Identification of plant promoter constituents by analysis of local distribution of short sequences.
Identification of plant promoter constituents by analysis of local distribution of short sequences.
复制标题
DOI：
10.1186/1471-2164-8-67
复制
发表时间：
2007-03-08
期刊：
影响因子：
4.4
通讯作者：
Abe T
中科院分区：
文献类型：
--
作者：
Yamamoto YY;Ichida H;Matsui M;Obokata J;Sakurai T;Satou M;Seki M;Shinozaki K;Abe T
植物启动子结构对于理解启动子的调控和进化是重要的，但是我们目前对植物启动子结构的了解，特别是关于核心启动子的了解，是不够的。TATA盒等启动子元件和多种转录调控元件在启动子中的局部分布已被发现，这一特性已被成功地用于从人类基因组中提取启动子组分。已经通过计算机分析了短序列沿着植物启动子的LDSS（Local Distribution of Short Sequences，短序列的局部分布）谱，并且已经鉴定出数百个六聚体和八聚体序列在拟南芥和水稻的启动子内具有局部分布。根据它们的定位模式，所鉴定的序列可以分为三组，嘧啶补丁（Y补丁），TATA盒，和REG（调节元件组）。TATA盒组的序列与先前研究中报道的序列一致。REG组包括200多个序列，其中一半对应于已知的顺式元件。其他REG亚组，连同约100个未分类的序列，被认为是新的顺式调控元件。拟南芥和水稻之间的LDSS阳性序列的比较揭示了中度保守的元件和共同的启动子结构。此外，在转录起始位点（-1/+1）处已经鉴定了称为YR规则（C/TA/G）的二聚体基序。这一规则也适用于拟南芥和水稻启动子。LDSS已成功地应用于植物基因组和数百个推定的启动子元件已被提取为LDSS阳性八聚体。已鉴定的单子叶植物和双子叶植物的启动子结构是很保守的，但在所利用的序列中存在适度的变异。
Plant promoter architecture is important for understanding regulation and evolution of the promoters, but our current knowledge about plant promoter structure, especially with respect to the core promoter, is insufficient. Several promoter elements including TATA box, and several types of transcriptional regulatory elements have been found to show local distribution within promoters, and this feature has been successfully utilized for extraction of promoter constituents from human genome. LDSS (Local Distribution of Short Sequences) profiles of short sequences along the plant promoter have been analyzed in silico, and hundreds of hexamer and octamer sequences have been identified as having localized distributions within promoters of Arabidopsis thaliana and rice. Based on their localization patterns, the identified sequences could be classified into three groups, pyrimidine patch (Y Patch), TATA box, and REG (Regulatory Element Group). Sequences of the TATA box group are consistent with the ones reported in previous studies. The REG group includes more than 200 sequences, and half of them correspond to known cis-elements. The other REG subgroups, together with about a hundred uncategorized sequences, are suggested to be novel cis-regulatory elements. Comparison of LDSS-positive sequences between Arabidopsis and rice has revealed moderate conservation of elements and common promoter architecture. In addition, a dimer motif named the YR Rule (C/T A/G) has been identified at the transcription start site (-1/+1). This rule also fits both Arabidopsis and rice promoters. LDSS was successfully applied to plant genomes and hundreds of putative promoter elements have been extracted as LDSS-positive octamers. Identified promoter architecture of monocot and dicot are well conserved, but there are moderate variations in the utilized sequences.
登录
查看更多内容
影响因子：
46.9
作者：
Bajic, VB;Tan, SL;Sugano, S
通讯作者：
Sugano, S
影响因子：
64.8
作者：
Kellis, M;Patterson, N;Lander, ES
通讯作者：
Lander, ES
影响因子：
30.8
作者：
Ioshikhes, IP;Zhang, MQ
通讯作者：
Zhang, MQ
影响因子：
4.4
作者：
Fujimori, S;Washio, T;Tomita, M
通讯作者：
Tomita, M
影响因子：
7
作者：
Blanchette, M;Bataille, AR;Robert, FO
通讯作者：
Robert, FO