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A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures.

ABSTRACT: A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and non-canonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these non-standard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via introduction of a 2-dimensional hydrophobic end-labeling strategy into traditional mass spectrometry-based sequencing (2D HELS MS Seq) to allow de novo sequencing of RNA mixtures and enhance sample usage efficiency. Our method can directly read out the complete sequence, while identifying, locating, and quantifying base modifications accurately in both single and mixed RNA samples containing multiple different modifications at single-base resolution. Our method can also quantify stoichiometry/percentage of modified RNA versus its canonical counterpart RNA, simulating a real biological sample where modifications exist but may not be 100% at a particular site in the RNA. This method is a critical step towards fully sequencing real complex cellular RNA samples of any type and containing any modification type and can also be used in the quality control of modified therapeutic RNAs.

SUBMITTER: Zhang N

PROVIDER: S-EPMC6847078 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures.

Zhang Ning N Shi Shundi S Jia Tony Z TZ Ziegler Ashley A Yoo Barney B Yuan Xiaohong X Li Wenjia W Zhang Shenglong S

Nucleic acids research 20191101 20

A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and non-canonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these non-standard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via introduction of a 2-dimensional hydrophobic end-labeling strategy int ...[more]

PMID: 31504795

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Project description:Exposure to natural food contaminants during infancy may influence health consequences later in life. Hence, breast milk may serve as a vehicle to transport these contaminants, including mycotoxins, from mothers to their infants. Analytical methods mostly focused on single exposures in the past, thus neglecting co-occurrences and mixture effects. Here, we present a highly sensitive multi-biomarker approach by a sophisticated combination of steps during sample preparation including a Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) extraction followed by a solid phase extraction (SPE) cleanup and utilizing stable isotopes for compensating challenging matrix effects. The assay was validated in-house, reaching limits of detection (LOD) for all 34 analytes in the range of 0.1 to 300 ng/L with satisfying extraction efficiencies (75-109%) and stable intermediate precisions (1-18%) for most analytes. Compared to a similar multi-mycotoxin assay for breast milk, LOD values were decreased by a factor of 2-60x enabling the assessment of chronic low-dose exposures. The new method was applied to a small set of Nigerian breast milk samples (n = 3) to compare results with already published data. Concentration levels of samples that were found to be contaminated before could be confirmed. In addition, other mycotoxins were determined in all three samples, for example the newly investigated alternariol monomethyl ether (AME) was found for the first time in this biological fluid at concentrations up to 25 ng/L. Moreover, in a pooled Austrian sample obtained from a milk bank, trace amounts of multiple mycotoxins including AME (1.9 ng/L), beauvericin (5.4 ng/L), enniatin B (4.7 ng/L), enniatin B1 (<LOQ), ochratoxin A (<LOQ) and the estrogenic zearalenone (<LOQ) confirmed co-occurrence and exposure even in a country with high food safety standards. In conclusion, the method facilitates the determination of mycotoxins at ultra-trace levels in breast milk, enabling the generation of occurrence data necessary for comprehensive co-exposure assessment.

Dataset Information

A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures.

Publications

A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures.

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