High-Throughput Mapping of 2'-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
- Publikationstyp:
- Kapitel
- Metadaten:
-
- Autoren
- Virginie Marchand
- Lilia Ayadi
- Aseel El Hajj
- Florence Blanloeil-Oillo
- Mark Helm
- Yuri Motorin
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000417675100013&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1007/978-1-4939-6807-7_12
- ISBN-13
- 978-1-4939-6805-3
- Schlüsselwörter
- 2'-O-Methylation
- High-throughput sequencing
- RNA modification
- Ribose methylation
- Alkaline fragmentation
- Paginierung
- 171 - 187
- Buchtitel
- RNA METHYLATION: METHODS AND PROTOCOLS
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Titel
- High-Throughput Mapping of 2'-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
- Ausgabe der Zeitschrift
- 1562
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Virginie Marchand
- Lilia Ayadi
- Aseel El Hajj
- Florence Blanloeil-Oillo
- Mark Helm
- Yuri Motorin
- DOI
- 10.1007/978-1-4939-6807-7_12
- ISBN-13
- 9781493968053
- Online publication date
- 2017
- Paginierung
- 171 - 187
- Buchtitel
- Methods in Molecular Biology
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Herausgeber
- Springer New York
- Herausgeber URL
- http://dx.doi.org/10.1007/978-1-4939-6807-7_12
- Datum der Datenerfassung
- 2017
- Titel
- High-Throughput Mapping of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
Datenquelle: Crossref
- Abstract
- Detection of RNA modifications in native RNAs is a tedious and laborious task, since the global level of these residues is low and most of the suitable physico-chemical methods require purification of the RNA of interest almost to homogeneity. To overcome these limitations, methods based on RT-driven primer extension have been developed and successfully used, sometimes in combination with a specific chemical treatment. Nowadays, some of these approaches have been coupled to high-throughput sequencing technologies, allowing the access to transcriptome-wide data. RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from bacteria, archaea, and eukarya. Here, we describe a reliable and optimized protocol based on alkaline fragmentation of total RNA coupled to a commonly used ligation approach followed by Illumina sequencing. We describe the methodology for detection and relative quantification of 2'-O-methylations with a high sensitivity and reproducibility even with a limited amount of starting material (1 ng of total RNA). Altogether this technique unlocks a technological barrier since it will be applicable for routine parallel treatment of biological and clinical samples to decipher the functions of 2'-O-methylations in pathologies.
- Addresses
- IMoPA UMR7365 CNRS-UL, BioPole Lorraine University, 9 Avenue de la Foret de Haye, 54505, Vandoeuvre-Les-Nancy, France.
- Autoren
- Virginie Marchand
- Lilia Ayadi
- Aseel El Hajj
- Florence Blanloeil-Oillo
- Mark Helm
- Yuri Motorin
- DOI
- 10.1007/978-1-4939-6807-7_12
- Open access
- false
- Schlüsselwörter
- RNA
- Sequence Analysis, RNA
- Computational Biology
- Methylation
- Hydrolysis
- Gene Library
- Quality Control
- Software
- High-Throughput Nucleotide Sequencing
- Medium
- Paginierung
- 171 - 187
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Datum der Datenerfassung
- 2017
- Titel
- High-Throughput Mapping of 2'-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol).
- Ausgabe der Zeitschrift
- 1562
Datenquelle: Europe PubMed Central
- Abstract
- Detection of RNA modifications in native RNAs is a tedious and laborious task, since the global level of these residues is low and most of the suitable physico-chemical methods require purification of the RNA of interest almost to homogeneity. To overcome these limitations, methods based on RT-driven primer extension have been developed and successfully used, sometimes in combination with a specific chemical treatment. Nowadays, some of these approaches have been coupled to high-throughput sequencing technologies, allowing the access to transcriptome-wide data. RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from bacteria, archaea, and eukarya. Here, we describe a reliable and optimized protocol based on alkaline fragmentation of total RNA coupled to a commonly used ligation approach followed by Illumina sequencing. We describe the methodology for detection and relative quantification of 2'-O-methylations with a high sensitivity and reproducibility even with a limited amount of starting material (1 ng of total RNA). Altogether this technique unlocks a technological barrier since it will be applicable for routine parallel treatment of biological and clinical samples to decipher the functions of 2'-O-methylations in pathologies.
- Autoren
- Virginie Marchand
- Lilia Ayadi
- Aseel El Hajj
- Florence Blanloeil-Oillo
- Mark Helm
- Yuri Motorin
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/28349461
- DOI
- 10.1007/978-1-4939-6807-7_12
- Schlüsselwörter
- 2′-O-Methylation
- Alkaline fragmentation
- High-throughput sequencing
- RNA modification
- Ribose methylation
- Computational Biology
- Gene Library
- High-Throughput Nucleotide Sequencing
- Hydrolysis
- Methylation
- Quality Control
- RNA
- Sequence Analysis, RNA
- Software
- Paginierung
- 171 - 187
- Datum der Veröffentlichung
- 2017
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2018
- Titel
- High-Throughput Mapping of 2'-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol).
- Ausgabe der Zeitschrift
- 1562
Datenquelle: PubMed
- Beziehungen:
- Eigentum von