The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
Open accessAbstract
Many biological processes are RNA-mediated, but higher-order structures for most RNAs are unknown, which makes it difficult to understand how RNA structure governs function. Here we describe selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) that makes possible de novo and large-scale identification of RNA functional motifs. Sites of 2′-hydroxyl acylation by SHAPE are encoded as noncomplementary nucleotides during cDNA synthesis, as measured by massively parallel sequencing. SHAPE-MaP–guided modeling identified greater than 90% of accepted base pairs in complex RNAs of known structure, and we used it to define a new model for the HIV-1 RNA genome. The HIV-1 model contains all known structured motifs and previously unknown elements, including experimentally validated pseudoknots. SHAPE-MaP yields accurate and high-resolution secondary-structure models, enables analysis of low-abundance RNAs, disentangles sequence polymorphisms in single experiments and will ultimately democratize RNA-structure analysis.
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Cites
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Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
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Amplification of complex gene libraries by emulsion PCR
Williams, R., Peisajovich, S. G., Miller, O. J., Magdassi, S., Tawfik, D. S., & Griffiths, A. D. (2006) · Nature Methods · doi:10.1038/nmeth896 · Cited by 358
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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892
mRNA structure regulates protein expression through changes in functional half-life
Mauger, D. M., Cabral, B. J., Presnyak, V., Su, S. V., Reid, D. W., Goodman, B., Link, K., Khatwani, N., Reynders, J., Moore, M. J., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1908052116 · Cited by 555
Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines
Nance, K. D., & Meier, J. L. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00197 · Cited by 466
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
Metadata
- Authors
- Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E., & Weeks, K. M.
- Venue
- Nature Methods
- Published
- 2014-07-13
- Volume
- 11
- Issue
- 9
- Pages
- 959-965
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1985278607
- Cited by
- 654
- References
- 6
- FWCI
- 13.99
- Type
- journal article
- Language
- en
- Open access
- green
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