RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

By Nathan A. Siegfried, Steven Busan, Greggory M. Rice, J. Nelson, Kevin M. Weeks. Nature Methods, 2014

550 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c821135ba3132bb7744e6183400c4740fb551b3d

Citations in the corpus

• Pervasive tertiary structure in the dengue virus RNA genome (2018, unknown): “The minimum free-energy secondary structure (inverted black arcs) was obtained using both 1M7 and differential SHAPE reactivities as constraints (1, 12, 13).”
• RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (2017, unknown): “Before the experiment, homologous structures identical to this particular riboswitch were already available (Stoddard et al. 2010).”
• Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus (2018, unknown): “(ii) RNA was converted to cDNA using Superscript III (Thermo) using a manganese reverse transcriptase protocol (Siegfried et al., 2014) to promote reverse-transcription through formaldehyde crosslinks on RNA.”
• The Landscape of long non-coding RNA classification (2015, unknown): “Among others, these methods include CLIP-seq [131] for detection and measurement of RNA – protein interactions, SHAPE-seq [132] for analysis of RNA secondary structure, ChIRP [133] for measurement of RNA–chromatin interactions, and GRO-seq (Box 1) to measure transcription [134].”
• Recent advances in RNA structurome (2022, unknown): “RNA structurome, high-throughput techniques, genome-wide, 3D structure, RNA secondary structure, SARS-CoV-2, decoding, function © Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2022 life.scichina.com link.springer.com SCIENCE CHINA Life Sciences †Contributed equally to”