Bioinformatic analyses of CRISPR elements

CRISPR元件的生物信息分析

• 批准号: 206968047
• 负责人: Professor Dr. Rolf Backofen
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Research Units
• 财政年份: 2011
• 资助国家: 德国
• 起止时间: 2010-12-31 至 2020-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/206968047?language=en
• 关键词: Bioinformatic; analyses; CRISPR; elements

Most archaea and many bacteria have a defence system against a variety of invading genetic elements called CRISPR-Cas systems, which is based on RNA. This project aims at a better understanding of the CRISPR-Cas system by using highly advanced bioinformatics approaches. First, we will develop a fully automated annotation pipeline for CRISPR-Cas systems. There is a severe deficit in convenient annotation applications for CRISPR-Cas systems. In addition to our automated characterization of CRISPR evolution (CRISPRmap), we intend to develop a web-server toolbox for a comprehensive automatic in silico characterization of many other important aspects of CRISPR-Cas systems, including the prediction of the CRISPR orientation, the leader sequence and the first automated annotation of CRISPR-Cas subtypes.Second, we want to identify CRISPR targets (i.e. protospacers) and characterize associated protospacer-adjacent motif, PAM, important for both adaptation and interference. Our goal is to first collect a set of protospacers from viral genomes and metagenomics data. Subsequently, we will identify and analyze patterns of associated PAMs. Characterized PAM motifs and their properties will be validated the groups of Schmitz-Streit and Randau.Third, we want to detect requirements of a CRISPR array that lead to efficient cleavage in a cell. These requirements do not only help to expand our knowledge of the diverse CRISPR processing mechanisms, but also aid in the design of artificial arrays for experiments. With experiments performed by the Hess and Marchfelder groups, we will measure the effect of detailed sequence and structure constraints on processing efficiency.Finally, we want to, in collaboration with Jörg Vogel/Nadja Heidrich and Emmanuelle Charpentier, characterize further type II systems that require a non-coding RNA (tracrRNA). These systems are especially interesting since they are widely used for genome editing.

大多数古细菌和许多细菌都有一种防御系统，可以抵御各种入侵的遗传因子，称为CRISPR-Cas系统，该系统基于RNA。该项目旨在通过使用高度先进的生物信息学方法更好地了解CRISPR-Cas系统。首先，我们将为CRISPR-Cas系统开发一个完全自动化的注释管道。CRISPR-Cas系统在方便的注释应用方面存在严重缺陷。除了我们对CRISPR进化的自动化表征之外，（CRISPRmap），我们打算开发一个网络服务器工具箱，用于CRISPR-Cas系统的许多其他重要方面的全面自动计算机表征，包括CRISPR方向的预测，前导序列和CRISPR-Cas亚型的第一个自动注释。我们希望识别CRISPR靶点（即原型间隔区）并表征相关的原型间隔区邻近基序（PAM），这对适应和干扰都很重要。我们的目标是首先从病毒基因组和宏基因组学数据中收集一组原型间隔区。随后，我们将识别和分析相关PAM的模式。表征的PAM基序及其性质将由Schmitz-Streit和Randau的小组进行验证。第三，我们希望检测导致细胞中有效切割的CRISPR阵列的要求。这些要求不仅有助于扩大我们对不同CRISPR处理机制的了解，还有助于设计用于实验的人工阵列。通过Hess和Marchfelder小组进行的实验，我们将测量详细序列和结构约束对处理效率的影响。最后，我们希望与Jörg Vogel/Nadja Heidrich和Emmanuelle Charpentier合作，进一步表征需要非编码RNA（tracrRNA）的II型系统。这些系统特别有趣，因为它们被广泛用于基因组编辑。