Learning the RNA World by structural covariations

Many apparently noncoding RNA transcripts are observed for which we don't know the purpose of their existence. Identifying an RNA transcript with a conserved structure is important support for a possible structural RNA function for that transcript. This question is different from structure prediction because any RNA folds into some structure, regardless of whether that structure has any conserved biological function. We have produced a statistical test to assess when an RNA alignment presents evidence of a conserved RNA structure. The program named R-scape (RNA structural covariations above phylogenetic expectation) is computationally lightweight (which is unusual for structural RNA applications). And here is R-scape's webserver.

As more noncoding RNA transcripts are investigated, a picture emerges in which a substantial number of transcripts appear to perform roles where neither the actual RNA sequence nor any RNA structure are relevant, instead depending just on the fact that they are transcribed. Others appear to encode some small previously unidentified peptides. In this context, identifying a (possibly scarce) subset of transcripts with a conserved RNA structure becomes a special pursuit that could unveil new RNA functions in a background of other noncoding RNA transcripts.

This laboratory develops computational probabilistic models to understand RNA structure. We also work with models of sequence evolution in order to bring phylogenetic power to the question of remote homology recognition. Lately, we are also very interested in asking causal questions to experimentally determined data.

Recent publications

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Department of Molecular & Cellular Biology
Northwest Building
52 Oxford Street
Harvard University
Cambridge MA 02138, USA


RNA Structural Covariations Above Phylogenetic Expectation.

Current version: 1.5.16 (August 2020).

R-scape version 1.5.16 , August 2020.
CaCoFold systematically finds RNA pseudoknots, triplets and alternative structures with covariation support. Fast.

See Coronavirus 3'UTR pseudoknot.

CaCoFold proposes one more helix with covariation support than the Rfam14.2 structure (RF00165).

RNA structure prediction using positive and negative evolutionary information UPDATED 25 May 2020.

Adds comparisons for 21 structural RNAs of the CaCoFold structure to crystal structures for 21 structural RNAs.

See CaCoFold analysis of the Cobalamin Riboswitch(RF00174).