Structural imprints in vivo decode RNA regulatory mechanisms

By R. Spitale, Ryan A. Flynn, Qiangfeng Cliff Zhang, Pete Crisalli, Byron Lee, Jong-Wha Jung, Hannes Y. Kuchelmeister, Pedro J. Batista, E. Torre, E. Kool and 1 more. Nature, 2015

670 citations recorded by the source corpus.

Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2′-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA–protein interactions and N6-methyladenosine (m6A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a2dc39fd57f1df90a58fc880ba40a26daa025524

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Citations in the corpus

SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features (2016, background): “have recently demonstrated that the RNA structural imprints as a powerful predictor of m6A sites (41).”
Mechanisms of long noncoding RNA function in development and disease (2016, methodology): “accelerated by recently developed techniques combined with high-throughput sequencing, such as SHAPE-MaP and icSHAPE [19, 20].”
Recent advances in RNA structurome (2022, methodology): “icSHAPE In vivo NAI-N3 Mouse cells, human embryonic stem cells (hESCs) SARS-CoV-2 (Spitale et al., 2015; Sun et al., 2021a; Wang et al., 2021b) Pros: In vivo, probe four nucleotides, high signalto-noise ratio Cons: No dsRNA information”
Rethinking m6A Readers, Writers, and Erasers (2017, background): “Subsequent transcriptome-wide structure mapping demonstrated that m6A is found in regions with reduced structure (Spitale et al. 2015), supporting the overall idea that m6A can create greater accessibility to a region of RNA by impairing local RNA folding.”
RNA duplex map in living cells reveals higher order transcriptome structure (2016, methodology): “Compared with icSHAPE and DMS-seq, which measure nucleotide flexibility (Ding et al., 2014; Rouskin et al., 2014; Spitale et al., 2015), PARIS directly determines the locations of long-range duplexes and can resolve complex structures such as pseudoknots and alternative structures.”
RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation (2015, background): “Indeed, structural mapping of mRNA insidemammalian cells has revealed that themethylation regions of mRNA tend to lack secondary structures, highlighting the potential role of m(6)A in shaping RNA structures (Schwartz et al. 2013; Wan et al. 2014; Spitale et al. 2015).”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “…1987; Latham and Cech, 1989; Moazed and Noller, 1986), have identified transcriptome-wide RNA base-pairing in vivo (Ding et al., 2014; Rouskin et al., 2014; Spitale et al., 2015; Wan et al., 2014) including within the coding region of mRNAs, suggesting a function independent of coding potential.”
Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions (2022, background): “The secondary structures of RNA are generated by icSHAPE (in vivo click selective 2’-hydroxyl acylation and profiling experiment) [57] in the HeLa cell environment.”