Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology

Gray, Elizabeth; Beringer, Daniel M; Meyer, Michelle M.

doi:10.1042/bst20191060

Cited by 4 publications

(1 citation statement)

References 60 publications

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“…The evolution of regulatory RNAs is highly dynamic and, when compared to their protein counterparts, only poorly understood [36,[60][61][62]. Regulatory RNAs can be expressed from IGRs, as well as from the 5'-and 3'UTRs of mRNAs, and the coding sequence [63].…”

Section: Discussionmentioning

confidence: 99%

ChimericFragments: Computation, analysis, and visualization of global RNA networks

Siemers,

Lippegaus,

Papenfort

2023

Preprint

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RNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.

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Section: Discussionmentioning

confidence: 99%

ChimericFragments: Computation, analysis, and visualization of global RNA networks

Siemers,

Lippegaus,

Papenfort

2023

Preprint

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Two for one: regulatory RNAs that encode small proteins

Aoyama,

Storz

2023

Trends in Biochemical Sciences

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A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding

Mukherjee

Retwitzer

Hubbell

et al. 2023

Briefings in Bioinformatics

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Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found to regulate a large number of genes/operons in bacteria. Presently, >50 bacterial riboswitch classes have been discovered, but only the thiamine pyrophosphate riboswitch class is detected in a few eukaryotes like fungi, plants and algae. One of the most important challenges in riboswitch research is to discover existing riboswitch classes in eukaryotes and to understand the evolution of bacterial riboswitches. However, traditional search methods for riboswitch detection have failed to detect eukaryotic riboswitches besides just one class and any distant structural homologs of riboswitches. We developed a novel approach based on inverse RNA folding that attempts to find sequences that match the shape of the target structure with minimal sequence conservation based on key nucleotides that interact directly with the ligand. Then, to support our matched candidates, we expanded the results into a covariance model representing similar sequences preserving the structure. Our method transforms a structure-based search into a sequence-based search that considers the conservation of secondary structure shape and ligand-binding residues. This method enables us to identify a potential structural candidate in fungi that could be the distant homolog of bacterial purine riboswitches. Further, phylogenomic analysis and evolutionary distribution of this structural candidate indicate that the most likely point of origin of this structural candidate in these organisms is associated with the loss of traditional purine riboswitches. The computational approach could be applicable to other domains and problems in RNA research.

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Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology

Cited by 4 publications

References 60 publications

ChimericFragments: Computation, analysis, and visualization of global RNA networks

ChimericFragments: Computation, analysis, and visualization of global RNA networks

Two for one: regulatory RNAs that encode small proteins

A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding

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