RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications
RNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search al...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/16/9249 |
| _version_ | 1797432072237744128 |
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| author | Qiyao Zhu Louis Petingi Tamar Schlick |
| author_facet | Qiyao Zhu Louis Petingi Tamar Schlick |
| author_sort | Qiyao Zhu |
| collection | DOAJ |
| description | RNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search algorithm that finds and ranks independent RNA substructures. Our expanded list of 183 existing dual graph motifs reveals five common motifs found in transfer RNA, riboswitch, and ribosomal 5S RNA components. Moreover, we identify three motifs for available viral frameshifting RNA elements, suggesting a correlation between viral structural complexity and frameshifting efficiency. We further partition the RNA substructures into 1844 distinct submotifs, with pseudoknots and junctions retained intact. Common modules are internal loops and three-way junctions, and three submotifs are associated with riboswitches that bind nucleotides, ions, and signaling molecules. Together, our library of existing RNA motifs and submotifs adds to the growing universe of RNA modules, and provides a resource of structures and substructures for novel RNA design. |
| first_indexed | 2024-03-09T09:55:02Z |
| format | Article |
| id | doaj.art-15299401827442a1918b8b6559cb04fd |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T09:55:02Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-15299401827442a1918b8b6559cb04fd2023-12-01T23:48:02ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-08-012316924910.3390/ijms23169249RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element ApplicationsQiyao Zhu0Louis Petingi1Tamar Schlick2Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USADepartment of Computer Science, College of Staten Island, City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USACourant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USARNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search algorithm that finds and ranks independent RNA substructures. Our expanded list of 183 existing dual graph motifs reveals five common motifs found in transfer RNA, riboswitch, and ribosomal 5S RNA components. Moreover, we identify three motifs for available viral frameshifting RNA elements, suggesting a correlation between viral structural complexity and frameshifting efficiency. We further partition the RNA substructures into 1844 distinct submotifs, with pseudoknots and junctions retained intact. Common modules are internal loops and three-way junctions, and three submotifs are associated with riboswitches that bind nucleotides, ions, and signaling molecules. Together, our library of existing RNA motifs and submotifs adds to the growing universe of RNA modules, and provides a resource of structures and substructures for novel RNA design.https://www.mdpi.com/1422-0067/23/16/9249coarse-grained RNA motifsdual graphs and subgraphsviral frameshifting elementsriboswitch structures |
| spellingShingle | Qiyao Zhu Louis Petingi Tamar Schlick RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications International Journal of Molecular Sciences coarse-grained RNA motifs dual graphs and subgraphs viral frameshifting elements riboswitch structures |
| title | RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications |
| title_full | RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications |
| title_fullStr | RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications |
| title_full_unstemmed | RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications |
| title_short | RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications |
| title_sort | rna as graphs motif atlas dual graph library of rna modules and viral frameshifting element applications |
| topic | coarse-grained RNA motifs dual graphs and subgraphs viral frameshifting elements riboswitch structures |
| url | https://www.mdpi.com/1422-0067/23/16/9249 |
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