scholarly journals The Maize Imprinted Gene Floury3 Encodes a PLATZ Protein Required for tRNA and 5S rRNA Transcription through Interaction with RNA Polymerase III

2017 ◽  
Vol 29 (10) ◽  
pp. 2661-2675 ◽  
Author(s):  
Qi Li ◽  
Jiechen Wang ◽  
Jianwei Ye ◽  
Xixi Zheng ◽  
Xiaoli Xiang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Imprinted Gene ◽  
Rrna Transcription ◽  
Polymerase Iii

DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene

FEBS Letters ◽  
1990 ◽  
Vol 269 (2) ◽  
pp. 358-362 ◽  
Author(s):  
Daniel Besser ◽  
Frank Götz ◽  
Kai Schulze-Forster ◽  
Herbert Wagner ◽  
Hans Kröger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Trna Gene ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Polymerase Iii ◽  
5S Rrna Gene

scholarly journals Transcription of genomic bovine and Xenopus laevis DNA species by RNA polymerase III in HeLa-cell cytosol extracts

1986 ◽  
Vol 237 (3) ◽  
pp. 827-835 ◽  
Author(s):  
J J Furth ◽  
C Y Su
Keyword(s):  
Xenopus Laevis ◽  
Rna Polymerase ◽  
Hela Cell ◽  
Rna Polymerase Iii ◽  
5S Rdna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Polymerase Iii ◽  
Repeat Dna ◽  
Cell Cytosol

RNA transcribed from genomic Xenopus laevis DNA by RNA polymerase III in HeLa-cell extract was found in discrete size classes and was transcribed from at least two different Xenopus repeat DNA species. Very little 5S ribosomal RNA was transcribed, contrasting with results obtained on transcription of genomic Xenopus DNA by Xenopus extract [Bogenhagen et al. (1982) Cell 28, 413-421]. The low transcription was not due to an inability to use 5S rDNA templates, since the cloned Xenopus 5S ribosomal gene and pseudogene were effective templates for RNA polymerase III in HeLa extract. RNA transcribed from genomic bovine DNA by RNA polymerase III in HeLa-cell cytosol extract consisted of 120-nucleotide RNA and a larger amount of heterogeneously sized RNA (180-650 nucleotides). Only a small portion of the 120-nucleotide RNA was 5S rRNA. Most of the 120-nucleotide RNA and the larger RNA species were transcribed from one bovine repeat DNA. Genes for 5S rRNA and bovine repeat DNA were transcribed roughly in proportion to their frequency in Bos, contrasting with results in a homologous system in which transcription of repeat genes is repressed [Furth (1985) Biochem. Biophys. Res. Commun. 131, 551-556]. Bovine 5S rRNA genes appear to be concentrated on one DNA fragment obtained by restriction-enzyme-HindIII digestion of genomic bovine DNA.

Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition

1992 ◽  
Vol 12 (5) ◽  
pp. 2260-2272
Author(s):  
F E Campbell ◽  
D R Setzer
Keyword(s):  
Rna Polymerase ◽  
Transcription Termination ◽  
Transcription Elongation ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Signal Recognition ◽  
Polymerase Iii ◽  
5S Rrna Gene ◽  
Nascent Rna

Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.

scholarly journals Displacement of Xenopus transcription factor IIIA from a 5S rRNA gene by a transcribing RNA polymerase.

1991 ◽  
Vol 11 (8) ◽  
pp. 3978-3986 ◽  
Author(s):  
F E Campbell ◽  
D R Setzer
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Internal Control ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Transcription Factor Iiia ◽  
Polymerase Iii ◽  
5S Rrna Gene

In the absence of other components of the RNA polymerase III transcription machinery, transcription factor IIIA (TFIIIA) can be displaced from both strands of its DNA-binding site (the internal control region) on the somatic-type 5S rRNA gene of Xenopus borealis during transcription elongation by bacteriophage T7 RNA polymerase, regardless of which DNA strand is transcribed. Furthermore, substantial displacement is observed after the template has been transcribed only once. Since the complete 5S rRNA transcription complex has previously been shown to remain stably bound to the gene during repeated rounds of transcription by either RNA polymerase III or bacteriophage SP6 RNA polymerase, these results indicate that a factor(s) in addition to TFIIIA is required to create a complex that will remain stably associated with the template during transcription. Thus, transcription complex stability during passage of RNA polymerase cannot be explained solely on the basis of the DNA-binding properties of TFIIIA.

