Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Page 11 of 15 Table 4 Conservation of the three [-39, -26]-PLM classes in orthologous gene pairs between A. thaliana and O. sativa. Number of ortholog pairs with PLM in A. thaliana (a) O. sativa (b) Both species (c) 393 343 997 531 655 602 Only TATAWA 82 6% Only TATAΔ-PLMs 138 11% Only TC[-39,-26]-PLMs 98 12% In the 5805 pairs of orthologous genes between A. thaliana and O. sativa, we searched for the number of genes containing a given [-39,-26]-PLM (a) in A. thaliana but not in their respective O. sativa ortholog, (b) in O. sativa but not in their respective A. thaliana ortholog and (c) in both orthologous genes. The c/(a+c) ratio indicates the level of observed conservation for each PLM class in O. sativa in regard to A. thaliana. Then we compared the ratio to the by chance value, i.e. the ratio b/(5805-a-c): the presence of a given PLM in O. sativa orthologous genes from the PLM-less A. thaliana genes. We performed two one-sided Fisher exact tests allowing the identification of significantly different percentages. The underlined data indicate that the observed percentage is higher than expected. NS indicates non-significant difference. P-values in parenthesis are less than 5% with the Bonferroni correction. Percentage of PLM conservation Observed Expected by chance: 17% (7e-15) 12% (NS) 13% (NS) [53] and that the correlation between transcriptional range and intensity is rather weak [51]. Nevertheless, TATAΔ- and TC[-39,-26]-PLMs are conserved, both at the sequence level per se and at the occurrence level within the whole genome. Discussion and conclusions In A. thaliana and O. sativa, we identified a novel class of putative TFBS involving TC-elements that are prefer- entially located within the same core-promoter region as TATA-boxes. We showed that these TC-elements are structurally distinct from the previously described TC-microsatellites observed in the 5’UTR of plant genes. Nevertheless, the presence of both TC-elements and TC-microsatellites in higher plants but not in vertebrates suggests an evolu- tionary link between these two promoter elements. Previous reports have described the presence of a pyri- midine rich element, named the Y-patch, in plant core- promoters [21,26], and its tendency to be associated with both the TATA-box and the Inr motif [45]. Y- patch motifs and TC-microsatellites are two names used to globally describe T and C rich sequences widely sur- rounding the TSS. In promoters, these two elements are characterized by two non identical but overlapping groups of motifs. Our results show that the TC[-39,-26]- PLM exhibits specific characteristics distinguishing it from the other Y-patch motifs. Y-patch motifs show fre- quent occurrence in plant promoters, are present in a wide area around the TSS (see Figure 1) and may be extended from a 6- to a 10-base-long element without decreasing the score associated to their local overrepre- sentation (SMS). Indeed the TC[-39,-26]-PLMs were only observed in a sub-set of 18% of A. thaliana promoters at the TATA-box expected position, were associated with a sharp functional window, were 6-base-long and could not be extended without decreasing their SMS. Specific promoter features were frequently observed when genes were classified into groups, i.e. the TC-ele- ment-containing gene group, the TATA-box-containing gene group or the TATAΔ-PLMs-containing gene group. First, our data indicate that the TATA-box preferentially associates with a CA-TSS. Neither the TATAΔ- nor the TC-elements exhibited this apparent functional association. In addition, no association between the TATA-box and any of the three other YR- TSS was observed. Second, TC-element-containing genes were predominately large and involved in protein metabolism while TATA-box-containing genes were predominantly compact and involved in response to stress and stimulus. Indeed, gene function, specificity and level of expression are linked features. Using an ori- ginal approach we have been able to distinguish the pos- sible involvement of different [-39,-26]-elements in the control of either the level or the specificity of expres- sion. A global analysis of CATMA-transcriptome data indicated preferential links between the presence of: (i) a TATA-box and high gene expression; (ii) TC-elements and high specificity of gene expression; and (iii) TATAΔ-PLMs and broad expression patterns, as in housekeeping genes. All together our observations sug- gest that TC-elements might be considered as a novel class of plant promoter elements linked directly or indir- ectly to the regulation of gene expression. The presence of all three elements, i.e. TATA-boxes, TC- and TATAΔ-elements, have been observed in two plants that diverged about 150 millions of year ago [29]. We observed a global conservation, i.e. conservation in the relative number of genes containing one of the three motifs in the two genomes. Nevertheless, only the TATA-box showed a low level of conservation between orthologous gene pairs while conservation of either TC- or TATAΔ-elements between orthologous gene pairs was no higher than that found between any gene pair. On the one hand, the low level of conservation at the orthologous gene level is in line with the rapid evolution of core regulatory motifs after gene duplication in A. thaliana [43] and with the notion that A. thaliana and O. sativa may have independently evolved novel TSSs [54]. On the other hand, the conservation of the relative number of genes with either a TATA-box, a TC- or a TATAΔ-element suggests a global conservation of the interspecies variability, noise level and evolvability of gene expression; three processes involving TATA