Identification of polyadenylation signals and alternative polyadenylation in Vitis vinifera based on ESTs data
Identification of polyadenylation signals and alternative polyadenylation in Vitis vinifera based on ESTs data
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DOI：
10.1016/j.scienta.2007.10.009
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发表时间：
2008-02-01
影响因子：
4.3
通讯作者：
Yao, Quan-Hong
中科院分区：
文献类型：
--
作者：
Cai, Bin;Peng, Ri-He;Yao, Quan-Hong
多聚腺苷酸化是转录后加工事件之一，它需要前信使核糖核酸3‘端的一些序列信号来确定多聚腺苷化位点(PS)。一些前-mRNAs含有多个多聚腺苷酸化位点，产生具有可变长度的3‘端的成熟转录本。为了阐明葡萄多腺化信号和交替多腺化，我们在每个Unigene条目中提取了62,811个3‘表达序列标签(EST)，并对每个转录单位的EST进行了比对。在筛选人工聚(A)位点后，总共有27.9%的序列被发现含有替代的多聚腺苷基化位点。为了弄清多聚腺苷酸化信号的模式，建立了三个包含多聚腺苷酸化位点的序列数据集。对数据集中序列特征的分析表明，在PS之前，尿嘧啶的含量开始增加，最高可达40%-100Nt。近一半被检测的序列在切割和聚(A)加成部位对CA或UA有严格的要求。PS上游-15nT到-25nT的序列是一个富含A的基序，对应于动物体内严格的多聚腺苷信号AAUAAA。在葡萄中，大多数富含A的基序都是AAUAAA的变体。PS通常出现在富U元素之后和之前，没有显性的特定六核苷酸基序。葡萄多聚腺苷信号的整体模式更类似于酵母，而不是动物。(C)2007 Elsevier B.V.保留所有权利。
Polyadenylation, one of the post-transcriptional processing events, requires some sequence signals on the 3' end of pre-mRNA to determine the polyadenylation site (PS). Some pre-mRNAs contain multiple polyadenylation sites, producing mature transcripts with 3' end of variable length. To elucidate polyadenylation signals and alternative polyadenylation in Vitis vinifera, we extracted 62,811 3' expressed sequence tags (ESTs) of V vinifera in each UniGene entry and aligned the clustered ESTs of each transcription unit. After filtering artificial poly(A) sites, a total of 27.9% of the sequences examined were found to contain alternative polyadenylation sites. To clarify the pattern of polyadenylation signals, three datasets of sequences containing polyadenylation site were built. Analysis of sequence features in the datasets indicated that the content of uracil begins to increase up to 40% 100 nucleotides (nt) before the PS. Nearly half of the sequences examined showed stringent requirement of CA or UA at cleavage and poly(A) addition sites. The sequence at -15 nt to -25 nt upstream of the PS has been characterized as an A-rich motif, corresponding to the strict polyadenylation signal, AAUAAA, in animals. In grape, most A-rich motifs are variants of AAUAAA. PS commonly occurs following and preceding U-rich element, without a dominant specific hexanucleotide motif. The whole pattern of polyadenylation signals in V. vinifera is more similar to yeasts than animals. (c) 2007 Elsevier B.V. All rights reserved.