Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome
Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome
复制标题
DOI：
10.1046/j.1365-313x.2002.01417.x
复制
发表时间：
2002-10-01
期刊：
影响因子：
7.2
通讯作者：
Koncz, C
中科院分区：
文献类型：
--
作者：
Szabados, L;Kovács, I;Koncz, C
利用T-DNA插入突变技术诱导基因敲除突变被广泛应用于植物基因功能的研究。为了评估这种遗传方法的效率，我们对1000个T-DNA插入的PCR扩增接头进行了测序，并分析了它们在拟南芥基因组中的分布。973个标签的图谱位置可以明确地确定，表明大多数T-DNA插入降落在染色体域的高基因密度。只有4.7%的插入被发现在散置，着丝粒，端粒和rDNA重复序列，而0.6%的测序标签确定染色体整合段的细胞器DNA。35.4%的T-DNA位于预测基因的ATG和终止密码子之间，其中62.2%位于外显子，37.8%位于内含子。T-DNA标签在编码区和基因间区的频率与预测的这些序列在基因组中的大小分布表现出良好的相关性。然而，在基因的3 '和5'调控区，对应于终止密码子3'下游和ATG密码子5'上游的300 bp间隔，T-DNA插入的频率比基因组中其他任何类似间隔高1.7-2.3倍。在5 '调控区和编码区的插入频率的加和提供了突变率的估计，表明47.8%的映射T-DNA标签诱导敲除突变在拟南芥中。
Induction of knockout mutations by T-DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T-DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T-DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T-DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T-DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T-DNA insertions in 3'- and 5'-regulatory regions of genes, corresponding to 300 bp intervals 3' downstream of stop and 5' upstream of ATG codons, was 1.7-2.3-fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5'-regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T-DNA tags induced knockout mutations in Arabidopsis .