rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

Nat Methods. 2016 Oct;13(10):841-4. doi: 10.1038/nmeth.3965. Epub 2016 Aug 29.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cytosine / metabolism
  • G-Quadruplexes*
  • Guanine / metabolism
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • RNA Stability
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA / methods*
  • Transcriptome / genetics*


  • RNA, Messenger
  • Guanine
  • Cytosine