Computational prediction of nonenzymatic RNA degradation patterns

  • Agnieszka Rybarczyk Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61 704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, ul. Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Piotrowo 2, 60-965 Poznan, Poland
  • Paulina Jackowiak
  • Marek Figlerowicz
  • Jacek Blazewicz
Keywords: RNA degradation, nonenzymatic RNA hydrolysis, branch-and-cut algorithm


Since the beginning of XXI century, the increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins). More recently, it has been shown that small regulatory RNAs are also generated as stable intermediates of RNA degradation (so called RNA fragments originating from tRNA, snRNA, snoRNA etc.). Unfortunately, the mechanisms underlying biogenesis of the RNA fragments remain unclear. It is thought that several factors may be involved in the formation of the RNA fragments. The most important are specific RNases, RNA-protein interactions and RNA structure.  

In this work, we focus on RNA primary and secondary structures as factors influencing RNA stability and consequently the pattern of RNA fragmentation. Earlier, we identified major structural factors affecting non-enzymatic RNA degradation. Now based on these data we developed a new branch-and-cut algorithm that is able to predict the products of large RNA molecules hydrolysis in vitro. We also present the experimental data that verify the results generated using this algorithm.


Aalto AP, Pasquinelli AE (2012) Small non-coding RNAs mount a silent revolution in gene expression. Curr Opin Cell Biol. 24: 333-40. doi: 10.1016/

Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M (2014) RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. 42: W368-72. doi: 10.1093/nar/gku330

Bibillo A, Figlerowicz M, Ziomek K, Kierzek R (2000) The nonenzymatic hydrolysis of oligoribonucleotides. VII. Structural elements affecting hydrolysis. Nucleosides Nucleotides Nucleic Acids 19: 977–994. doi: 10.1080/15257770008033037

Bibillo A, Figlerowicz M, Kierzek R (1999) The non-enzymatic hydrolysis of oligoribonucleotides VI. The role of biogenic polyamines. Nucleic Acids Res. 27: 3931–3937. doi: 10.1093/nar/27.19.3931

Blazewicz J, Figlerowicz M, Kasprzak M, Nowacka M, Rybarczyk A (2011) RNA partial degradation problem: motivation, complexity, algorithm. Journal of Computational Biology 18: 821-834. doi: 10.1089/cmb.2010.0153

Blazewicz J, Formanowicz P, Guinand F, Kasprzak M (2002) A heuristic managing errors for DNA sequencing. Bioinformatics 18: 652-660.

Blazewicz J, Szachniuk M, Wojtowicz A (2005) RNA tertiary structure determination: NOE pathway construction by tabu search. Bioinformatics 21: 2356-2361. doi:10.1093/bioinformatics/bti351

Ciesiołka J, Michałowski D, Wrzesinski J, Krajewski J, Krzyzosiak WJ (1998) Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs. J Mol Biol. 275: 211-20.

Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs, RNA 15: 2147–2160.

Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12: 19-31. doi: 10.1038/nrg2916

Dutkiewicz M, Ciesiolka J (2005) Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5' end of the replicative viral strand, Nucleic Acids Res. 33: 693-703. doi: 10.1093/nar/gki218

Figlerowicz M (2000) Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus, Nucleic Acids Res. 28: 1714-1723.

Gendron P, Lemieux S, Major F (2001) Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 308: 919–36. doi: 10.1006/jmbi.2001.4626

Grunberg-Manago M (1999) Messenger RNA Stability and Its Role in Control of Gene Expression in Bacteria and Phages. Annu Rev Genet. 33: 193-227. doi:10.1146/annurev.genet.33.1.193

Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte Für Chem Chem Mon. 125: 167–88. doi: 10.1007/BF00818163

Houseley J, Tollervey D. (2009) The many pathways of RNA degradation. Cell 136: 763–776. doi: 10.1016/j.cell.2009.01.019

Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 151: 2120-32. doi: 10.1104/pp.109.147280

Hsieh LC, Lin SI, Kuo HF, Chiou TJ (2010) Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots. Plant Signal Behav. 5: 537-9. doi: 10.4161/psb.11029

Hui MP, Foley PL, Belasco JG (2014) Messenger RNA degradation in bacterial cells. Annu Rev Genet. 48: 537-59. doi: 10.1146/annurev-genet-120213-092340

Hurto RL (2011) Unexpected functions of tRNA and tRNA processing enzymes. Adv Exp Med Biol. 722: 137-55. doi: 10.1007/978-1-4614-0332-6_9

Jackowiak P, Nowacka M, Strozycki PM, Figlerowicz M (2011) RNA degradome-its biogenesis and functions. Nucleic Acids Res. 39: 7361-70. doi: 10.1093/nar/gkr450

Kaukinen U, Lyytikainen S, Mikkola S, Lonnberg H (2002) The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence. Nucleic Acids Res. 30: 468–474. doi: 10.1093/nar/30.2.468

Kazakov S, Altman S (1992) A trinucleotide can promote metal ion-dependent specific cleavage of RNA. Proc Natl Acad Sci U.S.A. 89: 7939-43.

