scholarly journals Epigenetic silencing of clustered tRNA genes in Arabidopsis

2020 ◽  
Vol 48 (18) ◽  
pp. 10297-10312
Author(s):  
Guillaume Hummel ◽  
Alexandre Berr ◽  
Stéfanie Graindorge ◽  
Valérie Cognat ◽  
Elodie Ubrig ◽  
...  
Keyword(s):  
Rna Polymerase Iii ◽  
Trna Genes ◽  
Biological Processes ◽  
Predominant Role ◽  
Genomic Features ◽  
Transfer Rnas ◽  
Regulatory Processes ◽  
Repressive Chromatin ◽  
Wide Range ◽  
Pol Iii

Abstract Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.

scholarly journals Epigenetic silencing of clustered tDNAs in Arabidopsis

2020 ◽  
Author(s):  
Guillaume Hummel ◽  
Alexandre Berr ◽  
Stéfanie Graindorge ◽  
Valérie Cognat ◽  
Elodie Ubrig ◽  
...  
Keyword(s):  
Rna Polymerase Iii ◽  
Trna Genes ◽  
Biological Processes ◽  
Predominant Role ◽  
Genomic Features ◽  
Transfer Rnas ◽  
Repressive Chromatin ◽  
Wide Range ◽  
Genomic Environment ◽  
Fine Tune

AbstractBeyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. Our data highlight that the combination of both genomic environment and epigenomic landscape contribute to fine tune the differential expression of dispersed versus clustered tDNAs in Arabidopsis.

scholarly journals Involvement of RNA Polymerase III in Immune Responses

2015 ◽  
Vol 35 (10) ◽  
pp. 1848-1859 ◽  
Author(s):  
Damian Graczyk ◽  
Robert J. White ◽  
Kevin M. Ryan
Keyword(s):  
Transcription Factor ◽  
Immune Responses ◽  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Trna Genes ◽  
Malignant Cells ◽  
Polymerase Iii ◽  
Mouse Macrophages ◽  
Tightly Coupled ◽  
Pol Iii

Inflammation in the tumor microenvironment has many tumor-promoting effects. In particular, tumor-associated macrophages (TAMs) produce many cytokines which can support tumor growth by promoting survival of malignant cells, angiogenesis, and metastasis. Enhanced cytokine production by TAMs is tightly coupled with protein synthesis. In turn, translation of proteins depends on tRNAs, short abundant transcripts that are made by RNA polymerase III (Pol III). Here, we connect these facts by showing that stimulation of mouse macrophages with lipopolysaccharides (LPS) from the bacterial cell wall causes transcriptional upregulation of tRNA genes. The transcription factor NF-κB is a key transcription factor mediating inflammatory signals, and we report that LPS treatment causes an increased association of the NF-κB subunit p65 with tRNA genes. In addition, we show that p65 can directly associate with the Pol III transcription factor TFIIIB and that overexpression of p65 induces Pol III-dependent transcription. As a consequence of these effects, we show that inhibition of Pol III activity in macrophages restrains cytokine secretion and suppresses phagocytosis, two key functional characteristics of these cells. These findings therefore identify a radical new function for Pol III in the regulation of macrophage function which may be important for the immune responses associated with both normal and malignant cells.

scholarly journals Structural basis of RNA polymerase III transcription repression by Maf1

2019 ◽  
Author(s):  
Matthias K. Vorländer ◽  
Florence Baudin ◽  
Robyn D. Moir ◽  
René Wetzel ◽  
Wim J. H. Hagen ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Binding Site ◽  
Transcription Initiation ◽  
Rna Polymerase Iii ◽  
Structural Basis ◽  
Metabolic Efficiency ◽  
Transcription Repression ◽  
Polymerase Iii ◽  
Wide Range ◽  
Pol Iii

