Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets.
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets.
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DOI：
10.1093/nar/gkl1096
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发表时间：
2007
影响因子：
14.9
通讯作者：
Cossart P
中科院分区：
文献类型：
--
作者：
Mandin P;Repoila F;Vergassola M;Geissmann T;Cossart P
为了鉴定致病性单核细胞增生李斯特菌中的非编码RNA（ncRNA），我们通过基于计算机的方法分析了菌株EGD-e的基因间区域（IGRs）。在所发现的12个ncRNA中，9个是新的并且对李斯特菌属是特异性的，并且这些ncRNA中的两个以生长依赖性方式表达。其中三个ncRNA以与重叠开放阅读框（ORF）相反的方向转录，表明它们在相应的mRNA上充当反义。其他ncRNA基因表现为单个转录单位。其中一个显示29个核苷酸的5个重复。这些新的ncRNA中有五种在非致病性物种L中不存在。无害，提高了它们可能参与毒性的可能性。为了预测ncRNA的mRNA靶点，我们开发了一种基于热力学配对能和已知ncRNA-mRNA杂交的计算方法。三个ncRNA，包括一个假定的反义ncRNA，预测有一个以上的mRNA的目标。其中几个被证明有效地结合到ncRNA，这表明我们的计算机模拟方法可以用作搜索ncRNA的mRNA靶标的通用工具。
To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA–mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.
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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：
5.6
作者：
Argaman, L;Altuvia, S
通讯作者：
Altuvia, S
DOI：
10.1073/pnas.170281497
发表时间：
2000-08-29
影响因子：
11.1
作者：
Lease, RA;Belfort, M
通讯作者：
Belfort, M
影响因子：
3.2
作者：
Christiansen, JK;Larsen, MH;Kallipolitis, BH
通讯作者：
Kallipolitis, BH
影响因子：
2.8
作者：
Kim, H;Marquis, H;Boor, KJ
通讯作者：
Boor, KJ