Abstract
BackgroundIn 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.ResultsWe 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 Ls-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.ConclusionsWe 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.
Highlights
In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S ribosomal DNA (rDNA) units (L-type)
The monomeric bands were amplified in A. absinthium, H. bracteatum, M. matricarioides and T. patula
In the case of tandem arrangement, mono and oligomeric products would be formed, the latter originating from polymerase read-through into neighboring units. This situation occurred in Linum alpinum, a species that typically evolved a separate arrangement of DNA units and which showed several oligomeric bands extending to a smear of an unresolved high-molecular-weight fraction (Figure 1C)
Summary
The 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S5 S units. Their methylation status was determined using bisulfite sequencing. Physical linkage of 5 S and 35 S genes predominates the organization of rDNA in streptophyte algae and early diverging land plants such as mosses [10,11] These studies led to the hypothesis that “liberation” of 5 S genes from the 35 S unit might have occurred in a common angiosperm ancestor after the separation from early diverging plants. The linked arrangement of 35 S-5 S units (hereafter L-type) was later found in several species from the genus Artemisia
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