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RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions

Authors Kimon Boehmer, Sarah J. Berkemer , Sebastian Will , Yann Ponty

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Author Details

Kimon Boehmer
  • Laboratoire d'Informatique de l'Ecole Polytechnique (LIX UMR 7161), Institut Polytechnique de Paris, France
Sarah J. Berkemer
  • Laboratoire d'Informatique de l'Ecole Polytechnique (LIX UMR 7161), Institut Polytechnique de Paris, France
Sebastian Will
  • Laboratoire d'Informatique de l'Ecole Polytechnique (LIX UMR 7161), Institut Polytechnique de Paris, France
Yann Ponty
  • Laboratoire d'Informatique de l'Ecole Polytechnique (LIX UMR 7161), Institut Polytechnique de Paris, France

Funding

  • Boehmer, Kimon: ANR-funded SYNORG project (ANR-23-CE44-0027).
  • Berkemer, Sarah J.: ANR-funded SYNORG project (ANR-23-CE44-0027).
  • Will, Sebastian: ANR-funded SYNORG project (ANR-23-CE44-0027).
  • Ponty, Yann: ANR-funded SYNORG project (ANR-23-CE44-0027).

Cite AsGet BibTex

Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 18:1-18:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.WABI.2024.18

Abstract

RNAs composed of Triplet Repeats (TR) have recently attracted much attention in the field of synthetic biology. We study the mimimum free energy (MFE) secondary structures of such RNAs and give improved algorithms to compute the MFE and the partition function. Furthermore, we study the interaction of multiple RNAs and design a new algorithm for computing MFE and partition function for RNA-RNA interactions, improving the previously known factorial running time to exponential. In the case of TR, we show computational hardness but still obtain a parameterized algorithm. Finally, we propose a polynomial-time algorithm for computing interactions from a base set of RNA strands and conduct experiments on the interaction of TR based on this algorithm. For instance, we study the probability that a base pair is formed between two strands with the same triplet pattern, allowing an assessment of a notion of orthogonality between TR.

Subject Classification

ACM Subject Classification
  • Applied computing → Bioinformatics
  • Theory of computation → Dynamic programming
  • Applied computing → Molecular sequence analysis
  • Theory of computation → Problems, reductions and completeness
Keywords
  • RNA folding
  • RNA interactions
  • triplet repeats
  • dynamic programming
  • NP-hardness

