Abstract
BackgroundShort interstitial telomere motifs (telo 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 cis-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of telo boxes within Arabidopsis thaliana and Oryza sativa genomes and their association with genes involved in the biogenesis of the translational apparatus.ResultsOur analysis showed that the distribution of the telo box (AAACCCTA) in different genomic regions of A. thaliana and O. sativa 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 Arabidopsis, a conserved topological association of telo boxes with site II or TEF cis-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in O. sativa. 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 telo 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 telo boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters.ConclusionsThe data reported in this work support the model previously proposed for the spreading of telo boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of telo boxes with site II or TEF cis-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.
Highlights
Short interstitial telomere motifs are short sequences identical to plant telomere repeat units
These cis-acting elements include the TEF1 box identified in promoters of the translation elongation factor EF1a [14], the Trap1 box in the promoter of a rp gene [15] and redundant site II motifs initially characterized in the promoter of the proliferating cellular nuclear antigen gene (PCNA) [16] and subsequently in most Arabidopsis rp genes [11]
A chi-square test was used to determine whether the observed frequencies of telobox in the different compartments markedly differ from the frequencies that we would expect by chance
Summary
Short interstitial telomere motifs (telo boxes) are short sequences identical to plant telomere repeat units. The telo box (AAACCCTA), was first observed within the promoter of the four Arabidopsis genes encoding the translation elongation factor EF1apromoters [3,4] and subsequently within a few plant rp promoters [5] This short motif is identical to the repeat (AAACCCT)n of plant telomeres [6] but differs from long interstitial telomere repeats (ITRs) which are found at discrete intrachromosomal sites in many eukaryotic species [7,8] and probably result from chromosomal rearrangements such as end-fusions and segmental duplications. Experimental data indicated that the telo box was involved in the expression in cycling cells [11,12,13] By itself this motif is not able to activate the transcription by RNA pol II but acts in synergy with various cis-acting elements to increase the expression. These cis-acting elements include the TEF1 box identified in promoters of the translation elongation factor EF1a [14], the Trap box in the promoter of a rp gene [15] and redundant site II motifs initially characterized in the promoter of the proliferating cellular nuclear antigen gene (PCNA) [16] and subsequently in most Arabidopsis rp genes [11]
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