Structural Properties Of Promoters In Arabidopsis Thaliana-A Genome-scale Analysis

During the last 20 years, the research of promoter and regulation of gene expression has attracted more and more research interest. The core promoter region is a key component in the regulation region of gene transcription initialized by RNA polymerase II, which includes DNA sequence elements that extend ~35bp upstream and downstream of the transcription start site (TSS). It is still unclear about how the special binding site on the wide promoter of genes recognized by specific transcription factors. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties.In our research, the structural properties of the promoters of Arabidopsis, such as the free energy distribution, bendability around the transcription start site and nucleotide compositions of promoter were studied in genome scale. All the promoter sequences used in this study are 1000 nt long, starting from 500 nt upstream (position -500) and extending up to 500 nt downstream (position +500) of the TSS.These results were compared with the properties from the vertebrates and E.coli promoters. It indicated that the structural profiles are much conserved within Arabidopsis and vertebrates, but differ considerably between Arabidopsis and E.coli. The results suggested that the promoter sequence from Arabidopsis showed the most stability, but the trends of the free energy and bendability distribution around the transcription start sites were conserved among the three groups. The obviously differences between upstream region and downstream region were observed, too.We also studied a GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residues. It showed significant GC-skew near the transcription start sites (TSS) of Arabidopsis genes but not in E.coli and vertebrate.We found the percentage occurrence of each dinucleotide in upstream was more than downstream region in the near vicinity of TSS in Arabidopsis and a similar AT-skew has been observed in Arabidopsis and E.coli. It might be caused by mutations during transcription initiation or the frequent use of transcription factor-biding sites having a strand preference.Finally, we used the free energy properties of promoter sequences to divide the total more than 29000 genes into 10 clusters. The genes expression levels were considered to implore the relationship between gene expression pattern and structural properties of promoters. Our results showed that the distribution of gene expression level in each cluster has no significant differences, which probably suggested that there were no direct correlations between gene expression and structural properties of promoters.The common properties and specificities of the promoters analyzed in our study give out some interesting clues about structural properties among different species, which would be provided as the complimentary materials for promoter analysis and transcription start sites prediction in the further research.