rRNA Genes: Evolution

Abstract

The large ribosomal ribonucleic acid (rRNA) gene arrays undergo concerted evolution on both homologous and nonhomologous chromosomes, but coding and noncoding parts of the ribosomal deoxyribonucleic acid (rDNA) unit are not homogenized to the same extent and at the same rate. We do not know if this is due to selection pressure, to localized recombination or gene conversions. New findings regarding array organization have raised the possibility that there are isolated clusters that only homogenize among/within themselves. It is not known if these noncanonical clusters are functional or not.

Keywords: rRNA; rDNA; ribosome; acrocentric; evolution

Figure 1.

Production of rRNAs from rDNA. Transcription from the rDNA repeats (top) produces primary transcript (middle), which then yields the processed rRNAs (bottom). ETS: external transcribed spacer; IGS: intergenic spacer; ITS: internal transcribed spacer.

Figure 2.

Structural analysis of the human rDNA locus by molecular combing. (a) Schematic representation of two canonical rDNA units. Restriction with EcoR1 (sites E) yields four distinct fragments spanning the transcribed region (thick line) and the intergenic spacer or IGS (thin line). The orientation of the rRNA transcript and the positions of the ribosomal genes (black boxes) are shown. (b) Two‐colour hybridization on combed human DNA. The red probe is the 5′ EcoR1 fragment B detected with Texas Red. The green probe is the 3′ fragment A detected with fluorescein isothiocyanate (FITC). The image displays 10 canonical rDNA units in tandem, each composed of a dual fluorescent signal and the adjacent nonhybridizing spacer segments. (c) Hybridization of the probes on human DNA that illustrates noncanonical units. The image displays a region containing two canonical units (left) followed by seven palindromic units, with each half joined by its 3′ region (3′‐3′ palindromes) and separated by short IGS segments. (d) Hybridizations illustrating successive inverted units with gaps. The image displays five canonical units, followed by a series of seven palindromic units separated by short gaps. (e) Hybridizations illustrating 5′‐5′ palindromic units. The image displays six canonical units (left), followed by two gapless palindromic units joined at their 5′ extremities and two canonical units (separated by a short IGS) in an inverted orientation with respect to the canonical units on the left. (f) Hybridizations illustrating 5′‐5′ palindromic units with gaps. The image displays six canonical units, followed by a single 3′ fragment and three 5′‐5′ palindromes with short central gaps separated by short IGS segments. (g) Hybridization illustrating complex recombinant structures. The image displays closely spaced, inverted units (left), followed by two complex units with alternating 5′ and 3′ coding sequences, separated by short IGS sequences, and one canonical unit (right). Scale bar, 10 kb, applicable to all images. (Figure from Caburet et al. () Reproduced by permission of Cold Spring Harbor Laboratory Press © 2005).

Figure 3.

Variability in palindromic rDNA spacer length. (a) A series of hybridization signals depicting the variability in the lengths for 3′‐3′ palindromes. (b) Signals for 5′‐5′ palindromes. (c) Bar graphs of the distribution of palindromic signals with respect to the total length between the outer probes, for 5′‐5′ palindromes in red and 3′‐3′ palindromes in green. The data represent a compilation of measurements on 306 individual palindromes. (Figure from Caburet et al. () Reproduced by permission of Cold Spring Harbor Laboratory Press © 2005).

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Gonzalez, Iris L, and Sylvester, James E(Dec 2007) rRNA Genes: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006131.pub2]