ABSTRACTMaf1 is a highly conserved central regulator of transcription by RNA polymerase III (Pol III), and Maf1 activity influences a wide range of phenotypes from metabolic efficiency to lifespan. Here, we present a 3.3 Å cryo-EM structure of yeast Maf1 bound to Pol III, which establishes how Maf1 achieves transcription repression. In the Maf1-bound state, Pol III elements that are involved in transcription initiation are sequestered, and the active site is sealed off due to ordering of the mobile C34 winged helix 2 domain. Specifically, the Maf1 binding site overlaps with the binding site of the Pol III transcription factor TFIIIB and DNA in the pre-initiation complex, rationalizing that binding of Maf1 and TFIIIB to Pol III are mutually exclusive. We validate our structure using variants of Maf1 with impaired transcription-inhibition activity. These results reveal the exact mechanism of Pol III inhibition by Maf1, and rationalize previous biochemical data.

scholarly journals Transcriptional activation of a moderately expressed tRNA gene by a positioned nucleosome

2006 ◽  
Vol 396 (3) ◽  
pp. 439-447 ◽  
Author(s):  
Akhila Parthasarthy ◽  
Karumathil P. Gopinathan
Keyword(s):  
Transcriptional Activation ◽  
Multigene Family ◽  
Rna Polymerase Iii ◽  
Upstream Region ◽  
Trna Genes ◽  
Naked Dna ◽  
Gene Copies ◽  
Direct Binding ◽  
Pol Iii ◽  
Mulberry Silkworm

All of the members of a tRNA1Gly multigene family from the mulberry silkworm, Bombyx mori, have identical coding regions and consequently identical internal promoter elements, but are transcribed at different levels. A moderately expressed copy, tRNA1Gly-4 from within this multigene family, which was transcribed to 30–50% of the highly transcribed gene copies harboured two typical TATAA box sequences in the 5′ upstream region at positions −27 nt and −154 nt with respect to the +1 nt of mature tRNA. Deletion of the distal TATAA sequence at −154 nt brought down the transcription more than 70%, whereas mutation of the proximal element did not affect transcription. tRNA1Gly-4 could be readily assembled into chromatin, with a positioned nucleosome in the upstream region, and the assembled nucleosome formed stable complexes with the transcription factors TFIIIC and TFIIIB. Organization of the gene into nucleosomes also enhanced transcription significantly above that of the naked DNA, reaching transcription levels comparable with those of the highly transcribed copies. This nucleosome-mediated enhancement in transcription was absent when the distal TATAA sequences were deleted, whereas mutation of the proximal TATAA element showed no effect. In the absence of the distal TATAA sequences, assembly into the nucleosome inhibited transcription of tRNA1Gly-4. TFIIIB bound directly through the distal TATAA sequence at −154 nt and the positioned nucleosome facilitated its interaction with TFIIIC. The direct binding of TFIIIB to the DNA provided anchoring of the factor to the template DNA which conferred a higher stability on the TFIIIB–TFIIIC–DNA complex. We have proposed a novel mechanism for the nucleosome-mediated stimulation of pol III (RNA polymerase III) transcription of tRNA genes, a model not presented previously.

scholarly journals Noncanonical Roles of tRNAs: tRNA Fragments and Beyond

2020 ◽  
Vol 54 (1) ◽  
pp. 47-69 ◽  
Author(s):  
Zhangli Su ◽  
Briana Wilson ◽  
Pankaj Kumar ◽  
Anindya Dutta
Keyword(s):  
Sequence Variation ◽  
Protein Translation ◽  
Nutrient Sensing ◽  
Trna Genes ◽  
Biological Processes ◽  
Messenger Rnas ◽  
Regulatory Pathways ◽  
Transfer Rnas ◽  
Rna Molecules

As one of the most abundant and conserved RNA species, transfer RNAs (tRNAs) are well known for their role in reading the codons on messenger RNAs and translating them into proteins. In this review, we discuss the noncanonical functions of tRNAs. These include tRNAs as precursors to novel small RNA molecules derived from tRNAs, also called tRNA-derived fragments, that are abundant across species and have diverse functions in different biological processes, including regulating protein translation, Argonaute-dependent gene silencing, and more. Furthermore, the role of tRNAs in biosynthesis and other regulatory pathways, including nutrient sensing, splicing, transcription, retroelement regulation, immune response, and apoptosis, is reviewed. Genome organization and sequence variation of tRNA genes are also discussed in light of their noncanonical functions. Lastly, we discuss the recent applications of tRNAs in genome editing and microbiome sequencing.

