In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

By Yiliang Ding, Yin Tang, C. Kwok, P. Bevilacqua, S. Assmann. Nature, 2013

765 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9487a3a4fc32e41a9cd949d3045e994b12db50e8

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In Molecular Biology

Citations in the corpus

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.”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, neutral): “, 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.”
Structural imprints in vivo decode RNA regulatory mechanisms (2015, methodology): “Metagene analysis of translation sites, pause site, m6A sites and protein binding sites—We calculated metagene structure profile around different functional sits by averaging all valid reactivity score R: (1), 10 nts upstream and downstream of the RNA methylation m6A site, as determined in by our la”
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) (2014, neutral): “3b ) has not been implemented in prior massively parallel sequencing-based RNA structure analyses 5,7,8,10,11,50 ; the authors of SHAPE-seq 8 and Mod-seq 51 have independently noted the importance of read depth in obtaining quantitative RNA structure probing information.”
Recent advances in RNA structurome (2022, background): “Structure-seq In vivo DMS Arabidopsis, rice (Deng et al., 2018; Ding et al., 2015; Ding et al., 2014; Tack et al., 2020) Pros: In vivo Cons: Only probe A and C, no dsRNA information”
NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017, methodology): “DMS-seq or Structure-seq uses the small molecule dimethyl sulfate (DMS) to modify adenines and cytosines in single-stranded states both in vivo and in vitro (64,65).”