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High efficient determination of target binding regions of bacterial sRNAs in sRNA-mRNA interactions

High efficient determination of target binding regions of ba...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xiaomin Ying Yuan Cao Jiayao Wu Lei Cha Qian Liu Wuju Li Center of Computational Biology Institute of Basic Medical SciencesAcademy of Military Medical Sciences Department of Clinical Laboratory the 90th Hospital of Jinan

Background:Bacterial sRNAs are a novel class of small regulatory RNAs 40-500nt in *** play important roles in gene regulation such as regulation of biogenesis of outer membrane proteins,quorum sensing,and expression of virulence-related genes. Most sRNAs act in trans via base-pairing with their target mRNAs,leading to repression or activation of translation or mRNA *** prediction is a labor-saving strategy for sRNA target *** computational methods have been developed. However,all these methods predict targets with lots of false *** improve the performance of the present prediction methods,we systematically analyzed 91 experimentally validated sRNA-mRNA interactions,and found that most sRNAs bound distinct targets via common regions and the common regions were ***,we present a novel method to determine target binding regions of sRNAs by conservation analysis. Methods:Firstly,we searched similar fragments against all bacterial genomes using WUblast with E-value less than *** sRNAs with rho-independent terminators,the similarity of terminator stems were required to be greater than 66%.Secondly,we perform multiple sequence alignment for all the similar fragments using *** rhoindependent terminators were aligned ***,we removed conserved stems from the consensus sequences using EMBOSS einverted ***,we expanded the conservative segments centered at consensus segments in the sequences with conservation score greater than *** the gaps of two adjacent segments were less than 3nt,the two adjacent segments were merged into one conservative segment. Results:We performed the conservation analysis as described in Methods for all the sRNAs with experimentally validated targets in sRNATarBase developed by our *** all 46 sRNAs,the conservative segments of 45(97.8%) sRNAs overlapped more than 50% with experimentally validated target binding *** all 91 sRNA-mRN

关键词： sRNAs bacteria target binding regions target prediction sRNA-mRNA interactions

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