DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

Nat Methods. 2017 Jan;14(1):75-82. doi: 10.1038/nmeth.4057. Epub 2016 Nov 7.


Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

Publication types

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

MeSH terms

  • Computational Biology
  • Genome, Human*
  • HEK293 Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mutation / genetics
  • Nucleic Acid Conformation
  • Protein Biosynthesis
  • RNA / chemistry*
  • RNA / genetics*
  • RNA-Binding Proteins / genetics*
  • Sequence Analysis, RNA
  • Sulfuric Acid Esters / chemistry*


  • FXR2 protein, human
  • RNA-Binding Proteins
  • Sulfuric Acid Esters
  • RNA
  • dimethyl sulfate