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Abstract
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.
Highlights
Experimental work and genomic sequence analysis have revealed that RNAs have a widespread role inside the cell [1,2,3,4,5]
For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information
Using a rigorously selected set of riboswitch families with complex structures, we show that Direct Coupling Analysis (DCA) can efficiently be integrated into existing tools for RNA secondary- and tertiary-structure prediction
Summary
Experimental work and genomic sequence analysis have revealed that RNAs have a widespread role inside the cell [1,2,3,4,5]. In addition to the transmission of genetic information, non-coding RNAs catalyze biochemical reactions and have a crucial role in a multitude of regulatory processes. While some functional RNA act essentially via their single-stranded information or in the context of RNA-protein complexes, in other cases function is directly tied to three-dimensional (3D) RNA structure [6]. Gaining such structural knowledge is important for understanding function. Experimental determination of RNA structure, remains challenging. Thanks to advances in sequencing technology, many RNAs have been sequenced in different organisms and classified into homologous families in the
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