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Elife. 2015 Jun 2;4:e07600. doi: 10.7554/eLife.07600.

Consistent global structures of complex RNA states through multidimensional chemical mapping.

Author information

1
Department of Biochemistry, Stanford University, Stanford, United States.
2
Biomedical Informatics Program, Stanford University, Stanford, United States.

Abstract

Accelerating discoveries of non-coding 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 internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

KEYWORDS:

biochemistry; biophysics; high-throughput; next-generation sequencing; non-coding RNA; none; riboswitches; ribozymes; structural biology; structure prediction

Comment in

PMID:
26035425
PMCID:
PMC4495719
DOI:
10.7554/eLife.07600
[Indexed for MEDLINE]
Free PMC Article

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