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Open Access Research article

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 and Alain Lecharny12*

Author affiliations

1 Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 -CNRS 8114 -UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France

2 Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP), UMR CNRS 8618 -UPS, Bâtiment 630, 91405 Orsay Cedex, France

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Citation and License

BMC Genomics 2010, 11:166  doi:10.1186/1471-2164-11-166

Published: 12 March 2010

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.