雷蒙德氏棉和拟南芥基因启动子中顺式作用元件的分布

doi:10.3724/SP.J.1005.2013.01226

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HEREDITAS ›› 2013, Vol. 35 ›› Issue (10): 1226-1236.doi: 10.3724/SP.J.1005.2013.01226

Analysis of cis-regulatory element distribution in gene promoters of Gossypium raimondii and Arabidopsis thaliana

SUN Gao-Fei^1,2, HE Shou-Pu¹, DU Xiong-Ming¹

1. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
2. Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang 455000, China

Received:2013-04-07 Revised:2013-07-22 Online:2013-10-20 Published:2013-10-25

Abstract

Abstract:

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)

SUN Gao-Fei HE Shou-Pu DU Xiong-Ming. Analysis of cis-regulatory element distribution in gene promoters of Gossypium raimondii and Arabidopsis thaliana[J]. HEREDITAS, 2013, 35(10): 1226-1236.

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Analysis of cis-regulatory element distribution in gene promoters of Gossypium raimondii and Arabidopsis thaliana

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