Expressed retrotransposed 5S rRNA genes in the mouse and rat genomes

The 5S ribosomal RNA gene(s) and their associated intergenic spacer regions were amplified from Carica papaya and Carica quercifolia by polymerase chain reaction. Both Carica species exhibited differently sized amplification products. Sequence analysis of these PCR products revealed that the 5S rRNA genes are arranged as tandem repeats in these regions. Sequence data revealed that the 5S rRNA gene from Carica quercifolia was 119 bp in length. Sequence variation was observed in various 5S rRNA gene copies cloned from Carica quercifolia. Only truncated 5S rRNA gene but with its full spacer region was recovered from Carica papaya. Interestingly, intergenic spacer sequence cloned from Carica papaya contained two specific domains, a 30bp “CT” rich domain exhibiting 95-100% homology to several human chromosomes and a domain matching with mitrocomin precursor, a photo-protein from Mitrocoma cellularia. The role of 5S rRNA gene and their spacer regions in discerning the germplasm and in adaptation of the species is discussed.

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A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication

Molecular and Cellular Biology ◽

10.1128/mcb.9.10.4416-4421.1989 ◽

1989 ◽

Vol 9 (10) ◽

pp. 4416-4421

Author(s):

W S Grayburn ◽

E U Selker

Keyword(s):

Dna Methylation ◽

Tandem Duplication ◽

De Novo ◽

5S Rrna ◽

Rrna Genes ◽

Structural Basis ◽

Rrna Gene ◽

Oak Ridge ◽

5S Rrna Gene ◽

5S Rrna Genes

5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.

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Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes

Genome ◽

10.1139/g05-068 ◽

2006 ◽

Vol 49 (1) ◽

pp. 79-86 ◽

Cited By ~ 41

Author(s):

Manuel Manchado ◽

Eugenia Zuasti ◽

Ismael Cross ◽

Alejandro Merlo ◽

Carlos Infante ◽

...

Keyword(s):

5S Rdna ◽

5S Rrna ◽

Rrna Genes ◽

Solea Senegalensis ◽

Rrna Gene ◽

Small Nuclear Rna ◽

5S Rrna Gene ◽

Nuclear Rna ◽

Pcr Products ◽

Rna Genes

Some units of the 5S rDNA of Solea senegalensis were amplified by PCR and sequenced. Three main PCR products (227, 441, and 2166 bp) were identified. The 227- and 441-bp fragments were characterized by highly divergent nontranscribed spacer sequences (referred to as NTS-I and NTS-II) that were 109 and 324 bp long, respectively, yet their coding sequences were nearly identical. The 2166-bp 5S rDNA unit was composed of two 5S rRNA genes separated by NTS-I and followed by a 1721-bp spacer containing the U2, U5, and U1 small nuclear RNA genes (snRNAs). They were inverted and arranged in the transcriptional direction opposite that of the 5S rRNA gene. This simultaneous linkage of 3 different snRNAs had never been observed before. The PCR products were used as probes in fluorescence in situ hybridization experiments to locate the corresponding loci on the chromosomes of S. senegalensis. A major 5S rDNA chromosomal site was located along most of the short arm of a submetacentric pair, while a minor site was detected near the centromeric region of an acrocentric pair.Key words: soleidae, pleuronectiformes, 5S rDNA, Solea, snRNAs linkage.

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Isolation of Euglena gracilis chloroplast 5S ribosomal RNA and mapping the 5S rRNA gene on chloroplast DNA

Biochemistry ◽

10.1021/bi00576a029 ◽

1979 ◽

Vol 18 (9) ◽

pp. 1820-1825 ◽

Cited By ~ 27

Author(s):

Patrick W. Gray ◽

Richard B. Hallick

Keyword(s):

Chloroplast Dna ◽

Ribosomal Rna ◽

Euglena Gracilis ◽

5S Rrna ◽

Rrna Gene ◽

5S Ribosomal Rna ◽

5S Rrna Gene

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A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication.

Molecular and Cellular Biology ◽

10.1128/mcb.9.10.4416 ◽

1989 ◽

Vol 9 (10) ◽

pp. 4416-4421 ◽

Cited By ~ 28

Author(s):

W S Grayburn ◽

E U Selker

Keyword(s):

Dna Methylation ◽

Tandem Duplication ◽

De Novo ◽

5S Rrna ◽

Rrna Genes ◽

Structural Basis ◽

Rrna Gene ◽

Oak Ridge ◽

5S Rrna Gene ◽

5S Rrna Genes

5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.

