Evidence for strong purifying selection of human <i>47S</i> ribosomal RNA genes.

Abstract

The multicopy <i>47S</i> ribosomal RNA (rRNA) genes are among the most highly expressed genes in the human genome, yet to-date essentially no disease-causing sequence variants have been identified. This lack of disease association is surprising, as defects in <i>47S</i> rRNA transcription and changes in ribosomal protein dosage, as well as nucleotide changes in the mitochondrial rRNA, all result in disease. The failure to identify rRNA-associated diseases may thus primarily stem from the experimental challenges associated with analyzing this chromosomally isolated high-copy gene family. Here, we used an evolutionary approach to test whether mutations in the human <i>47S</i> genes can have phenotypic consequences. By analyzing sequence variants among rRNA genes across >3,000 individuals from the high-coverage 1,000 Genomes Project, we demonstrate highly stratified variant abundance across the <i>47S</i> rRNA genes. In individual genomes, variants were frequently amplified in the transcribed spacer sequences and the evolutionarily young expansion segments, but rarely across the conserved <i>18S</i>, <i>5.8S</i>, and <i>28S</i> rRNA-encoding sequences. Variant numbers and amplification were lowest in evolutionarily highly constrained nucleotide elements that are identical across >90% of sequenced eukaryotes. These results indicate that strong purifying selection acts to suppress copy number expansion of deleterious variants among the hundreds of <i>47S</i> rRNA copies and imply that deleterious variants in the <i>47S</i> rRNA have the potential to cause phenotypic consequences at very low copy numbers. As low-copy variant calls are rarely considered in association studies, this may explain why disease associations with <i>47S</i> rRNA variants have so far escaped detection.