Transcription factor requirements for in vitro formation of transcriptionally competent 5S rRNA gene chromatin

1990 ◽  
Vol 10 (5) ◽  
pp. 2390-2401
Author(s):  
S J Felts ◽  
P A Weil ◽  
R Chalkley
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Active Chromatin ◽  
Polymerase Iii ◽  
Protein Dna Interactions ◽  
5S Rrna Gene

The Saccharomyces cerevisiae 5S rRNA gene was used as a model system to study the requirements for assembling transcriptionally active chromatin in vitro with purified components. When a plasmid containing yeast 5S rDNA was assembled into chromatin with purified core histones, the gene was inaccessible to the yeast class III gene transcription machinery. Preformation of a 5S rRNA gene-TFIIIA complex was not sufficient for the formation of active chromatin in this in vitro system. Instead, a complete transcription factor complex consisting of TFIIIA, TFIIIB, and TFIIIC needed to be formed before the addition of histones in order for the 5S chromatin to subsequently be transcribed by RNA polymerase III. Various 5S rRNA maxigenes were constructed and used for chromatin assembly studies. In vitro transcription from these assembled 5S maxigenes revealed that RNA polymerase III was readily able to transcribe through one, two, or four nucleosomes. However, we found that RNA polymerase III was not able to efficiently transcribe a chromatin template containing a more extended array of nucleosomes. In vivo expression experiments indicated that all in vitro-constructed maxigenes were transcriptionally competent. Analyses of protein-DNA interactions formed on these maxigenes in vivo by indirect end labeling indicated that there are extensive interactions throughout the length of these maxigenes. The patterns of protein-DNA interactions formed on these genes are consistent with these DNAs being assembled into extensive nucleosomal arrays.

scholarly journals TFIIIB Subunit Bdp1 Participates in RNA Polymerase III Transcription in the Protozoan Parasite Leishmania major

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Fiordaliso C. Román-Carraro ◽  
Luis E. Florencio-Martínez ◽  
Gabriela Romero-Meza ◽  
Tomás Nepomuceno-Mejía ◽  
Julio C. Carrero ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Cell Line ◽  
Leishmania Major ◽  
Mutant Cell ◽  
Rna Polymerase Iii ◽  
Protozoan Parasite ◽  
5S Rrna ◽  
Mutant Cell Line ◽  
Polymerase Iii ◽  
Pol Iii

Leishmania major, a protozoan parasite that diverged early from the main eukaryotic lineage, exhibits unusual mechanisms of gene expression. Little is known in this organism about the transcription factors involved in the synthesis of tRNA, 5S rRNA, and snRNAs, transcribed by RNA Polymerase III (Pol III). Here we identify and characterize the TFIIIB subunit Bdp1 in L. major (LmBdp1). Bdp1 plays key roles in Pol III transcription initiation in other organisms, as it participates in Pol III recruitment and promoter opening. In silico analysis showed that LmBdp1 contains the typical extended SANT domain as well as other Bdp1 conserved regions. Nevertheless, LmBdp1 also displays distinctive features, including the presence of only one aromatic residue in the N-linker region. We were not able to produce null mutants of LmBdp1 by homologous recombination, as the obtained double replacement cell line contained an extra copy of LmBdp1, indicating that LmBdp1 is essential for the viability of L. major promastigotes. Notably, the mutant cell line showed reduced levels of the LmBdp1 protein, and its growth was significantly decreased in relation to wild-type cells. Nuclear run-on assays demonstrated that Pol III transcription was affected in the mutant cell line, and ChIP experiments showed that LmBdp1 binds to 5S rRNA, tRNA, and snRNA genes. Thus, our results indicate that LmBdp1 is an essential protein required for Pol III transcription in L. major.

scholarly journals RNA Polymerase III Transcription Complexes on Chromosomal 5S rRNA Genes In Vivo: TFIIIB Occupancy and Promoter Opening

2001 ◽  
Vol 21 (9) ◽  
pp. 3166-3178 ◽  
Author(s):  
G. Costanzo ◽  
S. Camier ◽  
P. Carlucci ◽  
L. Burderi ◽  
R. Negri
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Dimethyl Sulfate ◽  
Experimental System ◽  
5S Rrna ◽  
Rrna Genes ◽  
Polymerase Iii ◽  
5S Rrna Genes ◽  
Transcription Complexes

