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Method Article
Shankar Balasubramanian
Department of Chemistry, University of Cambridge, Cambridge, UK. Cancer Research UK, Cambridge Institute, Cambridge, UK.
Corresponding Author
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Alternative RNA structures such as RNA G-quadruplexes (rG4s) are often important in gene regulation and cellular processes, however, there is no experimental method for transcriptome-wide assessment of rG4 structures. Here, we introduce a novel approach called rG4-seq, which marries rG4-mediated reverse transcriptase stalling with next-generation sequencing to enable in vitro profiling of rG4 structures on a transcriptomic scale at nucleotide resolution. Upon high-throughput sequencing and bioinformatic analysis, the structural features and distribution of rG4s could be determined, as recently reported using extracted polyadenylated-enriched RNA from HeLa cells (Kwok et al, 2016). rG4-seq is readily applicable to any transcriptome, allowing global studies of rG4 structures and their potential regulatory roles in biology.
Keywords
RNA structure, G-quadruplex, transcriptome, gene regulation, rG4-seq, next-generation sequencing
The authors declare no competing financial interests.
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Associated Publications
rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome
by Chun Kit Kwok, Giovanni Marsico, Aleksandr B Sahakyan, +2
Nature Methods (20 September, 2016)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Shankar Balasubramanian
Department of Chemistry, University of Cambridge, Cambridge, UK. Cancer Research UK, Cambridge Institute, Cambridge, UK.
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 20 Sep, 2016
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
Alternative RNA structures such as RNA G-quadruplexes (rG4s) are often important in gene regulation and cellular processes, however, there is no experimental method for transcriptome-wide assessment of rG4 structures. Here, we introduce a novel approach called rG4-seq, which marries rG4-mediated reverse transcriptase stalling with next-generation sequencing to enable in vitro profiling of rG4 structures on a transcriptomic scale at nucleotide resolution. Upon high-throughput sequencing and bioinformatic analysis, the structural features and distribution of rG4s could be determined, as recently reported using extracted polyadenylated-enriched RNA from HeLa cells (Kwok et al, 2016). rG4-seq is readily applicable to any transcriptome, allowing global studies of rG4 structures and their potential regulatory roles in biology.
The authors declare no competing financial interests.
Loading...
Associated Publications
rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome
by Chun Kit Kwok, Giovanni Marsico, Aleksandr B Sahakyan, +2
Nature Methods (20 September, 2016)