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Literature DB >> 28504680

Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

Qing Dai^1,2, Sharon Moshitch-Moshkovitz^3,4, Dali Han^1,2, Nitzan Kol³, Ninette Amariglio^3,4,5, Gideon Rechavi^3,4,6, Dan Dominissini^3,4,6, Chuan He^1,2,7,8.

Abstract

The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Substances：

Year: 2017 PMID： 28504680 PMCID： PMC5712428 DOI： 10.1038/nmeth.4294

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

34 in total

1. Post-transcriptional modification of spliceosomal RNAs is normal in SMN-deficient cells.

Authors: Svetlana Deryusheva; Maria Choleza; Adrien Barbarossa; Joseph G Gall; Rémy Bordonné
Journal: RNA Date: 2011-11-28 Impact factor: 4.942

2. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing.

Authors: Xue-Hai Liang; Qing Liu; Maurille J Fournier
Journal: RNA Date: 2009-07-23 Impact factor: 4.942

3. Understanding the effect of locked nucleic acid and 2'-O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein.

Authors: Santosh Kumar; Koyeli Mapa; Souvik Maiti
Journal: Biochemistry Date: 2014-03-07 Impact factor: 3.162

4. Fast gapped-read alignment with Bowtie 2.

Authors: Ben Langmead; Steven L Salzberg
Journal: Nat Methods Date: 2012-03-04 Impact factor: 28.547

5. Absolute and relative quantification of RNA modifications via biosynthetic isotopomers.

Authors: Stefanie Kellner; Antonia Ochel; Kathrin Thüring; Felix Spenkuch; Jennifer Neumann; Sunny Sharma; Karl-Dieter Entian; Dirk Schneider; Mark Helm
Journal: Nucleic Acids Res Date: 2014-08-16 Impact factor: 16.971

6. Reovirus mRNA can be covalently crosslinked via the 5' cap to proteins in initiation complexes.

Authors: N Sonenberg; A J Shatkin
Journal: Proc Natl Acad Sci U S A Date: 1977-10 Impact factor: 11.205

7. Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5.

Authors: Roland Züst; Luisa Cervantes-Barragan; Matthias Habjan; Reinhard Maier; Benjamin W Neuman; John Ziebuhr; Kristy J Szretter; Susan C Baker; Winfried Barchet; Michael S Diamond; Stuart G Siddell; Burkhard Ludewig; Volker Thiel
Journal: Nat Immunol Date: 2011-01-09 Impact factor: 25.606

8. HTSeq--a Python framework to work with high-throughput sequencing data.

Authors: Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal: Bioinformatics Date: 2014-09-25 Impact factor: 6.937

9. Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA.

Authors: Virginie Marchand; Florence Blanloeil-Oillo; Mark Helm; Yuri Motorin
Journal: Nucleic Acids Res Date: 2016-06-14 Impact factor: 16.971

10. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

Authors: Nathan D Berkowitz; Ian M Silverman; Daniel M Childress; Hilal Kazan; Li-San Wang; Brian D Gregory
Journal: BMC Bioinformatics Date: 2016-05-17 Impact factor: 3.169

91 in total

Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

1. Post-transcriptional modification of spliceosomal RNAs is normal in SMN-deficient cells.

2. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing.

3. Understanding the effect of locked nucleic acid and 2'-O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein.

4. Fast gapped-read alignment with Bowtie 2.

5. Absolute and relative quantification of RNA modifications via biosynthetic isotopomers.

6. Reovirus mRNA can be covalently crosslinked via the 5' cap to proteins in initiation complexes.

7. Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5.

8. HTSeq--a Python framework to work with high-throughput sequencing data.

9. Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA.

10. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

Review 1. The Untranslated Regions of mRNAs in Cancer.

2. Assessing 2'-O-Methylation of mRNA Using Quantitative PCR.

Review 3. Relating Structure and Dynamics in RNA Biology.

Review 4. Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA.

5. mRNA acetylation: a new addition to the epitranscriptome.

Review 6. The Epitranscriptome in Translation Regulation.

Review 7. RNA epigenetics and cardiovascular diseases.

Review 8. Chemical Modifications in the Life of an mRNA Transcript.

Review 9. Dynamic RNA Modifications in Gene Expression Regulation.

10. Occurrence and Functions of m⁶A and Other Covalent Modifications in Plant mRNA.