ABSTRACT Quantitative analysis of multiple-hit potassium permanganate (KMnO4) footprinting has been carried out in vivo onSaccharomyces cerevisiae 5S rRNA genes. The results fix the number of open complexes at steady state in exponentially growing cells at between 8 and 17% of the 150 to 200 chromosomal copies. UV and dimethyl sulfate footprinting set the transcription factor TFIIIB occupancy at 23 to 47%. The comparison between the two values suggests that RNA polymerase III binding or promoter opening is the rate-limiting step in 5S rRNA transcription in vivo. Inhibition of RNA elongation in vivo by cordycepin confirms this result. An experimental system that is capable of providing information on the mechanistic steps involved in regulatory events in S. cerevisiae cells has been established.

scholarly journals Transcription factor requirements for in vitro formation of transcriptionally competent 5S rRNA gene chromatin.

1990 ◽  
Vol 10 (5) ◽  
pp. 2390-2401 ◽  
Author(s):  
S J Felts ◽  
P A Weil ◽  
R Chalkley
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Active Chromatin ◽  
Polymerase Iii ◽  
Protein Dna Interactions ◽  
5S Rrna Gene

The Saccharomyces cerevisiae 5S rRNA gene was used as a model system to study the requirements for assembling transcriptionally active chromatin in vitro with purified components. When a plasmid containing yeast 5S rDNA was assembled into chromatin with purified core histones, the gene was inaccessible to the yeast class III gene transcription machinery. Preformation of a 5S rRNA gene-TFIIIA complex was not sufficient for the formation of active chromatin in this in vitro system. Instead, a complete transcription factor complex consisting of TFIIIA, TFIIIB, and TFIIIC needed to be formed before the addition of histones in order for the 5S chromatin to subsequently be transcribed by RNA polymerase III. Various 5S rRNA maxigenes were constructed and used for chromatin assembly studies. In vitro transcription from these assembled 5S maxigenes revealed that RNA polymerase III was readily able to transcribe through one, two, or four nucleosomes. However, we found that RNA polymerase III was not able to efficiently transcribe a chromatin template containing a more extended array of nucleosomes. In vivo expression experiments indicated that all in vitro-constructed maxigenes were transcriptionally competent. Analyses of protein-DNA interactions formed on these maxigenes in vivo by indirect end labeling indicated that there are extensive interactions throughout the length of these maxigenes. The patterns of protein-DNA interactions formed on these genes are consistent with these DNAs being assembled into extensive nucleosomal arrays.

scholarly journals Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition.

1992 ◽  
Vol 12 (5) ◽  
pp. 2260-2272 ◽  
Author(s):  
F E Campbell ◽  
D R Setzer
Keyword(s):  
Rna Polymerase ◽  
Transcription Termination ◽  
Transcription Elongation ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Signal Recognition ◽  
Polymerase Iii ◽  
5S Rrna Gene ◽  
Nascent Rna

Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.

Displacement of Xenopus transcription factor IIIA from a 5S rRNA gene by a transcribing RNA polymerase

1991 ◽  
Vol 11 (8) ◽  
pp. 3978-3986
Author(s):  
F E Campbell ◽  
D R Setzer
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Internal Control ◽  
Rna Polymerase Iii ◽  
5S Rrna ◽  
Rrna Gene ◽  
Transcription Factor Iiia ◽  
Polymerase Iii ◽  
5S Rrna Gene

In the absence of other components of the RNA polymerase III transcription machinery, transcription factor IIIA (TFIIIA) can be displaced from both strands of its DNA-binding site (the internal control region) on the somatic-type 5S rRNA gene of Xenopus borealis during transcription elongation by bacteriophage T7 RNA polymerase, regardless of which DNA strand is transcribed. Furthermore, substantial displacement is observed after the template has been transcribed only once. Since the complete 5S rRNA transcription complex has previously been shown to remain stably bound to the gene during repeated rounds of transcription by either RNA polymerase III or bacteriophage SP6 RNA polymerase, these results indicate that a factor(s) in addition to TFIIIA is required to create a complex that will remain stably associated with the template during transcription. Thus, transcription complex stability during passage of RNA polymerase cannot be explained solely on the basis of the DNA-binding properties of TFIIIA.

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