Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

Abstract

Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.

Ribosomal DNA methylation as stable biomarkers for detection of cancer in plasma

“…However, it was reported that rDNA sequence has a certain rate of mutations, especially in IGS [13]. Recently, two studies has explored the sequence variation in rDNA [48,49]. Researchers studied chromosome 21 of one individual and identified 101 and 235 variant positions in transcribed regions and IGS respectively [49].…”

“…Recently, two studies has explored the sequence variation in rDNA [48,49]. Researchers studied chromosome 21 of one individual and identified 101 and 235 variant positions in transcribed regions and IGS respectively [49]. By analyzing whole genome sequencing data from 1000 Genome Project, researchers also identified intra-and inter-individual nucleotide variations in transcribed regions and found variant ribosomal RNA alleles might be correlated with physiology and diseases [48].…”

Loss of m1acp3Ψ ribosomal RNA modification is a major feature of cancer

“…rDNA sequence variation at the intra-and inter-individual level has been documented in multiple species including humans [8][9][10][11][12] , but the functional implications of rDNA variation remain elusive.…”

Ribosomal DNA-connecting ribosome biogenesis and chromosome biology

“…Ribosomal RNA accounts for up to 60-80% of the total cellular RNA. While these RNAs have been widely assumed to be identical, recent work suggests that there may be more heterogeneity at the DNA (Kim et al 2018;Xu et al 2017) and RNA level (Kim et al 2018;Parks et al 2018) in the human genome than previously suspected (reviewed by Matthew Parks and colleagues). This has interesting implications for ribosomes, since ribosomes with different versions of the ribosomal RNAs have the potential to have different translational properties.…”