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An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons
Article

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs

1
Department of Chemistry, New York University, New York, NY 10003, USA
2
Computer Science Department, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
3
Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
4
NYU-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 3663, China
*
Author to whom correspondence should be addressed.
Current address: Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Genes 2018, 9(8), 371; https://doi.org/10.3390/genes9080371
Received: 7 May 2018 / Revised: 26 June 2018 / Accepted: 26 June 2018 / Published: 25 July 2018
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks up to nine vertices; among them, 22 are frequently occurring, 15 of which contain pseudoknots. We then catalog atomic fragments corresponding to the subgraph blocks to define a library of building blocks that can be used for RNA design, which we call RAG-3Dual, as we have done for tree graphs. As an application, we analyze the distribution of these subgraph blocks within ribosomal RNAs of various prokaryotic and eukaryotic species to identify common subgraphs and possible ancestry relationships. Other applications of dual graph partitioning and motif library can be envisioned for RNA structure analysis and design. View Full-Text
Keywords: RNA graphs; dual graphs; graph partitioning; RNA substructures and submotifs; pseudoknots; ribosomal RNAs RNA graphs; dual graphs; graph partitioning; RNA substructures and submotifs; pseudoknots; ribosomal RNAs
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MDPI and ACS Style

Jain, S.; Bayrak, C.S.; Petingi, L.; Schlick, T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes 2018, 9, 371. https://doi.org/10.3390/genes9080371

AMA Style

Jain S, Bayrak CS, Petingi L, Schlick T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes. 2018; 9(8):371. https://doi.org/10.3390/genes9080371

Chicago/Turabian Style

Jain, Swati, Cigdem S. Bayrak, Louis Petingi, and Tamar Schlick. 2018. "Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs" Genes 9, no. 8: 371. https://doi.org/10.3390/genes9080371

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