Consistent global structures of complex RNA states through multidimensional chemical mapping
- Stanford University, United States
Abstract
Accelerating discoveries of noncoding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D IRES regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.
Article and author information
Author details
Reviewing Editor
- Timothy W Nilsen, Case Western Reserve University, United States
Version history
- Received: March 19, 2015
- Accepted: June 2, 2015
- Accepted Manuscript published: June 2, 2015 (version 1)
- Version of Record published: July 8, 2015 (version 2)
Copyright
© 2015, Yu Cheng et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Consistent global structures of complex RNA states through multidimensional chemical mapping
eLife 4:e07600.
https://doi.org/10.7554/eLife.07600
Further reading
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- Biochemistry and Chemical Biology
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