Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of arabidopsis
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of arabidopsis
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DOI：
10.1104/pp.104.046466
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发表时间：
2004-10-01
期刊：
影响因子：
7.4
通讯作者：
Mayer, KFX
中科院分区：
文献类型：
--
作者：
Haberer, G;Hindemitt, T;Mayer, KFX
在植物中，单个基因、长染色体区域以及完整基因组的重复为进化创新提供了一个主要来源。我们利用大规模平行特征测序法所测得的全基因组大量表达数据，研究了拟南芥中两种不同类型的重复——串联重复和片段重复，以了解其表达特征的相关性、保守性和差异。我们的分析表明，很大一部分重复基因对仍然具有转录特征的相似性。然而，我们的结果也表明，重复基因对之间经常发生表达差异，这一过程可能经常被用于保留序列冗余的基因对。重复基因启动子之间总体相似性的保留以及各个启动子内单个顺式元件的保留表明，转录新功能化和亚功能化过程仅限于一部分顺式元件。我们表明，重复启动子内的序列相似性和共享的调控特性为通过应用基因组内系统发育足迹法进行大规模顺式调控元件鉴定提供了一种有力手段。我们的工作为未来的比较研究奠定了基础，以阐明重复基因调控相似性和差异性的分子表现。
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications, tandem and segmental duplications, in Arabidopsis for correlation, conservation, and differences of expression characteristics by making use of large genome-wide expression data as measured by the massively parallel signature sequencing method. Our analysis indicates that large fractions of duplicated gene pairs still share transcriptional characteristics. However, our results also indicate that expression divergence occurs frequently between duplicated gene pairs, a process which frequently might be employed for the retention of sequence redundant gene pairs. Preserved overall similarity between promoters of duplicated genes as well as preservation of individual cis-elements within the respective promoters indicates that the process of transcriptional neo- and subfunctionalization is restricted to only a fraction of cis-elements. We show that sequence similarities and shared regulatory properties within duplicated promoters provide a powerful means to undertake large-scale cis-regulatory element identification by applying an intragenomic phylogenetic footprinting approach. Our work lays a foundation for future comparative studies to elucidate the molecular manifestation of regulatory similarities and dissimilarities of duplicated genes.