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. 2003 May 1;31(9):2361-8.
doi: 10.1093/nar/gkg348.

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium

Richard Sucgang  1 , Guokai Chen, Wen Liu, Ryan Lindsay, Jing Lu, Donna Muzny, Gad Shaulsky, William Loomis, Richard Gibbs, Adam Kuspa
Affiliations

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium

Richard Sucgang et al. Nucleic Acids Res. .

Abstract

Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.

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Figures

Figure 1
Figure 1
Overview of the sequence of the rDNA palindrome. Only one arm is presented here. The other arm is an exact complement that extends to the left of the arm shown. The predicted restriction map agrees with previously published maps (B: BamHI, R: EcoRI, S: SalI). (A) The 42 bp central region of asymmetry (CRA) is shown in detail. (B) A Pustell DNA matrix (44) of the terminal sequences indicating the presence of a series of short repeats.
Figure 2
Figure 2
Validating the sequence of the central non-palindromic region of the rDNA element. (A) Oligonucleotides corresponding to each half of the central region were paired with oligonucleotides corresponding to sequences at predicted distances into the arms of the elements. (B) PCR amplification produced the predicted, identical DNA fragments. (C) The same predicted PCR fragments were amplified from YAC DNA derived from the chromosome 4 YACs. (D) Region of chromosome 4 containing the rDNA locus. The rDNA-containing YACs are shown above the chromosome map. The rDNA is located between the erkB and ubpA.
Figure 3
Figure 3
Structural features of the extrachromosomal rDNA element. (A) Pustell dot-matrix autocomparison of one arm of the palindrome shows the prevalence of short repeated regions throughout except for the region transcribed into rRNA (44). Longer repeats are found towards the center of the palindrome. Two packets of highly repetitive DNA bracket the transcribed region (gray circles). The upstream and downstream sequences are unrelated. (B) The A+T content is high except in the transcribed regions and a short region upstream.
Figure 4
Figure 4
Nuclear distribution of extrachromosomal rDNA in AX4 cells. (A) An interphase nucleus stained with DAPI and combined on the right with the signal obtained by FISH with a mixture of rDNA probes (green). (B) Two examples of condensed nuclear DNA in nocodazole-treated cells stained with DAPI displaying seven chromosome-sized DNA bodies. (C) Two examples of rDNA FISH of nuclei from nocodazole-treated cells with the denaturation step carried out at 70°C. DAPI staining displaying six chromosome-sized DNAs along with many smaller DNA fragments (left panels) and the FISH signal (red) that identifies the smaller fragments as rDNA (right panels). (D) An example of rDNA FISH of a nocodazole- treated cell, with denaturation carried out at 55°C, in which the rDNA appears as chromosome-sized DNAs.
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References

    1. Gall J.G. (1974) Free ribosomal RNA genes in the macronucleus of Tetrahymena. Proc. Natl Acad. Sci. USA, 71, 3078–3081. - PMC - PubMed
    1. Karrer K.M. and Gall,J.G. (1976) The macronuclear ribosomal DNA of Tetrahymena pyriformis is a palindrome. J. Mol. Biol., 104, 421–453. - PubMed
    1. Maizels N. (1976) Dictyostelium 17S, 25S, and 5S rDNAs lie within a 38,000 base pair repeated unit. Cell, 9, 431–438. - PubMed
    1. Cockburn A.F., Newkirk,M.J. and Firtel,R.A. (1976) Organization of the ribosomal RNA genes of Dictyostelium discoideum: mapping of the non transcribed spacer regions. Cell, 9, 605–613. - PubMed
    1. Vogt V.M. and Braun,R. (1976) Structure of ribosomal DNA in Physarum polycephalum. J. Mol. Biol., 106, 567–587. - PubMed

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