Transcription of specific adenovirus genes in isolated nuclei by exogenous RNA polymerases

The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance

A 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3'-ends during repair. Another is synthesis of 5'ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.

Milestones in transcription and chromatin published in the Journal of Biological Chemistry

During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.

RNA Polymerase III as a Gatekeeper to Prevent Severe VZV Infections

In most individuals, varicella zoster virus (VZV) causes varicella upon primary infection and zoster during reactivation. However, in a subset of individuals, VZV may cause severe disease, including encephalitis. Host genetics is believed to be the main determinant of exacerbated disease manifestations. Recent studies have demonstrated that defects in the DNA sensor RNA polymerase III (POL III) confer selective increased susceptibility to VZV infection, thus providing fundamental new insight into VZV immunity. Here we describe the roles of POL III in housekeeping and immune surveillance during VZV infection. We present the latest knowledge on the role of POL III in VZV infection and discuss outstanding questions related to the role of POL III in VZV immunity, and how this insight can be translated into clinical medicine.

Mutations in RNA Polymerase III genes and defective DNA sensing in adults with varicella-zoster virus CNS infection

Recently, deficiency in the cytosolic DNA sensor RNA Polymerase III was described in children with severe primary varicella-zoster virus (VZV) infection in the CNS and lungs. In the present study we examined adult patients with VZV CNS infection caused by viral reactivation. By whole exome sequencing we identified mutations in POL III genes in two of eight patients. These mutations were located in the coding regions of the subunits POLR3A and POLR3E. In functional assays, we found impaired expression of antiviral and inflammatory cytokines in response to the POL III agonist Poly(dA:dT) as well as increased viral replication in patient cells compared to controls. Altogether, this study provides significant extension on the current knowledge on susceptibility to VZV infection by demonstrating mutations in POL III genes associated with impaired immunological sensing of AT-rich DNA in adult patients with VZV CNS infection.

RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression

RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.

RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway

Type I interferons (IFNs) are important for antiviral and autoimmune responses. Retinoic acid-induced gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5'-triphosphate (5'-ppp). Cytosolic B form double-stranded DNA, such as poly(dA-dT)*poly(dA-dT) [poly(dA-dT)], can also induce IFN-beta, but the underlying mechanism is unknown. Here, we show that the cytosolic poly(dA-dT) DNA is converted into 5'-ppp RNA to induce IFN-beta through the RIG-I pathway. Biochemical purification led to the identification of DNA-dependent RNA polymerase III (Pol-III) as the enzyme responsible for synthesizing 5'-ppp RNA from the poly(dA-dT) template. Inhibition of RNA Pol-III prevents IFN-beta induction by transfection of DNA or infection with DNA viruses. Furthermore, Pol-III inhibition abrogates IFN-beta induction by the intracellular bacterium Legionella pneumophila and promotes the bacterial growth. These results suggest that RNA Pol-III is a cytosolic DNA sensor involved in innate immune responses.

Synthesis of 5S rRNA and putative precursor tRNAs in nuclei isolated from wheat embryos

Nuclei isolated from wheat embryos synthesize 4.5S precursor tRNAs and 5S rRNA in vitro. The precursor tRNAs can be processed to 4S tRNAs. Transcription of the tRNA and 5S rRNA genes is carried out by endogenous RNA polymerase III, and addition of exogenous wheat RNA polymerase III results in increased transcription on these genes. A number of experimental results suggest that proper initiation and accurate transcription of the tRNA and 5S rRNA genes occurs with isolated wheat nuclei.

Enhancement of RNA polymerase III transcription by the E1A gene product of adenovirus

Nuclear extracts from adenovirus-infected HeLa cells harvested early in infection demonstrated a markedly increased capacity for transcription by RNA polymerase III of exogenous VA RNA genes, as well as cloned tRNA and 5S RNA genes. In contrast, no enhanced transcription was observed in extracts from cells infected with an E1A deletion mutant. Moreover, cells co-transfected with the VA- and E1A-containing plasmids showed markedly higher levels of VA RNA synthesis than did cells transfected with the VA-containing plasmid alone. Although analysis of high ionic strength extracts revealed that the enhancement of pol III transcription persists late in infection, moderate ionic strength extracts indicated that transcription factor IIIC becomes limiting. Chromatographic fractionation and complementation analysis of extracts from mock- and virus-infected cells indicated that the factor(s) responsible for the enhanced activity was localized entirely in the fraction containing transcription factor IIIC.

Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state

Cloned 5S RNA genes added to Xenopus oocyte nuclear extract assemble into stable active transcription complexes that persist for many rounds of 5S RNA synthesis. This stability of the complex has been demonstrated by its resistance to dilution and to competitor DNA. A stable complex is formed within minutes and lasts for at least 40 rounds of transcription per template over several hours. Stable, transcriptionally inactive complexes can be formed by incubation of cloned 5S RNA genes in an oocyte nuclear extract depleted of a 5S-specific transcription factor and supplemented with histones. The stable, transcriptionally active and inactive states of 5S RNA gene complexes that can be formed in vitro are analogous to the states of the somatic and oocyte 5S RNA genes as they exist in somatic cell chromatin. Oocyte 5S RNa genes remain repressed in chromatin isolated from somatic cells, but can be activated by washing chromatin with high salt. Maintenance of the differentiated state of cell requires that selected genes remain stably active while others are stably repressed for long periods of time. We propose that stable transcription complexes may play an important role in the maintenance of the differentiated state in eucaryotic cells.

Identification of a functional promoter in the long terminal repeat of Rous sarcoma virus

Specific initiation of transcription of Rous sarcoma virus by RNA polymerase II was obtained in a cell-free system using cloned RSV DNA as template. The site of initiation is located in the common "C" region of the long terminal repeat (LTR), 23 bp downstream from the promoter-like sequence TATTTAAG. This finding indicates that the basic information necessary for RSV transcription lies within the viral genome.

Modulation of transcription from chromatin assembled in vitro

A small plasmid DNA was assembled into chromatin in vitro by incubation in an extract prepared frog eggs of Xenopus laevis. The plasmid DNA contrained the regulatory region of the Escherichia coli lac operon, the transcription of which is under positive regulation by catabolite activator protein (CAP) and negative regulation by lac repressor. After incubation in the egg extract the plasmid DNA acquired approximately 60% of the predicted maximum number of nucleosomes. Chromatin was treated with protein and DNA cross-linking agents prior to transcriptin in order to demonstrate that regions of the DNA organized into nucleosomes served as templates for transcription. Cross-linking abolished transcription of chromatin but had no effect on transcription of the DNA, suggesting that transcription of untreated chromatin was not solely attributable to nucleosome-free regions. In support of this conclusion, the average size of the RNA transcribed from chromatin was approximately 1000 bases, which was approximately 5 times longer than the average distance between nucleosomes. Transcription of in vitro assembled plasmid chromatin by E. coli RNA polymerase was stimulated by catabolite activator protein. The CAP-mediated stimulation of transcription was detectable as an increase in total transcription that was specific to chromatin made from a plasmid containing the lac regulatory DNA sequences. The specific increase in the amount of RNA whose synthesis was initiated within the lac region was demonstrated by hybridization of transcription products to complementary DNA fragments bound to nitrocellulose filters. Preliminary investigation of the action of lac repressor suggested that it also modulated transcription from the chromatin template.

Transcription in vitro of adenovirus-2 DNA by RNA polymerases class C purified from uninfected and adenovirus-infected HeLa cells

DNA-dependent RNA polymerase class C (or III) has been solubilized from either uninfected or adenovirus-2-infected HeLa cells and purified by chromatography on phosphocellulose, DNA-cellulose, CM-Sephadex and DEAE-Sephadex. The last column separated the enzyme into three forms CI, CII and CIII, which were completely free of RNA polymerases class A and B and of DNase and RNase. The total and the relative amount of these different enzyme C forms did not vary whether purified from uninfected or infected cells. Irrespective of the stage of purification, the three enzyme forms transcribed deproteinized adenovirus-2DNA very efficiently. This transcription was highly sensitive to elevated ionic strength (especially in the presence of Mg2+) and was accompanied by continuous reinitiation as shown by adding poly(rI), a potent inhibitor of initiation. In addition heparin-resistant initiation complexes could be formed at elevated temperature. The RNA synthesized in vitro on deproteinized intact adenovirus-2 DNA by the different forms of RNA polymerase class C, has been characterized. Analysis of the transcripts by gel electrophoresis, RNA self-annealing, hybridization to separated adenovirus-2 DNA strands and to restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that the various regions of the adenovirus-2 genome were randomly transcribed. In addition, hybridization of RNA transcripts labelled at their 5' end by either [gamma32P]ATP or [gamma-32P]GTP indicated that not only elongation but also initiation occurred randomly through the entire adenovirus-2 genome, irrespective of the form of the enzyme and of the origin of the cells (normal or infected). The results are discussed in terms of the components which are possibly involved in specific transcription.