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Björkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW. Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms. J Am Chem Soc 2015; 137:14430-8. [PMID: 26495937 PMCID: PMC7547889 DOI: 10.1021/jacs.5b09438] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS) is a powerful technique for characterizing noncanonical nucleobases and other chemical modifications in small RNAs, yielding rich chemical information that is complementary to high-throughput indirect sequencing. However, mass spectra are often prohibitively complex when fragment ions are analyzed following either solution phase hydrolysis or gas phase fragmentation. For all but the simplest cases, ions arising from multiple fragmentation events, alternative fragmentation pathways, and diverse salt adducts frequently obscure desired single-cut fragment ions. Here we show that it is possible to take advantage of predictable regularities in liquid chromatographic (LC) separation of optimized RNA digests to greatly simplify the interpretation of complex MS data. A two-dimensional analysis of extracted compound chromatograms permits straightforward and robust de novo sequencing, using a novel Monte Carlo algorithm that automatically generates bidirectional paired-end reads, pinpointing the position of modified nucleotides in a sequence. We demonstrate that these advances permit routine LC-MS sequencing of RNAs containing noncanonical nucleotides, and we furthermore examine the applicability of this approach to the study of oligonucleotides containing artificial modifications as well as those commonly observed in post-transcriptionally modified RNAs.
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Affiliation(s)
- Anders Björkbom
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.,Åbo Akademi University , Department of Biosciences, Artillerigatan 6, FI-20520 Åbo, Finland
| | - Victor S Lelyveld
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Shenglong Zhang
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Weicheng Zhang
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - J Craig Blain
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute , Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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Zhang Q, Wang Y. Differentiation of 2'-O- and 3'-O-methylated ribonucleosides by tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1096-1099. [PMID: 16750383 DOI: 10.1016/j.jasms.2006.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 04/06/2006] [Accepted: 04/07/2006] [Indexed: 05/10/2023]
Abstract
Recent studies revealed that the 3'-terminal nucleotides in plant microRNAs were methylated on the ribose at the 2' or 3' hydroxyl groups. Here we examined the fragmentation of the electrospray-produced [M + H]+ and [M - H]- ions of 2'- and 3'-O-methylated ribonucleosides. It turned out that the predominant fragmentation pathway for the [M + H]+ ions of ribose-methylated nucleosides was the neutral loss of the methylated ribose, which made it impossible to distinguish 2'-O-methylation from 3'-O-methylation by positive-ion MS/MS. However, characteristic fragment ions, resulting from the cleavage through the ribose rings, were produced for the [M - H]- ions of each pair of ribose-methylated nucleosides. In this respect, the neutral loss of a 90-Da fragment (C3H6O3) was observed for 2'-O-methylated cytidine, guanosine and adenosine, but not for their 3'-O-methylated counterparts. On the other hand, the neutral loss of a 60-Da fragment (C2H4O2) was found for 3'-O-methyluridine, but not for 2'-O-methyluridine.
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Affiliation(s)
- Qingchun Zhang
- Department of Chemistry-027, University of California at Riverside, 900 University Avenue, 92521-0403, Riverside, CA, USA
| | - Yinsheng Wang
- Department of Chemistry-027, University of California at Riverside, 900 University Avenue, 92521-0403, Riverside, CA, USA.
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