CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
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DOI：
10.4161/rna.24046
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发表时间：
2013-05
期刊：
影响因子：
4.1
通讯作者：
Brown CM
中科院分区：
文献类型：
--
作者：
Biswas A;Gagnon JN;Brouns SJ;Fineran PC;Brown CM
细菌和古生菌CRISPR/Cas适应性免疫系统针对入侵生物体中的特定原核糖体核苷酸序列。这需要在处理过的CRISPR RNA和目标Protspacer之间进行碱基配对。对于I型和II型CRISPR/CAS系统，Protspacer相邻基序(PAM)对于靶标识别是必不可少的，而对于III型CRISPR/CAS系统，侧翼序列的错配在抗病毒反应中是重要的。在这项研究中，我们检查了每一类CRISPR的属性。我们使用这些信息来提供一个工具(CRISPRTarget)来预测CRISPR RNAs(http://bioanalysis.otago.ac.nz/CRISPRTarget).最有可能的目标这可以用来在新测序的基因组或元基因组数据中发现靶标。为了测试它的实用性，我们发现了特征良好的嗜热链球菌和Sulfolobus solafaricus Type II和III CRISPR/CAS系统的特征和目标。最后，在细小杆菌物种中，我们识别了新的CRISPR靶标，并提出了一个温带噬菌体暴露和I型CRISPR/Cas系统随后抑制的模型。
The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.