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Role of Histone H1 as an Architectural Determinant of Chromatin Structure and as a Specific Repressor of Transcription onXenopus Oocyte 5S rRNA Genes

Molecular and Cellular Biology ◽

10.1128/mcb.18.7.3668 ◽

1998 ◽

Vol 18 (7) ◽

pp. 3668-3680 ◽

Cited By ~ 62

Author(s):

Takashi Sera ◽

Alan P. Wolffe

Keyword(s):

Chromatin Structure ◽

Regulatory Elements ◽

Histone H1 ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Nucleosome Core ◽

5S Rrna Gene ◽

5S Rrna Genes

ABSTRACT We explore the role of histone H1 as a DNA sequence-dependent architectural determinant of chromatin structure and of transcriptional activity in chromatin. The Xenopus laevis oocyte- and somatic-type 5S rRNA genes are differentially transcribed in embryonic chromosomes in vivo depending on the incorporation of somatic histone H1 into chromatin. We establish that this effect can be reconstructed at the level of a single nucleosome. H1 selectively represses oocyte-type 5S rRNA genes by directing the stable positioning of a nucleosome such that transcription factors cannot bind to the gene. This effect does not occur on the somatic-type genes. Histone H1 binds to the 5′ end of the nucleosome core on the somatic 5S rRNA gene, leaving key regulatory elements in the promoter accessible, while histone H1 binds to the 3′ end of the nucleosome core on the oocyte 5S rRNA genes, specifically blocking access to a key promoter element (the C box). TFIIIA can bind to the somatic 5S rRNA gene assembled into a nucleosome in the presence of H1. Because H1 binds with equivalent affinities to nucleosomes containing either gene, we establish that it is the sequence-selective assembly of a specific repressive chromatin structure on the oocyte 5S rRNA genes that accounts for differential transcriptional repression. Thus, general components of chromatin can determine the assembly of specific regulatory nucleoprotein complexes.

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Organization of 5S ribosomal RNA genes in tea (Camellia sinensis)

Genome ◽

10.1139/g00-095 ◽

2001 ◽

Vol 44 (1) ◽

pp. 143-146 ◽

Cited By ~ 2

Author(s):

Dharam Singh ◽

Mahipal Singh

Keyword(s):

Camellia Sinensis ◽

Tandem Repeats ◽

5S Rdna ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Repeat Units ◽

Camellia Species ◽

5S Rrna Genes ◽

Rna Genes

The 5S rRNA genes in the Camellia sinensis (L.) O. Kuntze (tea) genome are arranged as tandem repeat units of 300 and 325 bps. The 2 classes of tandem repeats were discovered by Southern hybridisation of tea genomic DNA with a 5S rRNA gene PCR product.Key words: Camellia species, 5S rDNA, multigene family, tandem repeats, spacers.

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Organization of the 18S, 5S, 4S rRNA genes and the tRNA-like repeat in the mitochondrial genomes of three lupin species.

Acta Biochimica Polonica ◽

10.18388/abp.1994_4689 ◽

1994 ◽

Vol 41 (4) ◽

pp. 433-440

Author(s):

B Karpińska ◽

K Leśniewicz ◽

G Pietkiewicz ◽

H Augustyniak

Keyword(s):

Restriction Enzymes ◽

18S Rrna Gene ◽

5S Rrna ◽

Lupinus Luteus ◽

Rrna Genes ◽

Northern Hybridization ◽

Mitochondrial Genomes ◽

Rrna Gene ◽

5S Rrna Gene ◽

5S Rrna Genes

Southern blots of mitochondrial (mt) DNAs of three Lupinus species cleaved with three restriction enzymes were probed with Lupinus luteus mtDNA fragments containing 18S, 5S rRNA genes or a tRNA-like repeat. Comparison of the number of hybridizing bands and their intensity suggested that the mt 18S and 5S rRNA genes occur mostly in one copy in the genomes of three lupin species. The exception concerned the Lupinus angustifolius 5S rRNA gene showing two hybridizing bands of unequal intensity. The results of hybridization of the lupin mitochondrial genomes with a probe specific for the Lupinus luteus tRNA-like repeat pointed to the presence of such a repeat in other parts of the genomes besides the vicinity of the 18S rRNA gene. Northern hybridization analysis showed the presence of 18S, 5S and tRNA-like repeat transcripts similar in size in all lupin species.

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