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
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(Beijing), 2013 , 35(10) : 1226 -1236 . DOI: 10.3724/SP.J.1005.2013.01226
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