Title

Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment

Authors

Authors

C. C. Zhong;S. J. Zhang

Comments

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Abbreviated Journal Title

Nucleic Acids Res.

Keywords

SARCIN-RICIN LOOP; CRYSTAL-STRUCTURE; BASE-PAIRS; ISOSTERICITY MATRICES; TERTIARY STRUCTURES; ELONGATION-FACTORS; CLASSIFICATION; SUBUNIT; IDENTIFICATION; DISCOVERY; Biochemistry & Molecular Biology

Abstract

RNA structural motifs are the building blocks of the complex RNA architecture. Identification of non-coding RNA structural motifs is a critical step towards understanding of their structures and functionalities. In this article, we present a clustering approach for de novo RNA structural motif identification. We applied our approach on a data set containing 5S, 16S and 23S rRNAs and rediscovered many known motifs including GNRA tetraloop, kink-turn, C-loop, sarcin-ricin, reverse kink-turn, hook-turn, E-loop and tandem-sheared motifs, with higher accuracy than the state-of-the-art clustering method. We also identified a number of potential novel instances of GNRA tetraloop, kink-turn, sarcin-ricin and tandem-sheared motifs. More importantly, several novel structural motif families have been revealed by our clustering analysis. We identified a highly asymmetric bulge loop motif that resembles the rope sling. We also found an internal loop motif that can significantly increase the twist of the helix. Finally, we discovered a subfamily of hexaloop motif, which has significantly different geometry comparing to the currently known hexaloop motif. Our discoveries presented in this article have largely increased current knowledge of RNA structural motifs.

Journal Title

Nucleic Acids Research

Volume

40

Issue/Number

3

Publication Date

1-1-2012

Document Type

Article

Language

English

First Page

1307

Last Page

1317

WOS Identifier

WOS:000300422400038

ISSN

0305-1048

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