Human ribosomal RNA gene arrays display a broad range of palindromic structures

Genome Res. 2005 Aug;15(8):1079-85. doi: 10.1101/gr.3970105. Epub 2005 Jul 15.

Abstract

The standard model of eukaryotic ribosomal RNA (rRNA) genes involves tandem arrays with hundreds of units in clusters, the nucleolus organizer regions (NORs). A first genomic overview for human cells is reported here for these regions, which have never been sequenced in their totality, by using molecular combing. The rRNA-coding regions are examined by fluorescence on single molecules of DNA with two specific probes that cover their entire length. The standard organization assumed for rDNA units is a transcribed region followed by a nontranscribed spacer. While we confirmed this arrangement in many cases, unorthodox patterns were also observed in normal individuals, with one-third of the rDNA units rearranged to form apparently palindromic structures (noncanonical units) independent of the age of the donors. In cells from individuals with a deficiency in the WRN RecQ helicase (Werner syndrome), the proportion of palindromes increased to one-half. These findings, supported by Southern blot analyses, show that rRNA genes are a mosaic of canonical and (presumably nonfunctional) palindromic units that may be altered by factors associated with genomic instability and pathology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Blotting, Southern
  • Cells, Cultured
  • DNA Probes
  • Gene Order
  • Gene Rearrangement
  • Genes, rRNA / genetics*
  • Humans
  • In Situ Hybridization, Fluorescence / methods
  • Nucleic Acid Conformation
  • RNA, Ribosomal / chemistry
  • Werner Syndrome / genetics*

Substances

  • DNA Probes
  • RNA, Ribosomal