Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome
Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome
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DOI：
10.1093/nar/gkg492
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发表时间：
2003-08-01
影响因子：
14.9
通讯作者：
Brendel, V
中科院分区：
文献类型：
--
作者：
Zhu, W;Brendel, V
U12依赖的内含子由微小的U12型剪接体剪接，存在于包括拟南芥在内的多种真核生物中。在本研究中，通过高通量生物信息学分析和人工筛选相结合的方法，从拟南芥基因组中大量经cDNA/EST证实的内含子集合中编辑了一组可能依赖于U12的内含子。根据严格的标准，共鉴定出165个U12型内含子。这个序列的数量远远超过了之前报道的植物U12型内含子的总数，并允许对U12型信号进行更全面的统计分析。特别值得注意的是，发现分支位点和受体位点之间的距离在10到39个核苷酸之间，显著长于先前假设的21个碱基的极限。进一步的分析表明，除了间距限制外，潜在受体位点的序列背景可能在3‘剪接位点的选择中起着重要作用。本研究还捕捉到了几种涉及U12型内含子的选择性剪接事件，这为U12依赖的受体位点也可以被U2型剪接体识别提供了证据。此外，系统发育分析表明，在一个动植物祖先体内同时存在U12型AT-AC和U12型GT-AG内含子，存在于Na+/H+逆向转运蛋白中。
U12-dependent introns are spliced by the minor U12-type spliceosome and occur in a variety of eukaryotic organisms, including Arabidopsis. In this study, a set of putative U12-dependent introns was compiled from a large collection of cDNA/EST- confirmed introns in the Arabidopsis thaliana genome by means of high-throughput bioinformatic analysis combined with manual scrutiny. A total of 165 U12-type introns were identified based upon stringent criteria. This number of sequences well exceeds the total number of U12-type introns previously reported for plants and allows a more thorough statistical analysis of U12-type signals. Of particular note is the discovery that the distance between the branch site adenosine and the acceptor site ranges from 10 to 39 nt, significantly longer than the previously postulated limit of 21 bp. Further analysis indicates that, in addition to the spacing constraint, the sequence context of the potential acceptor site may have an important role in 3' splice site selection. Several alternative splicing events involving U12-type introns were also captured in this study, providing evidence that U12-dependent acceptor sites can also be recognized by the U2-type spliceosome. Furthermore, phylogenetic analysis suggests that both U12-type AT-AC and U12-type GT-AG introns occurred in Na+/H+ antiporters in a progenitor of animals and plants.