Keck MV, Hecht SM (1995) Sequence-specific hydrolysis of yeast tRNA(Phe) mediated by metal-free bleomycin. Biochemistry 34: 12029-37. doi: 10.1021/bi00037a046

Kierzek R (1992) Nonenzymatic hydrolysis of oligoribonucleotides, Nucleic Acids Res 20: 5079–5084.

Kierzek R (2001) Nonenzymatic Cleavage of Oligoribonucleotides, Methods in Enzymology 341: 657-675. doi: 10.1016/S0076-6879(01)41183-9

Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals, Nat Rev Mol Cell Biol. 10: 126-39. doi: 10.1038/nrm2632

Li Z, Ender C, Meister G, Moore PS, Chang Y, John B (2012) Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 40: 6787-6799. doi: 10.1093/nar/gks307

Lorentzen E, Conti E (2006) The exosome and the proteosome: nanocompartments for degradation. Cell 125: 651-654. doi: 10.1016/j.cell.2006.05.002

Lu X-J, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31: 5108–21. doi: 10.1093/nar/gkg680

Maivali U, Paier A, Tenson T (2013) When stable RNA becomes unstable: the degradation of ribosomes in bacteria and beyond. Biol Chem. 394: 845-55. doi: 10.1515/hsz-2013-0133

Mattick JS, Makunin IV (2006) Non-coding RNA. Hum. Mol. Genet. 15: R17–R29.

Mattick JS (2009) The genetic signatures of noncoding RNAs. PLoS Genet. 5: e1000459. doi: 10.1371/journal.pgen.1000459

Mickiewicz A, Rybarczyk A, Sarzynska J, Figlerowicz M, Blazewicz J (2016) AmiRNA Designer - new method of artificial miRNA design. Acta Biochim Pol 63: 71-77. doi: 0.18388/abp.2015_989

Mikkola S, Kaukinen U, Lonnberg H (2001) The effect of secondary structure on cleavage of the phosphodiester bonds of RNA. Cell Biochem Biophys. 34: 95-119. doi: 10.1385/CBB:34:1:95

Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nature Reviews Genetics 15: 423–437. doi:10.1038/nrg3722

Nowacka M, Jackowiak P, Rybarczyk A, Magacz T, Strozycki PM, Barciszewski J, Figlerowicz M (2012) 2D-PAGE as an effective method of RNA degradome analysis. Molecular Biology Reports 39: 139-146. doi:10.1007/s11033-011-0718-1

Nowacka M, Strozycki PM, Jackowiak P, Hojka-Osinska A, Szymanski M, Figlerowicz M (2013) Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions. Plant Mol Biol. 83: 191–204. doi: 10.1007/s11103-013-0079-3

Pederson T. (2010) Regulatory RNAs derived from transfer RNA? RNA 16: 1865–1869. doi: 10.1261/rna.2266510

Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res. 40: e112. doi: 10.1093/nar/gks339

Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129. doi: 10.1186/1471-2105-11-129

Ross J (1995) mRNA stability in mammalian cells. Microbiol Rev. 59: 423-450.

Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak R, Blazewicz J, Szachniuk M (2015) New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics 16: 276. doi: 10.1186/s12859-015-0718-6

Sobala A, Hutvagner G (2011) Transfer RNA-derived fragments: Origins, processing, and functions. Wiley Interdiscip Rev RNA 2: 853-62. doi: 10.1002/wrna.96

Szostak N, Royo F, Rybarczyk A, Szachniuk M, Blazewicz J, del Sol A, Falcon-Perez JM (2014) Sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biol 11:836–844. doi: 10.4161/rna.29305

Schweingruber C, Rufener SC, Zund D, Yamashita A, Muhlemann O (2013) Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochim Biophys Acta 1829: 612-23. doi: 10.1016/j.bbagrm.2013.02.005

Szweykowska-Kulinska Z, Jarmolowski A, Figlerowicz M (2003) RNA interference and its role in the regulation of eukaryotic gene expression. Acta Biochim Pol 50: 217–229.

Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS (2009) Small RNAs derived from snoRNAs. RNA 15: 1233–1240. doi:10.1261/rna.1528909

Taguchi G. (1987) System of Experimental Design: Engineering Methods to Optimize Quality and Minimize Costs, UNIPUB/Kraus International Publications.

Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095–2103. doi:10.1261/rna.1232808

Winkler WC, Breaker RR (2005) Regulation Of Bacterial Gene Expression By Riboswitches. Annu Rev Microbiol. 59: 487-517. doi: 10.1146/annurev.micro.59.030804.121336

Yang H, Jossinet F, Leontis NB, Chen L, Westbrook J, Berman H, Westhof E (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31: 3450–60. doi: 10.1093/nar/gkg529

Zhang S, Sun L, Kragler F (2009) The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol 150: 378–387. doi:10.1104/pp.108.134767

Zok T, Popenda M, Szachniuk M (2014) MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research 22: 457-474. doi:10.1007/s10100-013-0296-5