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ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

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Cozen, Aaron E, Quartley, Erin, Holmes, Andrew D, Hrabeta-Robinson, Eva, Phizicky, Eric M, Lowe, Todd M·2015·Nature Methods
DOI 10.1038/nmeth.3508PMC PMC4553111
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Abstract

High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA methylation sequencing (ARM-seq), which uses pretreatment with Escherichia coli AlkB to demethylate N(1)-methyladenosine (m(1)A), N(3)-methylcytidine (m(3)C) and N(1)-methylguanosine (m(1)G), all commonly found in tRNAs. Comparative methylation analysis using ARM-seq provides the first detailed, transcriptome-scale map of these modifications and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-seq demonstrates that tRNA fragments accurately recapitulate the m(1)A modification state for well-characterized yeast tRNAs and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state and may reveal new roles for tRNA fragments as biomarkers or signaling molecules.

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  • AlkB-facilitated RNA methylation sequencing (ARM-seq) led to the discovery of novel tRNA fragments previously undetected due to methylation, as well as the development of a transcriptome-wide modification profile.

    “AlkB-facilitated RNA methylation sequencing (ARM-seq), a sequencing method that involves treatment with an Escherichia coli demethylase, led to the discovery of novel tRNA fragments that were previously undetected due to the presence of methylation, as well as the development of a transcriptome-wide modification profile (141).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [141]

  • High-throughput tRNA-specific sequencing techniques have been developed.

    “More recently, high-throughput tRNA-specific sequencing techniques have also been developed.”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [141]

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Authors
Cozen, A. E., Quartley, E., Holmes, A. D., Hrabeta-Robinson, E., Phizicky, E. M., & Lowe, T. M.
Affiliations
  • University of California, Santa Cruz (US)
  • University of Rochester Medicine (US)
Corresponding author
  • Phizicky, Eric M
  • Lowe, Todd M
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2015-08-03
Volume
12
Issue
9
Pages
879-884
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/nmeth.3508
PMC
PMC4553111
OpenAlex
W2108138064
Cited by
479
References
3
Citations by year
2026: 38 · 2025: 60 · 2024: 55 · 2023: 45 · 2022: 48 · 2021: 54 · 2020: 44 · 2019: 47 · 2018: 27 · 2017: 28 · 2016: 29 · 2015: 3
FWCI
12.74
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Human Genome Research Institute (R01HG006753)
  • National Institute of General Medical Sciences (GM052347, R01GM052347)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
RNA methylation, tRNA-derived fragments, N1-methyladenosine, modified nucleosides, tRNA precursors, mitochondrial tRNA, RNA-seq library preparation
MeSH terms
Algorithms, Base Sequence, Mixed Function Oxygenases, Molecular Sequence Data, RNA, Transfer, Software, DNA Methylation, Escherichia coli Proteins, High-Throughput Nucleotide Sequencing

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