Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro

Sarah E. Harris, Maria S. Alexis, Gilbert Giri, Francisco F. Cavazos, Yue Hu, Jernej Murn, Maria M. Aleman, Christopher B. Burge and Daniel Dominguez ()
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Sarah E. Harris: University of North Carolina
Maria S. Alexis: Massachusetts Institute of Technology
Gilbert Giri: University of North Carolina
Francisco F. Cavazos: University of North Carolina
Yue Hu: University of North Carolina
Jernej Murn: University of California
Maria M. Aleman: University of North Carolina
Christopher B. Burge: Massachusetts Institute of Technology
Daniel Dominguez: University of North Carolina

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examine interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstitute the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.

Date: 2024
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DOI: 10.1038/s41467-024-52231-7

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