Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?
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DOI：
10.4161/rna.20294
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发表时间：
2012-07
期刊：
影响因子：
4.1
通讯作者：
Backofen R
中科院分区：
文献类型：
--
作者：
Richter AS;Backofen R
细菌小RNA（sRNA）是一类结构性RNA，通常通过转录后碱基对相互作用调节mRNA靶点。我们确定了区分功能性和非功能性相互作用的特征，并评估了这些特征对全基因组靶点预测的影响。为此，我们编制了一套71实验验证的sRNA-target对大肠杆菌和沙门氏菌。此外，我们收集了全长5′非翻译区，通过使用全基因组实验验证的转录起始位点。 只有sRNA中的相互作用位点，而不是在目标，显示出显着的序列保守性。除了这一观察结果，我们还发现sRNA与其靶标之间的碱基配对在亲缘关系较远的物种中一般不保守。对RybB和RyhB sRNA及其靶标的更仔细的检查显示，碱基配对互补性仅在靶标的一小部分中是保守的。与保守性相反，与非功能性位点相比，在sRNA和靶标中功能性相互作用位点的可及性显著更高。基于上述观察，我们成功地使用了以下限制来提高全基因组靶点预测的特异性：相互作用起始区域必须位于（1）两个相互作用伴侣中高度可及的区域或（2）来自多个sRNA比对可靠性特征的非结构化保守sRNA区域。 同源sRNA、功能性和非功能性靶标的比对序列以及具有sup表、图和参考文献的sup文档可在www.bioinf.uni-freiburg.de/Supplements/srna-interact-feat/获得。
Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. We determined features that discriminate functional from non-functional interactions and assessed the influence of these features on genome-wide target predictions. For this purpose, we compiled a set of 71 experimentally verified sRNA–target pairs from Escherichia coli and Salmonella enterica. Furthermore, we collected full-length 5′ untranslated regions by using genome-wide experimentally verified transcription start sites. Only interaction sites in sRNAs, but not in targets, show significant sequence conservation. In addition to this observation, we found that the base pairing between sRNAs and their targets is not conserved in general across more distantly related species. A closer inspection of RybB and RyhB sRNAs and their targets revealed that the base pairing complementarity is only conserved in a small subset of the targets. In contrast to conservation, accessibility of functional interaction sites is significantly higher in both sRNAs and targets in comparison to non-functional sites. Based on the above observations, we successfully used the following constraints to improve the specificity of genome-wide target predictions: the region of interaction initiation must be located in (1) highly accessible regions in both interaction partners or (2) unstructured conserved sRNA regions derived from reliability profiles of multiple sRNA alignments. Aligned sequences of homologous sRNAs, functional and non-functional targets, and a sup document with sup tables, figures and references are available at www.bioinf.uni-freiburg.de/Supplements/srna-interact-feat/.
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影响因子：
14.9
作者：
Guillier, Maude;Gottesman, Susan
通讯作者：
Gottesman, Susan
DOI：
10.1093/bioinformatics/btr149
发表时间：
2011-05-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ellwanger DC;Büttner FA;Mewes HW;Stümpflen V
通讯作者：
Stümpflen V
影响因子：
46.9
作者：
Cho, Byung-Kwan;Zengler, Karsten;Qiu, Yu;Park, Young Seoub;Knight, Eric M.;Barrett, Christian L.;Gao, Yuan;Palsson, Bernhard O.
通讯作者：
Palsson, Bernhard O.
影响因子：
5.6
作者：
Argaman, L;Altuvia, S
通讯作者：
Altuvia, S
影响因子：
16
作者：
Bouvier, Marie;Sharma, Cynthia M.;Vogel, Joerg
通讯作者：
Vogel, Joerg