The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo
Open accessAbstract
Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.
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Cites
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., & Jaffrey, S. R. (2012) · Cell · doi:10.1016/j.cell.2012.05.003 · Cited by 4,223
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Self-citationCoding-Sequence Determinants of Gene Expression in Escherichia coli
Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2014) · Nature · doi:10.1038/nature12756 · Cited by 775
Landscape and variation of RNA secondary structure across the human transcriptome
Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R. C., Snyder, M. P., Segal, E., et al. (2014) · Nature · doi:10.1038/nature12946 · Cited by 555
Control of mammalian translation by mRNA structure near caps
Babendure, J. R., Babendure, J. L., Ding, J.-H., & Tsien, R. Y. (2006) · RNA · doi:10.1261/rna.2309906 · Cited by 339
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The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution
Safra, M., Sas-Chen, A., Nir, R., Winkler, R., Nachshon, A., Bar-Yaacov, D., Erlacher, M., Rossmanith, W., Stern-Ginossar, N., & Schwartz, S. (2017) · Nature · doi:10.1038/nature24456 · Cited by 646
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28776-w · Cited by 399
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2021) · doi:10.1101/2021.03.29.437587 · Cited by 399
Translational control through ribosome heterogeneity and functional specialization
Gay, D. M., Lund, A. H., & Jansson, M. D. (2022) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2021.07.001 · Cited by 141
Metadata
- Authors
- Zubradt, M., Gupta, P., Persad, S., Lambowitz, A. M., Weissman, J. S., & Rouskin, S.
- Venue
- Nature Methods
- Published
- 2016-11-07
- Volume
- 14
- Issue
- 1
- Pages
- 75-82
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2554920439
- Cited by
- 454
- References
- 6
- FWCI
- 13.09
- Type
- journal article
- Language
- en
- Open access
- green
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