Computational identification of riboswitches based on RNA conserved functional sequences and conformations

被引：45

作者：

Chang, Tzu-Hao ^{[2
]}

Huang, Hsien-Da ^{[1
]}

Wu, Li-Ching ^{[3
]}

Yeh, Chi-Ta ^{[2
]}

Liu, Baw-Jhiune ^{[4
]}

Horng, Jorng-Tzong ^{[2
,5
]}

机构：

[1] Natl Chiao Tung Univ, Dept Biol Sci & Technol, Inst Bioinformat & Syst Biol, Hsinchu 300, Taiwan

[2] Natl Cent Univ, Dept Comp Sci & Informat Engn, Jhongli 320, Taiwan

[3] Natl Cent Univ, Inst Syst Biol & Bioinformat, Jhongli 320, Taiwan

[4] Yuan Ze Univ, Dept Comp Sci & Engn, Jhongli 320, Taiwan

[5] Asia Univ, Dept Bioinformat, Wufeng 413, Taiwan

来源：

RNA | 2009年 / 15卷 / 07期

关键词：

riboswitch; RNA secondary structure; regulatory RNA; APTAMER DOMAIN; ELEMENTS; BINDING; PLANTS; LIGAND;

D O I：

10.1261/rna.1623809

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Riboswitches are cis-acting genetic regulatory elements within a specific mRNA that can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, an increasing number of riboswitches have been identified in different species and investigated for their roles in regulatory functions. Both the sequence contexts and structural conformations are important characteristics of riboswitches. None of the previously developed tools, such as covariance models (CMs), Riboswitch finder, and RibEx, provide a web server for efficiently searching homologous instances of known riboswitches or considers two crucial characteristics of each riboswitch, such as the structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method for identifying 12 kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction, which makes it possible to have an accurate and convenient web server for biologists to obtain the results of their analysis of a given mRNA sequence. RiboSW is now available on the web at http://RiboSW.mbc.nctu.edu.tw/.

引用

页码：1426 / 1430

页数：5

共 13 条

[11] Vitamin B1 biosynthesis in plants requires the essential iron-sulfur cluster protein, THIC [J].

Raschke, Maja ;

Buerkle, Lukas ;

Mueller, Nadine ;

Nunes-Nesi, Adriano ;

Fernie, Alisdair R. ;

Arigoni, Duilio ;

Amrhein, Nikolaus ;

Fitzpatrick, Teresa B. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (49) :19637-19642

[12] Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand [J].

Thore, Stephane ;

Leibundgut, Marc ;

Ban, Nenad .

SCIENCE, 2006, 312 (5777) :1208-1211

[13] Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs [J].

Wachter, Andreas ;

Tunc-Ozdemir, Meral ;

Grove, Beth C. ;

Green, Pamela J. ;

Shintani, David K. ;

Breaker, Ronald R. .

PLANT CELL, 2007, 19 (11) :3437-3450

← 1 2 →