Both maintenance and avoidance of RNA-binding protein interactions constrain coding region evolution

Rosina Savisaar, Laurence Hurst

Research output: Contribution to journalArticle

10 Citations (Scopus)
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Abstract

While the principal force directing coding sequence (CDS) evolution is selection on protein function, to ensure correct gene expression CDSs must also maintain interactions with RNA-binding proteins (RBPs). Understanding how our genes are shaped by these RNA-level pressures is necessary for diagnostics and for improving transgenes. However, the evolutionary impact of the need to maintain RBP interactions remains unresolved. Are coding sequences constrained by the need to specify RBP binding motifs? If so, what proportion of mutations are affected? Might sequence evolution also be constrained by the need not to specify motifs that might attract unwanted binding, for instance because it would interfere with exon definition? Here, we have scanned human CDSs for motifs that have been experimentally determined to be recognized by RBPs. We observe two sets of motifs - those that are enriched over nucleotide-controlled null and those that are depleted. Importantly, the depleted set is enriched for motifs recognized by non-CDS binding RBPs. Supporting the functional relevance of our observations, we find that motifs that are more enriched are also slower-evolving. The net effect of this selection to preserve is a reduction in the over-all rate of synonymous evolution of 2-3% in both primates and rodents. Stronger motif depletion, on the other hand, is associated with stronger selection against motif gain in evolution. The challenge faced by our CDSs is therefore not only one of attracting the right RBPs but also of avoiding the wrong ones, all while also evolving under selection pressures related to protein structure.
Original languageEnglish
Pages (from-to)1110-1126
JournalMolecular Biology and Evolution
Volume34
Issue number5
Early online date30 Jan 2017
DOIs
Publication statusPublished - 1 May 2017

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RNA-binding proteins
RNA-Binding Proteins
RNA
Maintenance
protein
Pressure
Amino Acid Motifs
protein binding
protein structure
Transgenes
Protein Binding
Primates
transgenes
exons
preserves
binding proteins
Exons
Rodentia
Carrier Proteins
Proteins

Cite this

Both maintenance and avoidance of RNA-binding protein interactions constrain coding region evolution. / Savisaar, Rosina; Hurst, Laurence.

In: Molecular Biology and Evolution, Vol. 34, No. 5, 01.05.2017, p. 1110-1126.

Research output: Contribution to journalArticle

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