Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 without Inr and TATA-less promoters. We observed the same relative representation of these three categories in Arabidopsis. Consistent with mammalian studies [44], recent evidence suggests that A. thaliana genes contain- ing a TATA-box tend to have a sharper dominant peak of TSS compared to that of other genes [45]. The distance between TATA-box and Inr is important for accurate transcription initiation [46]. We considered the distance between the Inr [21], called here YR-TSS, and the conserved PLMs characterized using our approach. As expected, the YR-TSS is a conserved PLM whose functional window is one base upstream of the TSS in both plants (data not shown). We first analysed the 1496 A. thaliana promoters containing a TATA-box and we represented the distances between each TATAWA in the [-39, -26] region and each dinucleotide CA, TA, TG and CG up to 70 bases downstream of the TATAWA (Figure 6.A). The dinucleotide CA, but not TA, TG or CG showed a strong preferred distance of 30 Figure 6 Distance between the four YR-TSSs relative to the three classes of [-39,-26]-PLMs in A. thaliana promoters. We computed the distance observed between each PLM of a given class of [-39,-26]-PLMs and all dinucleotides CA (red line), TG (yellow line), TA (blue line) and CG (green line) present downstream of the PLMs. The distance on the x-axis corresponds to the number of bases between the first base of a [-39,-26]-PLM and the first base of an YR-TSS. For instance, a distance of 8 bases between a TATAWA and a CA corresponds to the TATAWANNCA sequence in a promoter. We analysed the three gene sets containing a unique class of [-39,-26]-PLMs and represented the distance between (A) the TATAWA-, (B) the TATAΔ-, (C) the TC[-39,-26]-PLMs and the four YR- TSS sequences. Analyses done for each PLM led to the same representation as the global analysis done for the PLM class it belongs to: for instance, the analysis for the TTCTTC-PLM led to a (C) representation. Page 8 of 15 to 33 bases from TATAWA. This distance is consistent with the preferential position of both PLMs and with mammalian results [47]. Furthermore, none of the YR motifs showed a preferential distance either from TATAΔ- or from TC[-39,-26]-PLMs (Figure 6.B and 6.C). Finally, our results provide evidence of a link between the canonical TATA-box and the CA-TSS: 30 to 33 bases preferentially separate the CA from the first T of TATAWA. Genes containing the TC[-39,-26]-element are generally long In human, the presence of a TATA-box in promoters is often associated with a compact gene structure [6]. In A. thaliana, we observed the same bias towards a more compact structure of TATA-box-containing genes (Table 2). In contrast, the TC[-39,-26]-PLM-containing genes and the [-39,-26]-PLM-less genes were overall rela- tively longer while the gene structure of TATAΔ-PLM- containing genes showed no bias. When present, the bias in gene size was mainly explained by the 5’UTR and by the length of the coding sequence. However, to a lesser extent, the enrichment in compact genes amongst those containing a TATA-box may be explained by the shorter cumulative length of introns, and by the higher percentage of intronless genes (Table 2). Based on the counting of Expressed Sequence Tags (ESTs) [4] or on microarray data [6], gene size and gene expression levels have been shown previously to be inversely correlated in both human and yeast. This being the case, our observations could be due to the fact that, in general, TATA-box genes have higher expres- sion levels than other A. thaliana genes [19,21]. The dif- ferences in gene sizes we observed are consistent with a lower mean expression of TATAΔ-PLM- than of TATA-box-containing genes. Both TC[-39,-26]-PLM-con- taining and [-39,-26]-PLM-less genes could be expressed at lower levels. TATA-box-containing genes have been shown to generally display relatively high specificity of expression compared to housekeeping genes that fre- quently show high expression levels (Table 1). There- fore, the question remains as to understand whether the presence of regulatory elements in the [-39, -26] region of promoters is linked directly to gene function per se or to the transcription level that in turn is associated with gene function. To resolve this we analysed a large set of transcriptome data, distinguishing the two differ- ent components of transcription: specificity and level. Specific role played by each class of regulatory element found in the [-39, -26] region on different components of transcription In eukaryotic genomes, various TFBSs have been linked to specific gene expression patterns [4,6,9,48]. We