The Intergenic Spacer Region of the RDNA in Haplopappus Gracilis (Nutt.) Gray

Overview

Journal Protoplasma

Publisher Springer

Specialty Biology

Date 2012 Sep 6

PMID 22948831

Citations 3

Authors

M Ruffini Castiglione

M T Gelati

R Cremonini

M Frediani

Affiliations

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Abstract

In this paper, we provide further information on the genome organisation of Haplopappus gracilis, one of the six angiosperms showing the lowest chromosome number, i.e. 2n = 4, by determining the nucleotide sequence of the intergenic spacer region of the ribosomal RNA genes and its cytological localization on metaphase chromosomes. DNA sequence analysis reveals the occurring of a product of 4,382 bp in length, characterised by the presence of four blocks of different repeated sequences. Our analysis also evidenced putative promoter regions with three transcription initiation sites for polymerase I, as previously reported in Artemisia absinthium, belonging to the same Asteraceae family. A fluorescent in situ hybridization with the intergenic spacer probe indicates the presence of rDNA genes only in the satellited chromosomes of H. gracilis; besides, differences in the signal intensity between homologous chromosomes were frequently observed, thus suggesting for these chromosome sites the presence of a variable number of rDNA gene copies, even if a divergent chromatin organisation in corresponding regions cannot be ruled out.

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References

Ruffini Castiglione M, Kotseruba V, Cremonini R . Methylated-rich regions and tandem repeat arrays along the chromosome complement of Colpodium versicolor (Stev.) Schmalh. Protoplasma. 2009; 237(1-4):13-8. DOI: 10.1007/s00709-009-0063-6. View

Bennett S, Leitch I, Bennett M . Chromosome identification and mapping in the grass Zingeria biebersteiniana (2n = 4) using fluorochromes. Chromosome Res. 1995; 3(2):101-8. DOI: 10.1007/BF00710670. View

Ruffini Castiglione M, Frediani M, Venora G, Cremonini R . Cytological investigation of Haplopappus gracilis (Nutt.) Gray: 5-methylcytosine-rich regions, fluorochrome banding and chromatin sensitivity to DNase I digestion. Protoplasma. 2008; 233(1-2):107-13. DOI: 10.1007/s00709-008-0296-9. View

De Winter R, Moss T . Spacer promoters are essential for efficient enhancement of X. laevis ribosomal transcription. Cell. 1986; 44(2):313-8. DOI: 10.1016/0092-8674(86)90765-8. View

Panero J, Funk V . The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed. Mol Phylogenet Evol. 2008; 47(2):757-82. DOI: 10.1016/j.ympev.2008.02.011. View

Borisjuk N, Borisjuk L, Komarnytsky S, Timeva S, Hemleben V, Gleba Y . Tobacco ribosomal DNA spacer element stimulates amplification and expression of heterologous genes. Nat Biotechnol. 2000; 18(12):1303-6. DOI: 10.1038/82430. View

Komarova N, Grabe T, Huigen D, Hemleben V, Volkov R . Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids. Plant Mol Biol. 2004; 56(3):439-63. DOI: 10.1007/s11103-004-4678-x. View

Moss T . A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis. Nature. 1983; 302(5905):223-8. DOI: 10.1038/302223a0. View

Maluszynska J, Heslop-Harrison J . Physical mapping of rDNA loci in Brassica species. Genome. 1993; 36(4):774-81. DOI: 10.1139/g93-102. View

10.

Kato A, Nakajima T, Yamashita J, Yakura K, Tanifuji S . The structure of the large spacer region of the rDNA in Vicia faba and Pisum sativum. Plant Mol Biol. 1990; 14(6):983-93. DOI: 10.1007/BF00019395. View

11.

Gruendler P, Unfried I, Pascher K, Schweizer D . rDNA intergenic region from Arabidopsis thaliana. Structural analysis, intraspecific variation and functional implications. J Mol Biol. 1991; 221(4):1209-22. DOI: 10.1016/0022-2836(91)90929-z. View

12.

Garcia S, Panero J, Siroky J, Kovarik A . Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family. BMC Plant Biol. 2010; 10:176. PMC: 3095306. DOI: 10.1186/1471-2229-10-176. View

13.

Ueki M, Uchizawa E, Yakura K . The nucleotide sequence of the rDNA intergenic spacer region in a wild species of the genus Vicia, V. angustifolia. Plant Mol Biol. 1992; 18(1):175-8. DOI: 10.1007/BF00018476. View

14.

Hemleben V, Zentgraf U . Structural organization and regulation of transcription by RNA polymerase I of plant nuclear ribosomal RNA genes. Results Probl Cell Differ. 1994; 20:3-24. DOI: 10.1007/978-3-540-48037-2_1. View

15.

Markos S, Baldwin B . Structure, molecular evolution, and phylogenetic utility of the 5(') region of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Astereae). Mol Phylogenet Evol. 2002; 23(2):214-28. DOI: 10.1016/S1055-7903(02)00004-0. View

16.

Durante M, Cionini P, Avanzi S, Cremonini R, DAmato F . Cytological localization of the genes for the four classes of ribosomal RNA (25S, 18S, 5.8S and 5S) in polytene chromosomes of Phaseolus coccineus. Chromosoma. 1977; 60(3):269-82. DOI: 10.1007/BF00329775. View

17.

Lyon M . The William Allan memorial award address: X-chromosome inactivation and the location and expression of X-linked genes. Am J Hum Genet. 1988; 42(1):8-16. PMC: 1715299. View

18.

Ruffini Castiglione M, Venora G, Ravalli C, Stoilov L, Gecheff K, Cremonini R . DNA methylation and chromosomal rearrangements in reconstructed karyotypes of Hordeum vulgare L. Protoplasma. 2008; 232(3-4):215-22. DOI: 10.1007/s00709-007-0275-6. View

19.

Rogers S, Bendich A . Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol. 2013; 9(5):509-20. DOI: 10.1007/BF00015882. View

20.

Nardi I, Batistoni R, Andronico F . Chromosome location of the ribosomal RNA genes in Triturus vulgaris meridionalis (Amphibia, Urodela). II. Intraspecific variability in number and position of the chromosome loci for 18S + 28S ribosomal RNA. Chromosoma. 1977; 64(1):67-84. DOI: 10.1007/BF00292889. View