Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq

Sunny Y. Yang, David Monchaud, Judy M. Y. Wong

Published: 2022-02-08 DOI: 10.1038/s41596-021-00671-6

G-quadruplexes

G4RP-seq

RNA profiling

cross-linking

BioTASQ

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Guanine-rich RNAs can fold into four-stranded structures, termed G-nobreakquadruplexes (G4-RNAs), and participate in a wide range of biological processes. Here we describe in detail a G4-RNA-specific precipitation (G4RP) protocol, which enables the transc
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
References
ACKNOWLEDGMENTS

Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K. & Neidle, S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 34, 5402–5415 (2006).
Spiegel, J., Adhikari, S. & Balasubramanian, S. The structure and function of DNA G-quadruplexes. Trends Chem. 2, 123–136 (2020).
Rhodes, D. & Lipps, H. J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627–8637 (2015).
Fay, M. M., Lyons, S. M. & Ivanov, P. RNA G-quadruplexes in biology: principles and molecular mechanisms. J. Mol. Biol. 429, 2127–2147 (2017).
Marsico, G. et al. Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 47, 3862–3874 (2019).
Maizels, N. G4‐associated human diseases. EMBO Rep. 16, 910–922 (2015).
Raguseo, F., Chowdhury, S., Minard, A. & Di Antonio, M. Chemical-biology approaches to probe DNA and RNA G-quadruplex structures in the genome. Chem. Commun. 56, 1317–1324 (2020).
Puig Lombardi, E. & Londoño-Vallejo, A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res. 48, 1603 (2019).
Monchaud, D. Quadruplex detection in human cells. Annu. Rep. Med. Chem. http://doi.org/10.1016/bs.armc.2020.04.007 (2020).
Kwok, C. K. & Merrick, C. J. G-Quadruplexes: prediction, characterization, and biological application. Trends Biotechnol 35, 997–1013 (2017).
Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013).
Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877–881 (2015).
Hänsel-Hertsch, R., Spiegel, J., Marsico, G., Tannahill, D. & Balasubramanian, S. Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing. Nat. Protoc. 13, 551–564 (2018).
Zheng, K. et al. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res. http://doi.org/10.1093/nar/gkaa841 (2020).
Kwok, C. K., Marsico, G., Sahakyan, A. B., Chambers, V. S. & Balasubramanian, S. rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat. Methods 13, 841–844 (2016).
Yang, S. Y. et al. Transcriptome-wide identification of transient RNA G-quadruplexes in human cells. Nat. Commun. 9, 4730 (2018).
Mendoza, O., Bourdoncle, A., Boulé, J.-B., Brosh, R. M. & Mergny, J.-L. G-quadruplexes and helicases. Nucleic Acids Res. 44, 1989–2006 (2016).
Varshney, D., Spiegel, J., Zyner, K., Tannahill, D. & Balasubramanian, S. The regulation and functions of DNA and RNA G-quadruplexes. Nat. Rev. Mol. Cell Biol. 21, 459–474 (2020).
Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019).
Rodriguez, R. et al. A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. J. Am. Chem. Soc. 130, 15758–15759 (2008).
Guo, J. U. & Bartel, D. P. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science 353, aaf5371–aaf5371 (2016).
Umar, M. I., Ji, D., Chan, C.-Y. & Kwok, C. K. G-quadruplex-based fluorescent turn-on ligands and aptamers: from development to applications. Molecules 24, 2416 (2019).
Stefan, L. & Monchaud, D. Applications of guanine quartets in nanotechnology and chemical biology. Nat. Rev. Chem. 3, 650–668 (2019).
Haudecoeur, R., Stefan, L., Denat, F. & Monchaud, D. A model of smart G-quadruplex ligand. J. Am. Chem. Soc. 135, 550–553 (2013).
Laguerre, A. et al. A twice-as-smart synthetic G-quartet: PyroTASQ is both a smart quadruplex ligand and a smart fluorescent probe. J. Am. Chem. Soc. 136, 12406–12414 (2014).
Laguerre, A. et al. Visualization of RNA-quadruplexes in live cells. J. Am. Chem. Soc. 137, 8521–8525 (2015).
Renard, I. et al. Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol. Nucleic Acids Res. 47, 5502–5510 (2019).
Gilbert, C. & Svejstrup, J. Q. RNA immunoprecipitation for determining RNA–protein associations in vivo. Curr. Protoc. Mol. Biol. 75, 27.4.1–27.4.11 (2006).
Müller, S., Kumari, S., Rodriguez, R. & Balasubramanian, S. Small-molecule-mediated G-quadruplex isolation from human cells. Nat. Chem. 2, 1095–1098 (2010).
Neidle, S. Quadruplex nucleic acids as novel therapeutic targets. J. Med. Chem. 59, 5987–6011 (2016).
Kubota, M., Tran, C. & Spitale, R. C. Progress and challenges for chemical probing of RNA structure inside living cells. Nat. Chem. Biol. 11, 933–941 (2015).
Sharma, E., Sterne-Weiler, T., O’Hanlon, D. & Blencowe, B. J. Global mapping of human RNA–RNA interactions. Mol. Cell 62, 618–626 (2016).
Nguyen, T. C. et al. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO. Nat. Commun. 7, 12023 (2016).
Aw, J. G. A. et al. In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Mol. Cell 62, 603–617 (2016).
Lu, Z. et al. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell 165, 1267–1279 (2016).
Ruggiero, E. & Richter, S. N. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res. 46, 3270–3283 (2018).
Saranathan, N. & Vivekanandan, P. G-quadruplexes: more than just a kink in microbial genomes. Trends Microbiol. 27, 148–163 (2019).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2012).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Aranda, P. S., LaJoie, D. M. & Jorcyk, C. L. Bleach gel: a simple agarose gel for analyzing RNA quality. Electrophoresis 33, 366–369 (2012).
Goecks, J., Nekrutenko, A. & Taylor, J., Galaxy Team, T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
Read, M. et al. Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors. Proc. Natl Acad. Sci. USA 98, 4844–4849 (2001).
Heald, R. A. et al. Antitumor polycyclic acridines. 8.(1) Synthesis and telomerase-inhibitory activity of methylated pentacyclic acridinium salts. J. Med. Chem. 45, 590–597 (2002).

Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq

推荐阅读