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We introduce RNA G-quadruplex sequencing (rG4-seq), a transcriptome-wide RNA G-quadruplex (rG4) profiling method that couples rG4-mediated reverse transcriptase stalling with next-generation sequencing. Using rG4-seq on polyadenylated-enriched HeLa RNA, we generated a global in vitro map of thousands of canonical and noncanonical rG4 structures. We characterize rG4 formation relative to cytosine content and alternative RNA structure stability, uncover rG4-dependent differences in RNA folding and show evolutionarily conserved enrichment in transcripts mediating RNA processing and stability.

Original publication

DOI

10.1038/nmeth.3965

Type

Journal article

Journal

Nat Methods

Publication Date

10/2016

Volume

13

Pages

841 - 844

Keywords

Cytosine, G-Quadruplexes, Guanine, HeLa Cells, High-Throughput Nucleotide Sequencing, Humans, RNA Stability, RNA, Messenger, Sequence Analysis, RNA, Transcriptome