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农杆菌T-DNA在拟南芥中的整合与基因启动子区域频繁出现的DNA序列组成相关。

Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions.

作者信息

Schneeberger Richard G, Zhang Ke, Tatarinova Tatiana, Troukhan Max, Kwok Shing F, Drais Josh, Klinger Kevin, Orejudos Francis, Macy Kimberly, Bhakta Amit, Burns James, Subramanian Gopal, Donson Jonathan, Flavell Richard, Feldmann Kenneth A

机构信息

Ceres, Inc., Thousand Oaks, CA 91320, USA.

出版信息

Funct Integr Genomics. 2005 Oct;5(4):240-53. doi: 10.1007/s10142-005-0138-1. Epub 2005 Mar 3.

Abstract

Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5' and 3' flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5' upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration.

摘要

转座子和T-DNA等可移动插入元件能产生有用的遗传变异,是动植物功能基因组学研究的重要工具。在不同系统中获得的突变谱可能会受到DNA整合机制中固有的靶位点偏好的高度影响。我们研究了农杆菌T-DNA在模式植物拟南芥染色体中的插入靶位点偏好。计算了基因组基因区域和基因间区域的相对插入频率,并确定了与插入位点侧翼序列相关的DNA组成特征。全基因组的插入频率表明,T链整合在着丝粒和核糖体DNA位点附近受到抑制,向端粒方向逐渐增加,并且与基因密度高度相关。在基因水平上,T-DNA整合事件在蛋白质编码序列的5'和3'侧翼区域以及RNA聚合酶I转录的rRNA基因重复序列的启动子区域插入方面表现出统计学上的显著偏好。与编码序列相比,5'上游区域插入频率的增加与基因表达活性和DNA序列组成呈正相关。对DNA序列组成与基因活性之间关系的分析进一步表明,具有高CG偏斜率的DNA序列始终与T-DNA插入位点偏好和高基因表达相关。结果表明了T链整合在基因组和基因特异性方面的偏好,并表明在CG和AT偏斜率上有明显转变的DNA序列是T-DNA整合的优先靶标。

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