| Summary: | <p>Abstract</p> <p>Background</p> <p>Short interstitial telomere motifs (<it>telo </it>boxes) are short sequences identical to plant telomere repeat units. They are observed within the 5' region of several genes over-expressed in cycling cells. In synergy with various <it>cis</it>-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of <it>telo </it>boxes within <it>Arabidopsis thaliana </it>and <it>Oryza sativa </it>genomes and their association with genes involved in the biogenesis of the translational apparatus.</p> <p>Results</p> <p>Our analysis showed that the distribution of the <it>telo </it>box (AAACCCTA) in different genomic regions of <it>A. thaliana </it>and <it>O. sativa </it>is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in <it>Arabidopsis</it>, a conserved topological association of <it>telo </it>boxes with site II or TEF <it>cis</it>-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in <it>O. sativa</it>. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of <it>telo </it>boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between <it>telo </it>boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters.</p> <p>Conclusions</p> <p>The data reported in this work support the model previously proposed for the spreading of <it>telo </it>boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of <it>telo </it>boxes with site II or TEF <it>cis</it>-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.</p>
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