Analysis of the 5S RNA pool in Arabidopsis thaliana:: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA

One major SS RNA, 120 bases long, was revealed by an analysis of mature SS RNA from tissues, developmental stages, and polysomes in Arabidopsis thaliana. Minor SS RNA were also found, varying from the major one by one or two base substitutions; SS rDNA units from each SS array of the Arabidopsis genome were isolated by PCR using CIC yeast artificial chromosomes (YACs) mapped on the different loci. By using a comparison of the SS DNA and RNA sequences, we could show that both major and minor SS transcripts come from only two of the genomic SS loci: chromosome 4 and chromosome 5 major block. Other SS loci are either not transcribed or produce rapidly degraded SS transcripts. Analysis of the 5'- and 3'-DNA flanking Sequence has permitted the definition of specific signatures for each SS rDNA array.