Methods for Determination of 2′-O-Me in RNA
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Methods for Determination of 2′-O-Me in RNA. / Birkedal, Ulf; Krogh, Nicolai; Andersen, Kasper Langebjerg; Nielsen, Henrik.
Modified Nucleic Acids in Biology and Medicine. red. / Stefan Jurga ; Volker A. Erdmann ; Jan Barciszewski. switzerland : Springer Science+Business Media, 2016. s. 187-205 (RNA Technologies).Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt
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TY - CHAP
T1 - Methods for Determination of 2′-O-Me in RNA
AU - Birkedal, Ulf
AU - Krogh, Nicolai
AU - Andersen, Kasper Langebjerg
AU - Nielsen, Henrik
PY - 2016/7/30
Y1 - 2016/7/30
N2 - Ribose methylation is one of the most abundant RNA modifications and is found in all kingdoms of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. The most abundant mechanism of ribose methylation is found in rRNA of Archaea and Eukarya where a methyltransferase (fibrillarin) use sRNA (Archaea) or box C/D snoRNA (Eukarya) as guide RNAs to specify the site of modification. The general function of these modifications is to promote ribosome biogenesis, in particular folding of the ribosomal RNA. Furthermore, some modifications affect the fidelity of translation. The function of individual modifications has in many cases remained elusive, because genetic deletion of the modification has a weak phenotype or no phenotype at all. Another problem is that methods for mapping modifications and quantitating the fraction of RNA molecules modified in a population until recently remained poorly developed. Here, we review the methods that have been used to study 2′-O-Me in RNA starting with the original approach employing in vivo isotope labeling followed by paper chromatography. The next generation of methods typically addressed one nucleotide at a time and was mostly based on primer extension. Finally, more recent mass spectrometry and high-throughput sequencing methods hold promise to reveal a new biology of this widespread type of nucleotide modification.
AB - Ribose methylation is one of the most abundant RNA modifications and is found in all kingdoms of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. The most abundant mechanism of ribose methylation is found in rRNA of Archaea and Eukarya where a methyltransferase (fibrillarin) use sRNA (Archaea) or box C/D snoRNA (Eukarya) as guide RNAs to specify the site of modification. The general function of these modifications is to promote ribosome biogenesis, in particular folding of the ribosomal RNA. Furthermore, some modifications affect the fidelity of translation. The function of individual modifications has in many cases remained elusive, because genetic deletion of the modification has a weak phenotype or no phenotype at all. Another problem is that methods for mapping modifications and quantitating the fraction of RNA molecules modified in a population until recently remained poorly developed. Here, we review the methods that have been used to study 2′-O-Me in RNA starting with the original approach employing in vivo isotope labeling followed by paper chromatography. The next generation of methods typically addressed one nucleotide at a time and was mostly based on primer extension. Finally, more recent mass spectrometry and high-throughput sequencing methods hold promise to reveal a new biology of this widespread type of nucleotide modification.
U2 - 10.1007/978-3-319-34175-0_8
DO - 10.1007/978-3-319-34175-0_8
M3 - Book chapter
SN - 978-3-319-34173-6
T3 - RNA Technologies
SP - 187
EP - 205
BT - Modified Nucleic Acids in Biology and Medicine
A2 - Jurga , Stefan
A2 - Erdmann , Volker A.
A2 - Barciszewski, Jan
PB - Springer Science+Business Media
CY - switzerland
ER -
ID: 166272383