mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

Wan-Jung C. Lai, Mohammad Kayedkhordeh, Erica V. Cornell, Elie Farah, Stanislav Bellaousov, Robert Rietmeijer, Enea Salsi, David H. Mathews () and Dmitri N. Ermolenko ()
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Wan-Jung C. Lai: University of Rochester
Mohammad Kayedkhordeh: University of Rochester
Erica V. Cornell: University of Rochester
Elie Farah: University of Rochester
Stanislav Bellaousov: University of Rochester
Robert Rietmeijer: University of Rochester
Enea Salsi: University of Rochester
David H. Mathews: University of Rochester
Dmitri N. Ermolenko: University of Rochester

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract The 5′ and 3′ termini of RNA play important roles in many cellular processes. Using Förster resonance energy transfer (FRET), we show that mRNAs and lncRNAs have an intrinsic propensity to fold in the absence of proteins into structures in which the 5′ end and 3′ end are ≤7 nm apart irrespective of mRNA length. Computational estimates suggest that the inherent proximity of the ends is a universal property of most mRNA and lncRNA sequences. Only guanosine-depleted RNA sequences with low sequence complexity are unstructured and exhibit end-to-end distances expected for the random coil conformation of RNA. While the biological implications remain to be explored, short end-to-end distances could facilitate the binding of protein factors that regulate translation initiation by bridging mRNA 5′ and 3′ ends. Furthermore, our studies provide the basis for measuring, computing and manipulating end-to-end distances and secondary structure in RNA in research and biotechnology.

Date: 2018
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DOI: 10.1038/s41467-018-06792-z

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