RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

Nat Methods. 2014 Sep;11(9):959-65. doi: 10.1038/nmeth.3029. Epub 2014 Jul 13.


Many biological processes are RNA-mediated, but higher-order structures for most RNAs are unknown, which makes it difficult to understand how RNA structure governs function. Here we describe selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) that makes possible de novo and large-scale identification of RNA functional motifs. Sites of 2'-hydroxyl acylation by SHAPE are encoded as noncomplementary nucleotides during cDNA synthesis, as measured by massively parallel sequencing. SHAPE-MaP-guided modeling identified greater than 90% of accepted base pairs in complex RNAs of known structure, and we used it to define a new model for the HIV-1 RNA genome. The HIV-1 model contains all known structured motifs and previously unknown elements, including experimentally validated pseudoknots. SHAPE-MaP yields accurate and high-resolution secondary-structure models, enables analysis of low-abundance RNAs, disentangles sequence polymorphisms in single experiments and will ultimately democratize RNA-structure analysis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • DNA Mutational Analysis / methods*
  • HIV-1 / genetics*
  • Molecular Sequence Data
  • Nucleotide Motifs
  • RNA, Viral / genetics*
  • Sequence Analysis, RNA / methods*


  • RNA, Viral

Associated data

  • SRA/SRX554885