An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.
An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.
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DOI：
10.1093/nar/gkr1141
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Le Bouguénec C
中科院分区：
文献类型：
--
作者：
Pichon C;du Merle L;Caliot ME;Trieu-Cuot P;Le Bouguénec C
在高通量 RNA-seq 或平铺微阵列分析生成的大量数据中表征小非编码核糖核酸 (sRNA) 仍然是一个挑战。因此，仍然需要准确的计算机预测方法来识别给定细菌物种内的 sRNA。经过多年的努力，基于比较基因组分析或数学/统计模型开发了专用软件。尽管这些基因组分析能够有效识别基因间区域的 sRNA，但它们都未能预测反义 sRNA 基因 (asRNA)，即位于与编码蛋白质的 DNA 链互补的 RNA 基因。统计模型可以从理论上分析任何基因组区域，但效率不高。我们提出了一种新模型，用于在整个细菌基因组中对 sRNA 和 asRNA 候选物进行计算机识别。该模型成功用于分析革兰氏阴性大肠杆菌和革兰氏阳性无乳链球菌。在这两种细菌中，大量的 asRNA 是从位于致病岛的基因互补链转录而来，强烈表明这些 asRNA 是毒力表达的调节因子。特别是，我们鉴定了一种asRNA，它作为1型菌毛产生的增强子样调节剂，参与肠外致病性大肠杆菌的毒力。
Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. After years of effort, dedicated software were developed based on comparative genomic analyses or mathematical/statistical models. Although these genomic analyses enabled sRNAs in intergenic regions to be efficiently identified, they all failed to predict antisense sRNA genes (asRNA), i.e. RNA genes located on the DNA strand complementary to that which encodes the protein. The statistical models enabled any genomic region to be analyzed theorically but not efficiently. We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. This model was successfully used to analyze the Gram-negative Escherichia coli and Gram-positive Streptococcus agalactiae. In both bacteria, numerous asRNAs are transcribed from the complementary strand of genes located in pathogenicity islands, strongly suggesting that these asRNAs are regulators of the virulence expression. In particular, we characterized an asRNA that acted as an enhancer-like regulator of the type 1 fimbriae production involved in the virulence of extra-intestinal pathogenic E. coli.
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影响因子：
3.7
作者：
Beaume M;Hernandez D;Farinelli L;Deluen C;Linder P;Gaspin C;Romby P;Schrenzel J;Francois P
通讯作者：
Francois P
影响因子：
3.5
作者：
CHEREPANOV, PP;WACKERNAGEL, W
通讯作者：
WACKERNAGEL, W
通过比较基因组分析鉴定蓝细菌非编码RNA。
影响因子：
12.3
作者：
Axmann, Ilka M;Kensche, Philip;Vogel, Jorg;Kohl, Stefan;Herzel, Hanspeter;Hess, Wolfgang R
通讯作者：
Hess, Wolfgang R
影响因子：
14.9
作者：
Geissmann T;Chevalier C;Cros MJ;Boisset S;Fechter P;Noirot C;Schrenzel J;François P;Vandenesch F;Gaspin C;Romby P
通讯作者：
Romby P
DOI：
10.1073/pnas.0600927103
发表时间：
2006-05-02
影响因子：
11.1
作者：
Dühring, U;Axmann, IM;Wilde, A
通讯作者：
Wilde, A