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Supplementary Materials

References

  1. Dilimulati Aierken and Jerelle A Joseph. Accelerated simulations of rna phase separation: a systematic study of non-redundant tandem repeats. bioRxiv, pages 2023-12, 2023. Google Scholar
  2. Can Alkan, Emre Karakoc, Joseph H Nadeau, S Cenk Sahinalp, and Kaizhong Zhang. Rna-rna interaction prediction and antisense rna target search. Journal of Computational Biology, 13(2):267-282, 2006. Google Scholar
  3. Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. Soupfold. Software, version 1.0., ANR-funded SYNORG project (ANR-23-CE44-0027), swhId: https://archive.softwareheritage.org/swh:1:dir:3cb0c3e63356a53b4fa150d14e4c273678ef638d;origin=https://github.com/kimonboehmer/soupfold;visit=swh:1:snp:f794ddf74edf254cad245dde5b04e9246a8d5b3b;anchor=swh:1:rev:8f0ec2f33f598eb389f5c9ff379ea48d5770790e (visited on 2024-08-16). URL: https://github.com/kimonboehmer/soupfold/.
  4. Alin Bostan, Frédéric Chyzak, Gr égoire Lecerf, Bruno Salvy, and Éric Schost. Differential equations for algebraic functions. In C. W. Brown, editor, ISSAC'07: Proceedings of the 2007 international symposium on Symbolic and algebraic computation, pages 25-32. ACM Press, 2007. URL: https://doi.org/10.1145/1277548.1277553.
  5. Karl Bringmann, Fabrizio Grandoni, Barna Saha, and Virginia Vassilevska Williams. Truly subcubic algorithms for language edit distance and rna folding via fast bounded-difference min-plus product. SIAM Journal on Computing, 48(2):481-512, 2019. URL: https://doi.org/10.1137/17M112720X.
  6. Yi-Jun Chang. Hardness of rna folding problem with four symbols. Theoretical Computer Science, 757:11-26, 2019. URL: https://doi.org/10.1016/j.tcs.2018.07.010.
  7. Anne Condon, Monir Hajiaghayi, and Chris Thachuk. Predicting minimum free energy structures of multi-stranded nucleic acid complexes is apx-hard. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27)(2021). Schloss-Dagstuhl-Leibniz Zentrum für Informatik, 2021. Google Scholar
  8. A. Denise, Y. Ponty, and M. Termier. Controlled non-uniform random generation of decomposable structures. Theoretical Computer Science, 411(40):3527-3552, 2010. URL: https://doi.org/10.1016/j.tcs.2010.05.010.
  9. Robert M Dirks, Justin S Bois, Joseph M Schaeffer, Erik Winfree, and Niles A Pierce. Thermodynamic analysis of interacting nucleic acid strands. SIAM review, 49(1):65-88, 2007. Google Scholar
  10. Haotian Guo, Joseph C Ryan, Xiaohu Song, Adeline Mallet, Mengmeng Zhang, Victor Pabst, Antoine L Decrulle, Paulina Ejsmont, Edwin H Wintermute, and Ariel B Lindner. Spatial engineering of E. coli with addressable phase-separated RNAs. Cell, 185(20):3823-3837, 2022. Google Scholar
  11. Fanny Hauser, Ferdinand Ermel, and Kimon Boehmer. Clique cover based vertex cover solver. https://github.com/f-erm/CliqueCoverBasedVertexCoverSolver, 2024.
  12. Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David A Hendrix, and David H Mathews. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinformatics, 35(14):i295-i304, July 2019. URL: https://doi.org/10.1093/bioinformatics/btz375.
  13. Atagun U Isiktas, Aziz Eshov, Suzhou Yang, and Junjie U Guo. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. Cell Reports Methods, 2(11), 2022. Google Scholar
  14. Ryo Kurokawa, Mariko Kurokawa, Akihiko Mitsutake, Moto Nakaya, Akira Baba, Yasuhiro Nakata, Toshio Moritani, and Osamu Abe. Clinical and neuroimaging review of triplet repeat diseases. Japanese Journal of Radiology, 41(2):115-130, 2023. Google Scholar
  15. L. Lipshitz. D-finite power series. Journal of Algebra, 122(2):353-373, 1989. Google Scholar
  16. Jacob S Lu, Eckart Bindewald, Wojciech K Kasprzak, and Bruce A Shapiro. RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinformatics, 34(24):4297-4299, June 2018. URL: https://doi.org/10.1093/bioinformatics/bty468.
  17. Hiranmay Maity, Hung T Nguyen, Naoto Hori, and D Thirumalai. Odd-even disparity in the population of slipped hairpins in rna repeat sequences with implications for phase separation. Proceedings of the National Academy of Sciences, 120(24):e2301409120, 2023. Google Scholar
  18. Colin McDiarmid. Pattern minimisation in cutting stock problems. Discrete applied mathematics, 98(1-2):121-130, 1999. Google Scholar
  19. R Nussinov and A B Jacobson. Fast algorithm for predicting the secondary structure of single-stranded rna. Proceedings of the National Academy of Sciences, 77(11):6309-6313, 1980. URL: https://doi.org/10.1073/pnas.77.11.6309.
  20. B. Salvy and P. Zimmerman. GFUN: a Maple package for the manipulation of generating and holonomic functions in one variable. ACM Transactions on Mathematical Software, 20(2):163-177, 1994. Google Scholar
  21. Sharan R. Srinivasan, Claudio Melo de Gusmao, Joanna A. Korecka, and Vikram Khurana. Chapter 18 - repeat expansion disorders. In Michael J. Zigmond, Clayton A. Wiley, and Marie-Francoise Chesselet, editors, Neurobiology of Brain Disorders (Second Edition), pages 293-312. Academic Press, second edition edition, 2023. URL: https://doi.org/10.1016/B978-0-323-85654-6.00048-4.
  22. Douglas H. Turner and David H. Mathews. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Research, 38(suppl_1):D280-D282, October 2009. URL: https://doi.org/10.1093/nar/gkp892.
  23. Michael Zuker and Patrick Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research, 9(1):133-148, January 1981. URL: https://doi.org/10.1093/nar/9.1.133.
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