Fig 1.

(a) RNA molecules can have diverse structural landscapes that are linked to their biological functions. Some structural landscapes, such as those for stable ribosome domains, can have a single, stable structure that is critical for function. Others may have been selected to have an equilibrium of two or three structures, such as riboswitches, that enables them to fine tune their response to small molecules or macromolecular partners. There may be other RNAs with a heterogeneous landscape, such as random RNA sequences, that may require this heterogeneity for function. (b) Chemical mapping (footprinting) experiments for probing RNA structure can be conceptualized as linear combinations of the underlying structures in the RNA’s structural ensemble. The chemical mapping profiles of an ensemble of two structures, represented here as one-dimensional heat maps, are scaled by their respective Boltzmann weights, W₁ and W₂, and added together with experimental noise to form the observed chemical mapping pro?le of an RNA. (c) Mutate-and-map (M²) experiments are measurements of perturbed versions of an underlying structural landscape. A novel method, REEFFIT uses a blind source separation framework to automatically reconstruct this landscape by joint estimation of hidden reactivity profiles and fractions for a set of structures.