Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

Ulf Birkedal; Mikkel Christensen-Dalsgaard; Nicolai Krogh; Sabarinathan Radhakrishnan; Jan Gorodkin; Henrik Nielsen

doi:10.1002/anie.201408362

Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

Ulf Birkedal, Mikkel Christensen-Dalsgaard, Nicolai Krogh, Sabarinathan Radhakrishnan, Jan Gorodkin, Henrik Nielsen

Transcription, RNA, and Gene Medicine Program

112 Citations (Scopus)

Abstract

Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing-based method (RiboMeth-seq) and its application to yeast ribosomes, presently the best-studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth-seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth-seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.

Original language	English
Journal	Angewandte Chemie (International ed. in English)
Volume	54
Issue number	2
Pages (from-to)	451-455
Number of pages	5
ISSN	1433-7851
DOIs	https://doi.org/10.1002/anie.201408362
Publication status	Published - 7 Jan 2015

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title = "Profiling of Ribose Methylations in RNA by High-Throughput Sequencing",

abstract = "Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing-based method (RiboMeth-seq) and its application to yeast ribosomes, presently the best-studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth-seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth-seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.",

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T1 - Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

AU - Birkedal, Ulf

AU - Christensen-Dalsgaard, Mikkel

AU - Krogh, Nicolai

AU - Radhakrishnan, Sabarinathan

AU - Gorodkin, Jan

AU - Nielsen, Henrik

PY - 2015/1/7

Y1 - 2015/1/7

N2 - Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing-based method (RiboMeth-seq) and its application to yeast ribosomes, presently the best-studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth-seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth-seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.

AB - Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing-based method (RiboMeth-seq) and its application to yeast ribosomes, presently the best-studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth-seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth-seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.

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DO - 10.1002/anie.201408362

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Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

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