Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Page 10 of 15 Table 3 Expression of A. thaliana genes for the four promoter classes. Gene sets All genes HE LE SR WR WR-HE+ WR-LE+ SR-HE+ SR-LE+ 39.2% 60.8% 40.4% 11.1% 2.2% 3.4% 5.5% 7.4% Only TATA-box 53.8% (< 1e-30) 46.2% (2e-24) 41% (NS) 10.3% (NS) 2.4% (NS) 2.5% (NS) 8.5% (1e-5) 5% (< 1e-30) Only TC[-39,-26]-PLMs 36.7% (NS) 63.3% (NS) 44.1% (< 1e-30) 9.3% (NS) 1.6% (NS) 3.1% (NS) 5.3% (NS) 8.6% (NS) Only TATAΔ-PLMs 38.1% (NS) 61.9% (NS) 37.4% (< 1e-30) 13.2% (< 1e-30) 2.2% (NS) 4.0% (NS) 5.3% (NS) 6.8% (NS) [-39,-26]-PLM-less 34.5% (1e-22) 65.5% (< 1e-30) 40.2% (NS) 11.2% (NS) 2.3% (NS) 3.8% (NS) 4.6% (8e-6) 8.1% (< 1e-30) The 8 expression categories are described in the Figure 7. HE, High Expression; LE, Low Expression; SR Small Range of expression; WR, Wide Range of expression; HE+ Highest Expressions; LE+, Lowest Expressions. The whole gene set contains the 11161 genes for which we have both a known TSS and CATMA-expression data. We performed two one-sided Fisher exact tests allowing the identification of higher (bold) or lower (underlined) percentages in a gene set in comparison with all other genes, i.e. genes within the whole gene set minus genes within the considered gene set. NS indicates non-significant difference. P-values in parenthesis are less than 5% with the Bonferroni correction. contained TC[-39,-26]-PLM; (ii) genes within the tran- scriptional WR group, i.e. housekeeping genes predomi- nantly contained a TATAΔ-PLM; (iii) the transcriptional HE group was enriched with the TATA- box-containing genes and (iv) the transcriptional LE group was enriched with the [-39,-26]-PLM-less genes. These results clearly indicate a link between the differ- ent motifs within the core-promoter and transcriptional features of the gene and are in favour of a functionally independent role of the TATA-box, the TATAΔ- and the TC[-39,-26]-PLMs. Our observations provide further evidence for the involvement of the TATA-box in the regulation of transcription level. In addition, our results suggest that both TATAΔ- and TC[-39,-26]-PLMs might be involved in defining the specificity of transcription. The role of the TATAΔ-PLMs might be to promote a relatively wide range of expression while on the other hand TC[-39,-26]-PLMs may impose narrower limits. The adverse effect of TATAWA and [-39,-26]-PLM-less within genes on the extreme level of transcription (see Meth- ods section) was particularly evident in the SR group (Table 3, last two rows). The most Highly Expressed genes (HE+ genes) were predominantly those containing TATAWA whereas the most Lowly Expressed genes (LE+ genes) were mainly [-39,-26]-PLM-less genes. We propose that in the presence of a TATA-box, the recog- nition of the TSS depends directly on a small number of TBPs and/or of TBP-related protein(s). The relaxed recognition by TBPs in TATAΔ-containing promoters might be responsible for a bias towards the large range of expression. In the absence of TATA-box or TATAΔ, the recruitment of the TBP might be mediated by dif- ferent TBP-associated TFs depending on the gene. Interaction of the different TBP-associated TFs with other specific factors might therefore explain the rela- tively higher specificity of transcription observed for the TC[-39,-26]-PLM gene set. The class of regulatory element in the [-39, -26] region is not conserved in higher plant orthologous gene pairs With the increasing availability of transcriptome data, the search for conserved TFBSs within promoters of genes exhibiting similar transcriptional patterns has gathered much attention. Surprisingly, the conservation of core- promoter elements, widely considered as being those most conserved, has not received such large interest. One recent study addressing this question did cast doubt on this widely accepted notion [52]. Concordantly, in several studies on orthologous relationships between large gene families, we observed no significant conservation of the presence of a TATA-box between plant orthologues (data not shown). Even single copy genes present as orthologues in both A. thaliana and O. sativa are no more conserved than random pairs of genes [53]. The co-occurrence of different elements in the [-39, -26] pro- moter region could, at least in part, explain an apparent non-conservation at the gene level despite the observed conservation at the genomic one. This prompted us to reexamine the question comparing core-promoter ele- ments in the [-39, -26] region in A. thaliana and O. sativa. We analysed the conservation of the three classes of [-39,-26]-PLMs in 5805 pairs of orthologous genes in A. thaliana and O. sativa characterized by an experimentally supported TSS. While the conserva- tion of TATAWA appeared relatively low (17%), it was significantly higher than that expected by chance (6%) (Table 4). This was not the case for TATAΔ- or TC [-39,-26]-PLMs, which exhibited no conservation between orthologous genes (Table 4). Our results showing that the TATA-box is more involved at the transcriptional level and that both TATAΔ- and TC[-39,-26]-PLMs are more involved in specificity are in line with finding. All together our observations are in accordance with the fact that gene transcription levels are positively correlated between orthologous genes in A. thaliana and O. sativa