Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

ABSTRACT A key event in tRNA gene (tDNA) transcription by RNA polymerase (Pol) III is the TFIIIC-dependent assembly of TFIIIB upstream of the transcription start site. Different tDNA upstream sequences bind TFIIIB with different affinities, thereby modulating tDNA transcription. We found that in the absence of Nhp6 proteins, the influence of the 5′-flanking region on tRNA gene transcription is dramatically enhanced in Saccharomyces cerevisiae. Expression of a tDNA bearing a suboptimal TFIIIB binding site, but not of a tDNA preceded by a strong TFIIIB binding region, was strongly dependent on Nhp6 in vivo. Upstream sequence-dependent stimulation of tRNA gene transcription by Nhp6 could be reproduced in vitro, and Nhp6 proteins were found associated with tRNA genes in yeast cells. We also show that both transcription and silencing barrier activity of a tDNAThr at the HMR locus are compromised in the absence of Nhp6. Our data suggest that Nhp6 proteins are important components of Pol III chromatin templates that contribute both to the robustness of tRNA gene expression and to positional effects of Pol III transcription complexes.

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Relative Affinities of Nucleotide Substrates for the Yeast tRNA Gene Transcription Complex

Zeitschrift für Naturforschung C ◽

10.1515/znc-1992-3-426 ◽

1992 ◽

Vol 47 (3-4) ◽

pp. 320-322 ◽

Cited By ~ 1

Author(s):

Przemyslaw Szafranski ◽

W. Jerzy Smagowicz

Keyword(s):

Rna Polymerase ◽

Gene Transcription ◽

Trna Gene ◽

Rna Polymerase Iii ◽

Rna Polymerases ◽

Yeast Trna ◽

Polymerase Iii ◽

Michaelis Constants ◽

Auxiliary Protein

Abstract Apparent Michaelis constants for nucleotides in transcription of yeast tRN Agene by hom ologous RNA polymerase III with auxiliary protein factors, were found to be remarkably higher in initiation than in elongation of RNA chain. This supports presumptions regarding topological similarities between catalytic centers of bacterial and eukaryotic RNA polymerases.

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Upstream interactions of functional mammalian tRNA gene transcription complexes probed using a heterologous DNA-binding protein.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)31876-8 ◽

1994 ◽

Vol 269 (34) ◽

pp. 21812-21819

Author(s):

R.I. Tapping ◽

D.E. Syroid ◽

J.P. Capone

Keyword(s):

Dna Binding ◽

Gene Transcription ◽

Trna Gene ◽

Binding Protein ◽

Dna Binding Protein ◽

Transcription Complexes

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Transfer RNA genes are genomic targets for de Novo transposition of the yeast retrotransposon Ty3.

Genetics ◽

10.1093/genetics/126.4.837 ◽

1990 ◽

Vol 126 (4) ◽

pp. 837-850 ◽

Cited By ~ 4

Author(s):

D L Chalker ◽

S B Sandmeyer

Keyword(s):

Dna Sequences ◽

Southern Blot Analysis ◽

Trna Gene ◽

De Novo ◽

Insertion Site ◽

Trna Genes ◽

Coding Sequence ◽

Yeast Trna ◽

Genomic Insertions ◽

Rna Genes

Abstract Insertions of the yeast element Ty3 resulting from induced retrotransposition were characterized in order to identify the genomic targets of transposition. The DNA sequences of the junctions between Ty3 and flanking DNA were determined for two insertions of an unmarked element. Each insertion was at position -17 from the 5' end of a tRNA-coding sequence. Ninety-one independent insertions of a marked Ty3 element were studied by Southern blot analysis. Pairs of independent insertions into seven genomic loci accounted for 14 of these insertions. The DNA sequence flanking the insertion site was determined for at least one member of each pair of integrated elements. In each case, insertion was at position -16 or -17 relative to the 5' end of one of seven different tRNA genes. This proportion of genomic loci used twice for Ty3 integration is consistent with that predicted by a Poisson distribution for a number of genomic targets roughly equivalent to the estimated number of yeast tRNA genes. In addition, insertions upstream of the same tRNA gene in one case were at different positions, but in all cases were in the same orientation. Thus, genomic insertions of Ty3 in a particular orientation are apparently specified by the target, while the actual position of the insertion relative to the tRNA-coding sequence can vary slightly.

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Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽

10.1186/s12864-021-07859-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wen-Ge Dong ◽

Yalun Dong ◽

Xian-Guo Guo ◽

Renfu Shao

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Genome Organization ◽

Trna Gene ◽

Trna Genes ◽

Single Chromosome ◽

Gene Translocation ◽

Sucking Lice ◽

Different Types ◽

Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

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Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo.

Molecular and Cellular Biology ◽

10.1128/mcb.6.7.2663 ◽

1986 ◽

Vol 6 (7) ◽

pp. 2663-2673 ◽

Cited By ~ 49

Author(s):

M C Strobel ◽

J Abelson

Keyword(s):

Saccharomyces Cerevisiae ◽

Trna Gene ◽

Nuclear Extract ◽

Nonsense Suppression ◽

Trna Genes ◽

Suppressor Activity ◽

Specific Sequence ◽

Made In

The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.

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Transfer RNA genes experience exceptionally elevated mutation rates

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1801240115 ◽

2018 ◽

Vol 115 (36) ◽

pp. 8996-9001 ◽

Cited By ~ 12

Author(s):

Bryan P. Thornlow ◽

Josh Hough ◽

Jacquelyn M. Roger ◽

Henry Gong ◽

Todd M. Lowe ◽

...

Keyword(s):

Mutation Rate ◽

Trna Gene ◽

Gene Evolution ◽

Purifying Selection ◽

Mutation Rates ◽

Model Organisms ◽

Biological Synthesis ◽

Human Populations ◽

Trna Genes ◽

Simple Method

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.

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A transcriptionally active tRNA gene interferes with nucleosome positioning in vivo

Molecular and Cellular Biology ◽

10.1128/mcb.12.9.4015-4025.1992 ◽

1992 ◽

Vol 12 (9) ◽

pp. 4015-4025

Author(s):

R H Morse ◽

S Y Roth ◽

R T Simpson

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Trna Gene ◽

Rna Polymerase Iii ◽

Nucleosome Positioning ◽

Yeast Cells ◽

Trna Genes ◽

Start Site ◽

Cis Acting

Incorporation into a positioned nucleosome of a cis-acting element essential for replication in Saccharomyces cerevisiae disrupts the function of the element in vivo [R. T. Simpson, Nature (London) 343:387-389, 1990]. Furthermore, nucleosome positioning has been implicated in repression of transcription by RNA polymerase II in yeast cells. We have now asked whether the function of cis-acting elements essential for transcription of a gene transcribed by RNA polymerase III can be similarly affected. A tRNA gene was fused to either of two nucleosome positioning signals such that the predicted nucleosome would incorporate near its center the tRNA start site and essential A-box element. These constructs were then introduced into yeast cells on stably maintained, multicopy plasmids. Competent tRNA genes were transcribed in vivo and were not incorporated into positioned nucleosomes. Mutated, inactive tRNA genes were incorporated into nucleosomes whose positions were as predicted. This finding demonstrates that the transcriptional competence of the tRNA gene determined its ability to override a nucleosome positioning signal in vivo and establishes that a hierarchy exists between cis-acting elements and nucleosome positioning signals.

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