TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulationReport as inadecuate




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BMC Genomics

, 11:166

First Online: 12 March 2010Received: 27 July 2009Accepted: 12 March 2010

Abstract

BackgroundThe 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.

ResultsWe 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.

ConclusionsOur observations suggest that the TC-elements might constitute a class of novel regulatory elements participating towards the complex modulation of gene expression in plants.

AbbreviationsCATMAComplete Arabidopsis Transcriptome MicroArray

TFBSTranscription Factor Binding Site

GOGene Ontology

HEHigh Expression

LELow Expression

PLMPreferentially Located Motif

SMSScore of Maximal Square relative to the base line

SRSmall Range

TBPTATA-binding protein

TSSTranscriptional Start Site

WRWide Range

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-11-166 contains supplementary material, which is available to authorized users.

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Author: Virginie Bernard - Véronique Brunaud - Alain Lecharny

Source: https://link.springer.com/article/10.1186/1471-2164-11-166







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