雷蒙德氏棉和拟南芥基因启动子中顺式作用元件的分布
收稿日期: 2013-04-07
修回日期: 2013-07-22
网络出版日期: 2013-10-25
基金资助
Gossypium raimondii; genome-wide; cis-regulatory element (CRE)
Analysis of cis-regulatory element distribution in gene promoters of Gossypium raimondii and Arabidopsis thaliana
Received date: 2013-04-07
Revised date: 2013-07-22
Online published: 2013-10-25
随着雷蒙德氏棉(Gossypium raimondii)基因组草图的完成, 相关的基因组学研究已经全面展开。文章利用已公布的雷蒙德氏棉和拟南芥基因组序列, 结合顺式作用元件(cis-regulatory element, CRE)数据库PLACE中的CRE序列信息, 对两个物种中带有5′UTR注释的基因启动子上游1 000 bp序列进行CRE扫描和统计。结果表明, 雷蒙德氏棉和拟南芥基因组中分别有44(12.3%)和57(15.5%)个CRE在启动子的特定位置呈峰状分布, 其中在两个基因组均呈峰状分布的有34个, 这些CRE又可以根据核心序列分为4大类。TATABOX类CRE顶峰在启动子中出现的位置和其真实位置(~ -30 bp)具有一致性, 预示CRE真实位置在不同基因启动子中相对保守, 从而推测本研究中呈峰状分布CRE的顶峰位置可能就是转录因子和该CRE结合的真实位置。而同一CRE在两个基因组中存在的位置差异则主要源于雷蒙德氏棉基因的5′UTR长度变异大于拟南芥。另外, 文章还发现绝大多数峰状分布的CRE的位置都集中在-110 bp~0 bp之间, 这种集中的分布可能更有利于转录因子之间相互作用, 从而调控下游基因的表达。
孙高飞 何守朴 杜雄明 . 雷蒙德氏棉和拟南芥基因启动子中顺式作用元件的分布[J]. 遗传, 2013 , 35(10) : 1226 -1236 . DOI: 10.3724/SP.J.1005.2013.01226
Cotton genomic studies have boomed since the release of Gossypium raimondii draft genome. In this study, cis-regulatory element (CRE) in 1 kb length sequence upstream 5′ UTR of annotated genes were selected and scanned in the Arabidopsis thaliana (At) and Gossypium raimondii (Gr) genomes, based on the database of PLACE (Plant cis-acting Regulatory DNA Elements). According to the definition of this study, 44 (12.3%) and 57 (15.5%) CREs presented “peak-like” distribution in the 1 kb selected sequences of both genomes, respectively. Thirty-four of them were peak-like distributed in both genomes, which could be further categorized into 4 types based on their core sequences. The coincidence of TATABOX peak position and their actual position (~ -30 bp) indicated that the position of a common CRE was conservative in different genes, which suggested that the peak position of these CREs was their possible actual position of transcription factors. The position of a common CRE was also different between the two genomes due to stronger length variation of 5′ UTR in Gr than At. Furthermore, most of the peak-like CREs were located in the region of -110 bp~0 bp, which suggested that concentrated distribution might be conductive to the interaction of transcription factors , and then regulate the gene expression in downstream.
Key words： Gossypium raimondii; genome-wide; cis-regulatory element (CRE)
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