenerfassung
- 2019
- Titel
- Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation
- Ausgabe der Zeitschrift
- 7
Data source: Crossref
- Abstract
- Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2'-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
- Addresses
- IMoPA UMR7365 CNRS-UL, Biopole Lorraine University, 54505 Vandoeuvre-les-Nancy, France. Florian.Pichot5@etu.univ.
- Autoren
- Virginie Marchand
- Florian Pichot
- Kathrin Thüring
- Lilia Ayadi
- Isabel Freund
- Alexander Dalpke
- Mark Helm
- Yuri Motorin
- DOI
- 10.3390/biom7010013
- eISSN
- 2218-273X
- Externe Identifier
- PubMed Identifier: 28208788
- PubMed Central ID: PMC5372725
- Funding acknowledgements
- Deutsche Forschungsgemeinschaft: MH3397/14-1
- Deutsche Forschungsgemeinschaft: Da592/5
- Deutsche Forschungsgemeinschaft: SPP1784
- Agence Nationale de la Recherche: ANR-13-ISV8-0001
- Deutsche Forschungsgemeinschaft: MH3397/12-1
- Open access
- true
- ISSN
- 2218-273X
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- Biomolecules
- Schlüsselwörter
- Escherichia coli
- Saccharomyces cerevisiae
- RNA, Bacterial
- RNA, Fungal
- RNA, Transfer
- Sequence Analysis, RNA
- Computational Biology
- Methylation
- High-Throughput Nucleotide Sequencing
- Sprache
- eng
- Medium
- Electronic
- Online publication date
- 2017
- Open access status
- Open Access
- Paginierung
- E13
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2017
- Titel
- Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation.
- Sub types
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 7
Files
https://www.mdpi.com/2218-273X/7/1/13/pdf?version=1487072870 https://europepmc.org/articles/PMC5372725?pdf=render
Data source: Europe PubMed Central
- Abstract
- Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2'-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
- Date of acceptance
- 2017
- Autoren
- Virginie Marchand
- Florian Pichot
- Kathrin Thüring
- Lilia Ayadi
- Isabel Freund
- Alexander Dalpke
- Mark Helm
- Yuri Motorin
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/28208788
- DOI
- 10.3390/biom7010013
- eISSN
- 2218-273X
- Externe Identifier
- PubMed Central ID: PMC5372725
- Ausgabe der Veröffentlichung
- 1
- Zeitschrift
- Biomolecules
- Schlüsselwörter
- tRNA
- TrmH
- 2′‐O‐methylation
- RiboMethSeq
- TRM3
- deleted strain
- high‐throughput sequencing
- Computational Biology
- Escherichia coli
- High-Throughput Nucleotide Sequencing
- Methylation
- RNA, Bacterial
- RNA, Fungal
- RNA, Transfer
- Saccharomyces cerevisiae
- Sequence Analysis, RNA
- Sprache
- eng
- Country
- Switzerland
- PII
- biom7010013
- Datum der Veröffentlichung
- 2017
- Status
- Published online
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2017
- Titel
- Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 7
Data source: PubMed
- Beziehungen:
- Property of