摘要
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。
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 conser- vative in different genes, which suggested that the peak position of these CREs was their possible actual position of tran- scription factors. The position of a common CRE was also different between the two genomes due to stronger length varia- tion 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.
出处
《遗传》
CAS
CSCD
北大核心
2013年第10期1226-1236,共11页
Hereditas（Beijing)
基金
国家科技支撑计划项目(编号:2013BAD01B03)资助
关键词
雷蒙德氏棉
全基因组
顺式作用元件
Gossypium raimondii
genome-wide
cis-regulatory element （CRE）