scholarly journals Inhibition of tRNA Gene Transcription by the Immunosuppressant Mycophenolic Acid

2019 ◽  
Vol 40 (1) ◽  
Author(s):  
Aneta Jurkiewicz ◽  
Ewa Leśniewska ◽  
Małgorzata Cieśla ◽  
Neuton Gorjão ◽  
Theodoros Kantidakis ◽  
...  
Keyword(s):  
Mycophenolic Acid ◽  
Mammalian Cells ◽  
De Novo ◽  
Rna Polymerase Iii ◽  
Sharp Decrease ◽  
Trna Genes ◽  
Anticancer Chemotherapy ◽  
Transcriptional Inhibition ◽  
Cycle Arrest ◽  
Pol Iii

ABSTRACT Mycophenolic acid (MPA) is the active metabolite of mycophenolate mofetil, a drug that is widely used for immunosuppression in organ transplantation and autoimmune diseases, as well as anticancer chemotherapy. It inhibits IMP dehydrogenase, a rate-limiting enzyme in de novo synthesis of guanidine nucleotides. MPA treatment interferes with transcription elongation, resulting in a drastic reduction of pre-rRNA and pre-tRNA synthesis, the disruption of the nucleolus, and consequently cell cycle arrest. Here, we investigated the mechanism whereby MPA inhibits RNA polymerase III (Pol III) activity, in both yeast and mammalian cells. We show that MPA rapidly inhibits Pol III by depleting GTP. Although MPA treatment can activate p53, this is not required for Pol III transcriptional inhibition. The Pol III repressor MAF1 is also not responsible for inhibiting Pol III in response to MPA treatment. We show that upon MPA treatment, the levels of selected Pol III subunits decrease, but this is secondary to transcriptional inhibition. Chromatin immunoprecipitation (ChIP) experiments show that Pol III does not fully dissociate from tRNA genes in yeast treated with MPA, even though there is a sharp decrease in the levels of newly transcribed tRNAs. We propose that in yeast, GTP depletion may lead to Pol III stalling.

scholarly journals Role of maturation-promoting factor (p34cdc2-cyclin B) in differential expression of the Xenopus oocyte and somatic-type 5S RNA genes.

1994 ◽  
Vol 14 (7) ◽  
pp. 4704-4711 ◽  
Author(s):  
V J Wolf ◽  
T Dang ◽  
P Hartl ◽  
J M Gottesfeld
Keyword(s):  
Rna Polymerase Iii ◽  
Cyclin B ◽  
Trna Genes ◽  
5S Rna ◽  
Transcription System ◽  
Transcription Complexes ◽  
Pol Iii ◽  
Differential Transcription ◽  
5S Rna Genes ◽  
Rna Genes

Transcription of 5S rRNA and tRNA genes by RNA polymerase III (pol III) in cytosolic extracts of unfertilized Xenopus eggs and in a reconstituted system derived from Xenopus oocytes is repressed by the action of one or more mitotic protein kinases. Repression is due to the phosphorylation of a component of the pol III transcription apparatus. We find that the maturation/mitosis-promoting factor kinase (MPF, p34cdc2-cyclin B) can directly mediate this repression in vitro. Affinity-purified MPF and immune complexes formed with antibodies to the protein subunits of MPF (p34cdc2 and cyclin B) retain both histone H1 kinase activity and the capacity to repress transcription in the reconstituted transcription system. Transcription complexes of oocyte-type 5S RNA genes and tRNA genes are quantitatively more sensitive to MPF repression than the corresponding transcription complexes of the somatic-type 5S RNA gene. The differential transcription of oocyte- and somatic-type genes observed during early Xenopus embryogenesis has been reproduced with the reconstituted transcription system and affinity-purified MPF. This differential transcription may be due to the instability of transcription complexes on the oocyte-type genes and the heightened sensitivity of soluble transcription factors to inactivation by mitotic phosphorylation. Our results suggest that MPF may play a role in vivo in the establishment of the embryonic pattern of pol III gene expression.

scholarly journals Production and Purification of Endogenously Modified tRNA-Derived Small RNAs

