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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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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.
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)
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.
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)