2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction

Authors:
Ronny Lorenz;Stephan H. Bernhart;Jing Qin;Christian Honer zu Siederdissen;Andrea Tanzer;Fabian Amman;Ivo L. Hofacker;Peter F. Stadler
Affiliations:
University of Vienna, Vienna;University of Leipzig, Leipzig;Max Planck Institute for Mathematics in the Sciences, Leipzig and University of Leipzig, Leipzig;University of Vienna, Vienna;University of Vienna, Vienna and Center for Genomic Regulation (CRG), Barcelona;University of Vienna, Vienna;University of Vienna, Vienna and University of Copenhagen;University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2013

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Abstract

G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5脢鹿UTR of protein coding mRNAs.