2020 ◽  
Author(s):  
Aleksej Drino ◽  
Vera Oberbauer ◽  
Conor Troger ◽  
Eva Janisiw ◽  
Dorothea Anrather ◽  
...  
Keyword(s):  
Small Rnas ◽  
Molecular Level ◽  
Molecular Function ◽  
Biological Processes ◽  
Biological Impact ◽  
Rna Sequences ◽  
Preparative Scale ◽  
Transfer Rnas ◽  
Wide Range ◽  
Biological Sources

ABSTRACTDuring particular stress conditions, transfer RNAs (tRNAs) become substrates of stress-induced endonucleases, resulting in the production of distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide range of biological processes, but how isoacceptor and even isodecoder-specific tsRNAs act at the molecular level is still poorly understood. Importantly, stress-induced tRNA cleavage affects only a few tRNAs of a given isoacceptor or isodecoder, raising the question as to how such limited molecule numbers could exert measurable biological impact. While the molecular function of individual tsRNAs is likely mediated through association with other molecules, addressing the interactome of specific tsRNAs has only been attempted by using synthetic RNA sequences. Since tRNAs carry post-transcriptional modifications, tsRNAs are likely modified but the extent of their modifications remains largely unknown. Here, we developed a biochemical framework for the production and purification of specific tsRNAs using human cells. Preparative scale purification of tsRNAs from biological sources should facilitate experimentally addressing as to how exactly these small RNAs mediate the multitude of reported molecular functions.

scholarly journals Signaling to and from the RNA Polymerase III Transcription and Processing Machinery

2018 ◽  
Vol 87 (1) ◽  
pp. 75-100 ◽  
Author(s):  
Ian M. Willis ◽  
Robyn D. Moir
Keyword(s):  
Protein Synthesis ◽  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Negative Regulator ◽  
Energetic Cost ◽  
Regulatory Pathways ◽  
Transfer Rnas ◽  
Small Noncoding Rnas ◽  
Pol Iii ◽  
Robust Regulation

RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities. In this review, we consider how nutrients and stress control Pol III transcription via its factors and its negative regulator, Maf1. We highlight recent work showing that the composition of the tRNA population and the function of individual tRNAs is dynamically controlled and that unrestrained Pol III transcription can reprogram central metabolic pathways.

scholarly journals Role of maturation-promoting factor (p34cdc2-cyclin B) in differential expression of the Xenopus oocyte and somatic-type 5S RNA genes

1994 ◽  
Vol 14 (7) ◽  
pp. 4704-4711
Author(s):  
V J Wolf ◽  
T Dang ◽  
P Hartl ◽  
J M Gottesfeld
Keyword(s):  
Rna Polymerase Iii ◽  
Cyclin B ◽  
Trna Genes ◽  
5S Rna ◽  
Transcription System ◽  
Transcription Complexes ◽  
Pol Iii ◽  
Differential Transcription ◽  
5S Rna Genes ◽  
Rna Genes

Transcription of 5S rRNA and tRNA genes by RNA polymerase III (pol III) in cytosolic extracts of unfertilized Xenopus eggs and in a reconstituted system derived from Xenopus oocytes is repressed by the action of one or more mitotic protein kinases. Repression is due to the phosphorylation of a component of the pol III transcription apparatus. We find that the maturation/mitosis-promoting factor kinase (MPF, p34cdc2-cyclin B) can directly mediate this repression in vitro. Affinity-purified MPF and immune complexes formed with antibodies to the protein subunits of MPF (p34cdc2 and cyclin B) retain both histone H1 kinase activity and the capacity to repress transcription in the reconstituted transcription system. Transcription complexes of oocyte-type 5S RNA genes and tRNA genes are quantitatively more sensitive to MPF repression than the corresponding transcription complexes of the somatic-type 5S RNA gene. The differential transcription of oocyte- and somatic-type genes observed during early Xenopus embryogenesis has been reproduced with the reconstituted transcription system and affinity-purified MPF. This differential transcription may be due to the instability of transcription complexes on the oocyte-type genes and the heightened sensitivity of soluble transcription factors to inactivation by mitotic phosphorylation. Our results suggest that MPF may play a role in vivo in the establishment of the embryonic pattern of pol III gene expression.

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