PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

Abstract

Background: The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.

Results: This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial cis-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.

Conclusion: In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at http://PlantPAN.mbc.nctu.edu.tw.

Figure 1

System flow of PlantPAN. PlantPAN has two query interfaces. "Gene group analysis" discovers the co-occurrence of TFBSs in a group of gene promoters; "Promoter analysys" contains three subfunctions: "Search" and "Novel promoter sequence" search TFBSs, CpG/CpNpG islands and tandem repeats in a single input gene ID or a novel input promoter sequence; "Cross-Species" identifies TFBSs in conserved regions between homologous or two promoters.

Figure 2

Gene group analysis in PlantPAN. The "Gene group analysis" process has seven steps. Following GO function analysis, promoter extraction and TFBS scanning, the co-occurrence of TFBSs and combinatorial TFBSs in a group of gene promoters is tabulated and presented in two figures (with and without distance constraint).

Figure 3

Results of case study I in "Gene group analysis". (A) Reference case taken from Chawade et al., 2007 [10]. The genes used in the case study are At4g17550.1, At1g20450.1, At5g52310.1, At4g37150.1, and At1g20440.1. The origin of the arrow indicates the regulating TF family and the endpoint of the arrow indicates the target gene. The time scale shown on the vertical axis is cold treatment of plant. (B) CBFHV (AP2) displayed co-occurrences in At4g17550.1, At1g20450.1, At5g52310.1, At4g37150.1, and At1g20440.1 (C) CBFHV (AP2) and DOF represented combinatorial co-occurrences in At5g52310.1, At4g17550.1, At4g37150.1, and At1g20440.1 with 100 bp distance constraint between CBFHV and DOF.

Figure 4

Web interface for a search for a single gene in PlantPAN. The "Search" web tool can be used to search for general gene information and gene regulatory features; furthermore, (B) tabulated results contain general gene information and "Promoter Analysis" functions. The "Promoter analysis" functions can be used to identify regulatory elements in the promoter sequence.

Figure 5

Graphical view of a case (AT1G48990) of "Cross-Species" analysis. The conserved regions and TFBSs in the conserved regions are shown in a figure significantly. Each conserved site or TFBS can be further clicked for more detailed information.