Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 R E S E A R C H A R T I C L E Open Access TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation Virginie Bernard1, Véronique Brunaud1, Alain Lecharny1,2* Abstract Background: The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. Indeed different core-promoter elements are involved in the recruitment of the TATA-box-binding protein. Here we assessed the possibility of identifying novel functional motifs in plant genes, sharing the TATA-box topological constraints. Results: We developed an ab-initio approach considering the preferential location of motifs relative to the TSS. We identified motifs observed at the TATA-box expected location and conserved in both Arabidopsis thaliana and Oryza sativa promoters. We identified TC-elements within non-TA-rich promoters 30 bases upstream of the TSS. As with the TATA-box and TATA-variant sequences, it was possible to construct a unique distance graph with the TC- element sequences. The structural and functional features of TC-element-containing genes were distinct from those of TATA-box- or TATA-variant-containing genes. Arabidopsis thaliana transcriptome analysis revealed that TATA-box- containing genes were generally those showing relatively high levels of expression and that TC-element-containing genes were generally those expressed in specific conditions. Conclusions: Our observations suggest that the TC-elements might constitute a class of novel regulatory elements participating towards the complex modulation of gene expression in plants. Background Over the past genomics has markedly changed our view on core-promoter organization [1]. For instance, the TATA-box can no longer be regarded as a general fea- ture of polymerase II core-promoters [2]. Indeed, only a small fraction of eukaryotic genes actually harbour a TATA-box: less than 20% of genes in both human [3] and yeast [4]. While TATA-box-containing promoters support the direct binding of TATA-box-Binding Pro- teins (TBPs) and thereby also the formation of the pre- initiation complex, TATA-less promoters are recognized by multiple TBP-related proteins and other TBP-asso- ciated Transcription Factors (TFs) involved in the recruitment of TBP [5]. Indeed some TATA-variants and other alternative elements allow the initiation of * Correspondence: lecharny@evry.inra.fr 1Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 -CNRS 8114 -UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France transcription and participate towards defining distinct patterns of expression [4,6-9]. Several core-promoter elements or general Transcrip- tion Factor Binding Sites (TFBSs) have been previously identified in eukaryotes. They are characterized by a strong positional preference relative to the Transcrip- tional Start Site (TSS) as for instance the TATA-box in the [-30, -25] area [8], the Initiator element, (Inr), around the TSS [10], the downstream promoter element in the [+28, +33] area [11], or the IIB recognition ele- ment immediately upstream of certain TATA-boxes [12]. The position of binding sites of proteins belonging to the transcription complex is important for the func- tioning of promoters since it determines both the TSS location [13] and the transcription direction [5]. Thus, a strong positional conservation of a novel regulatory ele- ment would strongly indicate a functional role. This concept has led to a generation of tools that in contrast © 2010 Bernard et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.