Characterization of human 5S rRNA genes

Abstract

The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant with an additional nucleotide in the internal control region. A fragment from the 1.6 kb cluster contains a gene and is highly homologous to the 2.3 kb repeats, except for a large deletion in the 3'-flanking region starting 12 bp downstream of the gene. The number of genes and closely related gene variants is found to be 300-400 per haploid human genome. 100-150 of these are found in 2.3 kb repeats and 5-10 are found in 1.6 kb repeats. The total number of 5S rRNA sequences, including pseudogenes, is 1700-2000 per haploid genome. The genes and the gene variant are transcribed equally efficient in a HeLa cell extract. If 5'-flanking sequences, including a GC-motif in the -40 region, are removed from the genes, transcription is reduced with a factor 10 or more, suggesting that sequences upstream of the coding region are important for the level of transcription.

Characterization of Aequipecten opercularis (Bivalvia: Pectinidae) chromosomes by different staining techniques and fluorescent in situ hybridization.

“…Two independent clusters located on one arm of a single chromosome pair were also identified in humans (Lomholt et al, 1995;Pelliccia et al, 1997). However, in this case, molecular studies indicated that 5S rDNA show heterogeneity both in coding and spacer regions (Sorensen and Frederiksen, 1991). Whether or not this occurs in A. opercularis remains to be determined, but nucleotide sequence obtained for one repeat unit of 5S rDNA from A. opercularis (Insua et al, unpublished data) and the stringent conditions used here suggest that hybridization with sequences other than 5S rDNA is unlikely.…”

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

“…The only coleoptera investigated in this manuscript (Tribolium) is not assembled on chromosomal level; however, it shows also one huge cluster of 151 5S rRNA copies. Previous reports have shown that copy number is very variable among metazoans: 1700-2000 copies (including pseudogenes) in humans (Sorensen and Frederiksen, 1991), 50-100 copies in Macaca fascicularis (Jensen and Frederiksen, 2000), 35-41 copies in the chicken (Daniels and Delany, 2003), 24 000-61 000 copies (including pseudogenes) in three amphibians (24 000 in Xenopus laevis (Hilder et al, 1983)) and only three copies in Plasmodium falciparum (Shippen-Lentz and Vezza, 1988). However, these estimates relied on the method used and on the ability to differentiate among functional and non-functional copies.…”

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

“…In humans, the 18S, 5.8S and 28S rRNA molecules are encoded within tandemly repeated 43-kb nucleolar organizing regions residing on the five acrocentric autosomal chromosomes (13, 14, 15, 21 and 22) 2 (Fig. 1), while the 5S rRNA is encoded by a tandemly repeated B2.2-kb cluster on chromosome 1 (1q42 region) 3 . In addition, B150 proteins and B70 small nucleolar RNAs interact or are associated with the ribosome during its biogenesis 4 .…”