Human transcription factor TFIIIC2 specifically interacts with a unique sequence in the Xenopus laevis 5S rRNA gene

1989 ◽  
Vol 9 (11) ◽  
pp. 4941-4950
Author(s):  
L G Fradkin ◽  
S K Yoshinaga ◽  
A J Berk ◽  
A Dasgupta
Keyword(s):  
Transcription Factor ◽  
Xenopus Laevis ◽  
Binding Site ◽  
Gene Transcription ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
5S Rrna Gene ◽  
5S Rrna Genes ◽  
Type Gene

Transcription factor TFIIIC2 derived from human cells is required for tRNA-type gene transcription and binds with high affinity to the essential B-box promoter element of tRNA-type genes. Although 5S rRNA genes contain no homology with the tRNA-type gene B box, we show that TFIIIC2 is also required for Xenopus laevis 5S rRNA gene transcription. TFIIIC2 protected an approximately 30-base-pair (-10 to +18) region of a Xenopus 5S rRNA gene from DNase I digestion. This region, which spanned the transcription start site, included sequences that are highly conserved among eucaryotic 5S rRNA genes and have no homology with the B-box sequence of tRNA genes. Mutation of the TFIIIC2-binding site reduced transcription of the 5S rRNA gene by a factor of 10 in HeLa cell extracts. Methylation of C residues within the TFIIIC2-binding site interfered with binding of TFIIIC2. These results suggest a role of the TFIIIC2-binding sequence in 5S rRNA gene transcription. In addition, the 5S rRNA gene binding site and the tRNA-type gene B-box sequence did not compete with each other for binding to TFIIIC2 any better than did an unrelated DNA sequence, indicating that TFIIIC2 interacts with 5S rRNA genes and tRNA-type genes through separate DNA-binding domains or polypeptides.

scholarly journals Human transcription factor TFIIIC2 specifically interacts with a unique sequence in the Xenopus laevis 5S rRNA gene.

1989 ◽  
Vol 9 (11) ◽  
pp. 4941-4950 ◽  
Author(s):  
L G Fradkin ◽  
S K Yoshinaga ◽  
A J Berk ◽  
A Dasgupta
Keyword(s):  
Transcription Factor ◽  
Xenopus Laevis ◽  
Binding Site ◽  
Gene Transcription ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
5S Rrna Gene ◽  
5S Rrna Genes ◽  
Type Gene

Transcription factor TFIIIC2 derived from human cells is required for tRNA-type gene transcription and binds with high affinity to the essential B-box promoter element of tRNA-type genes. Although 5S rRNA genes contain no homology with the tRNA-type gene B box, we show that TFIIIC2 is also required for Xenopus laevis 5S rRNA gene transcription. TFIIIC2 protected an approximately 30-base-pair (-10 to +18) region of a Xenopus 5S rRNA gene from DNase I digestion. This region, which spanned the transcription start site, included sequences that are highly conserved among eucaryotic 5S rRNA genes and have no homology with the B-box sequence of tRNA genes. Mutation of the TFIIIC2-binding site reduced transcription of the 5S rRNA gene by a factor of 10 in HeLa cell extracts. Methylation of C residues within the TFIIIC2-binding site interfered with binding of TFIIIC2. These results suggest a role of the TFIIIC2-binding sequence in 5S rRNA gene transcription. In addition, the 5S rRNA gene binding site and the tRNA-type gene B-box sequence did not compete with each other for binding to TFIIIC2 any better than did an unrelated DNA sequence, indicating that TFIIIC2 interacts with 5S rRNA genes and tRNA-type genes through separate DNA-binding domains or polypeptides.

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

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.

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

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.

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

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 213-215 ◽  
Author(s):  
Guy Drouin
Keyword(s):  
Key Words ◽  
Ribosomal Rna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
5S Ribosomal Rna ◽  
Gene Copies ◽  
5S Rrna Gene ◽  
5S Rrna Genes ◽  
Rna Genes

The analyses of previously described 5S rRNA gene sequences show that some of the expressed 5S rRNA genes present in the mouse and rat genomes were derived from the retrotransposition of 5S rRNA transcripts. These analyses demonstrate that new 5S rRNA gene copies can originate by retrotransposition and that some of these retrotranscribed genes are expressed. Key words: 5S ribosomal RNA genes, retrotransposition, retroposons.

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

1998 ◽  
Vol 18 (7) ◽  
pp. 3668-3680 ◽  
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.

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

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.

scholarly journals Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

2012 ◽  
Vol 45 (4) ◽  
pp. 541-552 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Louise E. Mitchell ◽  
Tracy Berg ◽  
Niall S. Kenneth ◽  
Conrad von Schubert ◽  
...  
Keyword(s):  
Gene Transcription ◽  
5S Rrna ◽  
Rrna Gene ◽  
5S Rrna Gene ◽  
Direct Regulation

scholarly journals Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

2020 ◽  
Vol 21 (8) ◽  
pp. 2931 ◽  
Author(s):  
Ruslan Kalendar ◽  
Olga Raskina ◽  
Alexander Belyayev ◽  
Alan H. Schulman
Keyword(s):  
Copy Number ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Gene Copy ◽  
Rrna Gene ◽  
Long Terminal Repeats ◽  
5S Rrna Genes ◽  
Pol Iii ◽  
Tandem Arrays

Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

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