Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

摘要

Background In plants, the 5?S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35?S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5?S genes in several species from family Asteraceae known to contain linked 35?S-5?S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed L_s-type). The linked genes dominate 5?S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’) is proposed. The 5?S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35?S-5?S arrays with nucleolar periphery indicating that transcription of 5?S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5?S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5?S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.