Mapping circular RNA structures in living cells by SHAPE-MaP

Guo, Si-Kun; Fang, Nan; Liu, Chu-Xiao; Yang, Li

doi:10.1016/j.ymeth.2021.01.011

Cited by 10 publications

(8 citation statements)

References 23 publications

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“…NAI (2-methylnicotinic acid imidazolide) probing in vitro gave rise to consistent and reliable signals for SHAPE-MaP assays with $300 bp long tiling PCR products for each circular RNA, using POLR2A circles parallelly produced via different strategies as an example (Figure 3B). An in-house pipeline was developed to analyze in vitro SHAPE-MaP results (Guo et al, 2021). Examined structures of the spiked-in human 5S rRNA in circSHAPE-MaP duplicates were highly correlated and comparable to the reported 5S rRNA structure (Spitale et al, 2013) (Figure S5A), confirming that these independent SHAPE-MaP reactions were reliable for comparison among circular RNAs produced via methods I-III.…”

Section: Circularized Rnas Containing Unwanted Extra Fragments (E1 + ...mentioning

confidence: 65%

“…We performed in vitro circSHAPE-MaP (selective 2 0 -hydroxyl acylation analyzed by primer extension and mutational profiling for circular RNAs) to compare circular RNAs produced by these different methods (Figure 3A). Such in vitro circSHAPE-MaP assays were optimized from our previously developed in cell circSHAPE-MaP (Guo et al, 2021;Liu et al, 2019). In brief, two sets of divergent primers crossing the ligation junction site (JS) were designed for each circular RNA.…”

Section: Circularized Rnas Containing Unwanted Extra Fragments (E1 + ...mentioning

confidence: 99%

“…In vitro SHAPE probing (with/without proteins) In vitro SHAPE probing was performed as described (Guo et al, 2021;Liu et al, 2019;Smola et al, 2015) with modifications. In brief, in vitro produced and purified human 5S rRNA/circular RNAs were refolded in 3.3 3 folding buffer (333 mM HEPES, pH 8.0; 333 mM NaCl; 33 mM MgCl 2 ).…”

Section: In Vitro Activation Assay Of Pkrmentioning

confidence: 99%

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RNA circles with minimized immunogenicity as potent PKR inhibitors

et al. 2022

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Section: Circularized Rnas Containing Unwanted Extra Fragments (E1 + ...mentioning

confidence: 65%

Section: Circularized Rnas Containing Unwanted Extra Fragments (E1 + ...mentioning

confidence: 99%

Section: In Vitro Activation Assay Of Pkrmentioning

confidence: 99%

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RNA circles with minimized immunogenicity as potent PKR inhibitors

et al. 2022

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“…Chemical-based in vitro methods include structure-seq ( 134 ), dimethyl sulfate sequencing (DMS-seq) ( 135 ), and high-throughput sequencing for chemical probing of RNA structure (Mod-seq) ( 136 ). Chemical-based in vivo methods include chemical inference of RNA structures sequencing (CIRS-seq) ( 137 ), selective 20-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) ( 138 ), in vivo click selective 2-hydroxyl acylation and profiling experiment (icSHAPE) ( 139 ), and mapping RNA-RNA interactome and RNA structure in vivo (MARIO) ( 140 ). Combining data from both chemical- and enzyme- based sequencing approaches is considered ideal to gain a more comprehensive RNA structural information.…”

Section: Technology-based Omicsmentioning

confidence: 99%

Advances and Trends in Omics Technology Development

2022

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The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

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“…Furthermore, the functions of many of these RNA structures in the cell remain poorly defined, and many researchers are invesigating methodologies for the selective detection of these structures. [10][11][12][13][14] This motivated the authors to investigate the development of a methodology for selective chemical modification of these structures. This study designed the molecules to bind to each structure and react through proximity effects.…”

Section: Introductionmentioning

confidence: 99%

Selective Chemical Modification to the Higher‐Order Structures of Nucleic Acids

Nagatsugi

Onizuka

2022

The Chemical Record

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DNA and RNA can adopt a variety of stable higher‐order structural motifs, including G‐quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher‐order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher‐order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher‐order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher‐order structures of nucleic acids is also underway. In this personal account, we focus on the following higher‐order structures of nucleic acids, double‐stranded DNA containing the abasic site, T−T/U−U mismatch structure, and G‐quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.

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Mapping circular RNA structures in living cells by SHAPE-MaP

Cited by 10 publications

References 23 publications

RNA circles with minimized immunogenicity as potent PKR inhibitors

RNA circles with minimized immunogenicity as potent PKR inhibitors

Advances and Trends in Omics Technology Development

Selective Chemical Modification to the Higher‐Order Structures of Nucleic Acids

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