Phylogenetic Analysis with Improved Parameters Reveals Conservation in LncRNA Structures

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2019 Mar 21

PMID 30890332

Citations 31

Authors

Rafael C A Tavares

Anna Marie Pyle

Srinivas Somarowthu

Affiliations

Soon will be listed here.

Abstract

The existence of evolutionary conservation in base pairing is strong evidence for functional elements of RNA structure, although available tools for rigorous identification of structural conservation are limited. R-scape is a recently developed program for statistical prediction of pairwise covariation from sequence alignments, but it initially showed limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for a more powerful analysis of structure conservation in long RNA molecules, including mammalian lncRNAs.

Citing Articles

Identification of RNA structures and their roles in RNA functions.

Cao X, Zhang Y, Ding Y, Wan Y Nat Rev Mol Cell Biol. 2024; 25(10):784-801.

PMID: 38926530 DOI: 10.1038/s41580-024-00748-6.

Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA.

Bhatt U, Cucchiarini A, Luo Y, Evans C, Mergny J, Iyer K Genome Res. 2024; 34(2):217-230.

PMID: 38355305 PMC: 10984386. DOI: 10.1101/gr.278236.123.

Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1.

Weghorst F, Torres Marcen M, Faridi G, Lee Y, Cramer K J Mol Evol. 2024; 92(1):30-41.

PMID: 38189925 PMC: 10869381. DOI: 10.1007/s00239-023-10151-y.

DNABERT-based explainable lncRNA identification in plant genome assemblies.

Danilevicz M, Gill M, Fernandez C, Petereit J, Upadhyaya S, Batley J Comput Struct Biotechnol J. 2023; 21:5676-5685.

PMID: 38058296 PMC: 10696397. DOI: 10.1016/j.csbj.2023.11.025.

Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional Predictions Using Deep Learning Approaches.

Ramakrishnaiah Y, Morris A, Dhaliwal J, Philip M, Kuhlmann L, Tyagi S Epigenomes. 2023; 7(3).

PMID: 37754274 PMC: 10528440. DOI: 10.3390/epigenomes7030022.

References

Hofacker I, Fekete M, Stadler P . Secondary structure prediction for aligned RNA sequences. J Mol Biol. 2002; 319(5):1059-66. DOI: 10.1016/S0022-2836(02)00308-X. View

Washietl S, Hofacker I, Stadler P . Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A. 2005; 102(7):2454-9. PMC: 548974. DOI: 10.1073/pnas.0409169102. View

Lindgreen S, Gardner P, KROGH A . Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics. 2006; 22(24):2988-95. DOI: 10.1093/bioinformatics/btl514. View

Hofacker I . RNA consensus structure prediction with RNAalifold. Methods Mol Biol. 2007; 395:527-44. DOI: 10.1007/978-1-59745-514-5_33. View

Bernhart S, Hofacker I, Will S, Gruber A, Stadler P . RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008; 9:474. PMC: 2621365. DOI: 10.1186/1471-2105-9-474. View

Gruber A, Findeiss S, Washietl S, Hofacker I, Stadler P . RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput. 2009; :69-79. View

Harmanci A, Sharma G, Mathews D . TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinformatics. 2011; 12:108. PMC: 3120699. DOI: 10.1186/1471-2105-12-108. View

Novikova I, Hennelly S, Sanbonmatsu K . Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 2012; 40(11):5034-51. PMC: 3367176. DOI: 10.1093/nar/gks071. View

Kuraku S, Zmasek C, Nishimura O, Katoh K . aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Res. 2013; 41(Web Server issue):W22-8. PMC: 3692103. DOI: 10.1093/nar/gkt389. View

10.

Smith M, Gesell T, Stadler P, Mattick J . Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res. 2013; 41(17):8220-36. PMC: 3783177. DOI: 10.1093/nar/gkt596. View

11.

Ruzzo W, Gorodkin J . De novo discovery of structured ncRNA motifs in genomic sequences. Methods Mol Biol. 2014; 1097:303-18. DOI: 10.1007/978-1-62703-709-9_15. View

12.

Siegfried N, Busan S, Rice G, Nelson J, Weeks K . RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods. 2014; 11(9):959-65. PMC: 4259394. DOI: 10.1038/nmeth.3029. View

13.

Pyle A . Looking at LncRNAs with the ribozyme toolkit. Mol Cell. 2014; 56(1):13-7. DOI: 10.1016/j.molcel.2014.08.025. View

14.

Palazzo A, Lee E . Non-coding RNA: what is functional and what is junk?. Front Genet. 2015; 6:2. PMC: 4306305. DOI: 10.3389/fgene.2015.00002. View

15.

Somarowthu S, Legiewicz M, Chillon I, Marcia M, Liu F, Pyle A . HOTAIR forms an intricate and modular secondary structure. Mol Cell. 2015; 58(2):353-61. PMC: 4406478. DOI: 10.1016/j.molcel.2015.03.006. View

16.

Hezroni H, Koppstein D, Schwartz M, Avrutin A, Bartel D, Ulitsky I . Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep. 2015; 11(7):1110-22. PMC: 4576741. DOI: 10.1016/j.celrep.2015.04.023. View

17.

Fu Y, Xu Z, Lu Z, Zhao S, Mathews D . Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS One. 2015; 10(6):e0130200. PMC: 4468099. DOI: 10.1371/journal.pone.0130200. View

18.

Pirakitikulr N, Kohlway A, Lindenbach B, Pyle A . The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures. Mol Cell. 2016; 62(1):111-20. PMC: 4826301. DOI: 10.1016/j.molcel.2016.01.024. View

19.

Chillon I, Pyle A . Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Res. 2016; 44(19):9462-9471. PMC: 5100600. DOI: 10.1093/nar/gkw599. View

20.

Nitsche A, Stadler P . Evolutionary clues in lncRNAs. Wiley Interdiscip Rev RNA. 2016; 8(1). DOI: 10.1002/wrna.1376. View