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Literature DB >> 28349464

High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq).

Eva Hrabeta-Robinson¹, Erin Marcus², Aaron E Cozen¹, Eric M Phizicky², Todd M Lowe³.

Abstract

N 1-methyladenosine (m1A), N 3-methylcytidine (m3C), and N 1-methylguanosine (m1G) are common in transfer RNA (tRNA) and tRNA-derived fragments. These modifications alter Watson-Crick base-pairing, and cause pauses or stops during reverse transcription required for most high-throughput RNA sequencing protocols, resulting in inefficient detection of methyl-modified RNAs. Here, we describe a procedure to demethylate RNAs containing m1A, m3C, or m1G using the Escherichia coli dealkylating enzyme AlkB, along with instructions for subsequent processing with widely used protocols for small RNA sequencing.

Entities: CellLine Chemical Disease Gene Species

Keywords: AlkB; N 1-methyladenosine (m1A); N 1-methylguanosine (m1G); N 3-methylcytidine (m3C); RNA Sequencing; RNA demethylation; Transfer RNA (tRNA)

Mesh：

Substances：

Year: 2017 PMID： 28349464 PMCID： PMC5587177 DOI： 10.1007/978-1-4939-6807-7_15

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

9 in total

1. A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop.

Authors: Sonia D'Silva; Steffen J Haider; Eric M Phizicky
Journal: RNA Date: 2011-04-25 Impact factor: 4.942

Review 2. Identification of modified residues in RNAs by reverse transcription-based methods.

Authors: Yuri Motorin; Sébastien Muller; Isabelle Behm-Ansmant; Christiane Branlant
Journal: Methods Enzymol Date: 2007 Impact factor: 1.600

3. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA.

Authors: Per Arne Aas; Marit Otterlei; Pål O Falnes; Cathrine B Vågbø; Frank Skorpen; Mansour Akbari; Ottar Sundheim; Magnar Bjørås; Geir Slupphaug; Erling Seeberg; Hans E Krokan
Journal: Nature Date: 2003-02-20 Impact factor: 49.962

4. Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins.

Authors: Pål Ø Falnes
Journal: Nucleic Acids Res Date: 2004-12-01 Impact factor: 16.971

5. Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli.

Authors: James C Delaney; John M Essigmann
Journal: Proc Natl Acad Sci U S A Date: 2004-09-20 Impact factor: 11.205

6. Heterologous expression of L. major proteins in S. cerevisiae: a test of solubility, purity, and gene recoding.

Authors: Erin Quartley; Andrei Alexandrov; Maryann Mikucki; Frederick S Buckner; Wim G Hol; George T DeTitta; Eric M Phizicky; Elizabeth J Grayhack
Journal: J Struct Funct Genomics Date: 2009-08-22

7. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Authors: Michael I Love; Wolfgang Huber; Simon Anders
Journal: Genome Biol Date: 2014 Impact factor: 13.583

8. MODOMICS: a database of RNA modification pathways--2013 update.

Authors: Magdalena A Machnicka; Kaja Milanowska; Okan Osman Oglou; Elzbieta Purta; Malgorzata Kurkowska; Anna Olchowik; Witold Januszewski; Sebastian Kalinowski; Stanislaw Dunin-Horkawicz; Kristian M Rother; Mark Helm; Janusz M Bujnicki; Henri Grosjean
Journal: Nucleic Acids Res Date: 2012-10-30 Impact factor: 16.971

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

Authors: Aaron E Cozen; Erin Quartley; Andrew D Holmes; Eva Hrabeta-Robinson; Eric M Phizicky; Todd M Lowe
Journal: Nat Methods Date: 2015-08-03 Impact factor: 28.547

9 in total

7 in total

1. A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation.

Authors: Christopher P Watkins; Wen Zhang; Adam C Wylder; Christopher D Katanski; Tao Pan
Journal: Nat Commun Date: 2022-05-05 Impact factor: 17.694

High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq).

1. A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop.

Review 2. Identification of modified residues in RNAs by reverse transcription-based methods.

3. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA.

4. Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins.

5. Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli.

6. Heterologous expression of L. major proteins in S. cerevisiae: a test of solubility, purity, and gene recoding.

7. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

8. MODOMICS: a database of RNA modification pathways--2013 update.

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

1. A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation.

Review 2. Pathways to disease from natural variations in human cytoplasmic tRNAs.

3. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.

4. Pervasive Small RNAs in Cardiometabolic Research: Great Potential Accompanied by Biological and Technical Barriers.

Review 5. RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control.

6. Formation and persistence of polyglutamine aggregates in mistranslating cells.

7. A versatile tRNA modification-sensitive northern blot method with enhanced performance.