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 recombi...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nucleic acids research Jg. 46; H. 13; S. 6712 - 6725
Hauptverfasser: Kim, Jung-Hyun, Dilthey, Alexander T, Nagaraja, Ramaiah, Lee, Hee-Sheung, Koren, Sergey, Dudekula, Dawood, Wood III, William H, Piao, Yulan, Ogurtsov, Aleksey Y, Utani, Koichi, Noskov, Vladimir N, Shabalina, Svetlana A, Schlessinger, David, Phillippy, Adam M, Larionov, Vladimir
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 27.07.2018
Schlagworte:
Genomics
ISSN:0305-1048, 1362-4962, 1362-4962
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Present address: Alexander T. Dilthey, Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-UniversityDüsseldorf, Düsseldorf, Germany
The authors wish it to be known that, in their opinion, the first three authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gky442