[Analysis of cis-regulatory element distribution in gene promoters of Gossypium raimondii and Arabidopsis thaliana].
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.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy ofAgricultural Sciences, Anyang 455000, China. sungaofei@sina.com
Gao-Fei
GF
Sun
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy ofAgricultural Sciences, Anyang 455000, China.
Shou-Pu
SP
He
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy ofAgricultural Sciences, Anyang 455000, China.
Xiong-Ming
XM
Du
D017360:Arabidopsis / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D003368:Gossypium / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic; D016385:TATA Box
D010940:Plant Proteins