DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo
Top Cited Papers
- 7 November 2016
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 14 (1), 75-82
- https://doi.org/10.1038/nmeth.4057
Abstract
DMS-MaPseq enables genome-wide and target-specific RNA secondary structure probing of even rare or heterogeneously structured RNAs in vivo and was used to study structure involved in translation regulation as well as nascent transcripts. 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.Keywords
This publication has 47 references indexed in Scilit:
- SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing dataGenome Research, 2012
- Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop CodonsCell, 2012
- Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)Proceedings of the National Academy of Sciences of the United States of America, 2011
- A′-form RNA helices are required for cytoplasmic mRNA transport in DrosophilaNature Structural & Molecular Biology, 2010
- Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteineNucleic Acids Research, 2009
- VARNA: Interactive drawing and editing of the RNA secondary structureBioinformatics, 2009
- Coding-Sequence Determinants of Gene Expression in Escherichia coliScience, 2009
- Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome ProfilingScience, 2009
- Accurate SHAPE-directed RNA structure determinationProceedings of the National Academy of Sciences of the United States of America, 2009
- Messenger RNA targeting to endoplasmic reticulum stress signalling sitesNature, 2008