Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro.

Nuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I-III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.

Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae.

In archaea and bacteria the major classes of RNAs are synthesized by one DNA-dependent RNA polymerase (RNAP). In contrast, most eukaryotes have three highly specialized RNAPs to transcribe the nuclear genome. RNAP I synthesizes almost exclusively ribosomal (r)RNA, RNAP II synthesizes mRNA as well as many noncoding RNAs involved in RNA processing or RNA silencing pathways and RNAP III synthesizes mainly tRNA and 5S rRNA. This review discusses functional differences of the three nuclear core RNAPs in the yeast S. cerevisiae with a particular focus on RNAP I transcription of nucleolar ribosomal (r)DNA chromatin.

Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes.

In growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic "open" chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal "closed" chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.

Ultrafast Nanoscopy of High-Density Exciton Phases in WSe2.

The density-driven transition of an exciton gas into an electron-hole plasma remains a compelling question in condensed matter physics. In two-dimensional transition metal dichalcogenides, strongly bound excitons can undergo this phase change after transient injection of electron-hole pairs. Unfortunately, unavoidable nanoscale inhomogeneity in these materials has impeded quantitative investigation into this elusive transition. Here, we demonstrate how ultrafast polarization nanoscopy can capture the Mott transition through the density-dependent recombination dynamics of electron-hole pairs within a WSe2 homobilayer. For increasing carrier density, an initial monomolecular recombination of optically dark excitons transitions continuously into a bimolecular recombination of an unbound electron-hole plasma above 7 × 1012 cm-2. We resolve how the Mott transition modulates over nanometer length scales, directly evidencing the strong inhomogeneity in stacked monolayers. Our results demonstrate how ultrafast polarization nanoscopy could unveil the interplay of strong electronic correlations and interlayer coupling within a diverse range of stacked and twisted two-dimensional materials.

Proximity control of interlayer exciton-phonon hybridization in van der Waals heterostructures.

Van der Waals stacking has provided unprecedented flexibility in shaping many-body interactions by controlling electronic quantum confinement and orbital overlap. Theory has predicted that also electron-phonon coupling critically influences the quantum ground state of low-dimensional systems. Here we introduce proximity-controlled strong-coupling between Coulomb correlations and lattice dynamics in neighbouring van der Waals materials, creating new electrically neutral hybrid eigenmodes. Specifically, we explore how the internal orbital 1s-2p transition of Coulomb-bound electron-hole pairs in monolayer tungsten diselenide resonantly hybridizes with lattice vibrations of a polar capping layer of gypsum, giving rise to exciton-phonon mixed eigenmodes, called excitonic Lyman polarons. Tuning orbital exciton resonances across the vibrational resonances, we observe distinct anticrossing and polarons with adjustable exciton and phonon compositions. Such proximity-induced hybridization can be further controlled by quantum designing the spatial wavefunction overlap of excitons and phonons, providing a promising new strategy to engineer novel ground states of two-dimensional systems.

Tripartite Motif 22 (TRIM22) protein restricts herpes simplex virus 1 by epigenetic silencing of viral immediate-early genes.

Intrinsic resistance is a crucial line of defense against virus infections, and members of the Tripartite Ring Interaction Motif (TRIM) family of proteins are major players in this system, such as cytoplasmic TRIM5α or nuclear promyelocytic leukemia (PML/TRIM19) protein. Previous reports on the antiviral function of another TRIM protein, TRIM22, emphasized its innate immune role as a Type I and Type II interferon-stimulated gene against RNA viruses. This study shows that TRIM22 has an additional intrinsic role against DNA viruses. Here, we report that TRIM22 is a novel restriction factor of HSV-1 and limits ICP0-null virus replication by increasing histone occupancy and heterochromatin, thereby reducing immediate-early viral gene expression. The corresponding wild-type equivalent of the virus evades the TRIM22-specific restriction by a mechanism independent of ICP0-mediated degradation. We also demonstrate that TRIM22 inhibits other DNA viruses, including representative members of the ß- and γ- herpesviruses. Allelic variants in TRIM22 showed different degrees of anti-herpesviral activity; thus, TRIM22 genetic variability may contribute to the varying susceptibility to HSV-1 infection in humans. Collectively, these results argue that TRIM22 is a novel restriction factor and expand the list of restriction factors functioning in the infected cell nucleus to counter DNA virus infection.

Twist-tailoring Coulomb correlations in van der Waals homobilayers.

The recent discovery of artificial phase transitions induced by stacking monolayer materials at magic twist angles represents a paradigm shift for solid state physics. Twist-induced changes of the single-particle band structure have been studied extensively, yet a precise understanding of the underlying Coulomb correlations has remained challenging. Here we reveal in experiment and theory, how the twist angle alone affects the Coulomb-induced internal structure and mutual interactions of excitons. In homobilayers of WSe2, we trace the internal 1s-2p resonance of excitons with phase-locked mid-infrared pulses as a function of the twist angle. Remarkably, the exciton binding energy is renormalized by up to a factor of two, their lifetime exhibits an enhancement by more than an order of magnitude, and the exciton-exciton interaction is widely tunable. Our work opens the possibility of tailoring quasiparticles in search of unexplored phases of matter in a broad range of van der Waals heterostructures.

RNA polymerase I (Pol I) passage through nucleosomes depends on Pol I subunits binding its lobe structure.

RNA polymerase I (Pol I) is a highly efficient enzyme specialized in synthesizing most ribosomal RNAs. After nucleosome deposition at each round of rDNA replication, the Pol I transcription machinery has to deal with nucleosomal barriers. It has been suggested that Pol I-associated factors facilitate chromatin transcription, but it is unknown whether Pol I has an intrinsic capacity to transcribe through nucleosomes. Here, we used in vitro transcription assays to study purified WT and mutant Pol I variants from the yeast Saccharomyces cerevisiae and compare their abilities to pass a nucleosomal barrier with those of yeast Pol II and Pol III. Under identical conditions, purified Pol I and Pol III, but not Pol II, could transcribe nucleosomal templates. Pol I mutants lacking either the heterodimeric subunit Rpa34.5/Rpa49 or the C-terminal part of the specific subunit Rpa12.2 showed a lower processivity on naked DNA templates, which was even more reduced in the presence of a nucleosome. Our findings suggest that the lobe-binding subunits Rpa34.5/Rpa49 and Rpa12.2 facilitate passage through nucleosomes, suggesting possible cooperation among these subunits. We discuss the contribution of Pol I-specific subunit domains to efficient Pol I passage through nucleosomes in the context of transcription rate and processivity.

Multibranch pulse synthesis and electro-optic detection of subcycle multi-terahertz electric fields.

We present a robust, compact pulse synthesis scheme generating intense phase-locked subcycle multi-terahertz waveforms. The ultrabroadband laser fundamental is split into two parallel branches driving optical rectification in crystals of GaSe and LiGaS2, each operated at the group velocity matching point. The coherent combination of the resulting pulses yields a continuous multi-terahertz spectrum covering 1.5 optical octaves. The corresponding 0.8-cycle electric field waveform is directly mapped out by electro-optic sampling, revealing peak fields of 15 kV/cm at a repetition rate of 0.4 MHz. The multiplexable and power scalable scheme opens the door to strong-field custom-tailored waveforms driving nonlinear optics and light wave electronics.

Role for a Filamentous Nuclear Assembly of IFI16, DNA, and Host Factors in Restriction of Herpesviral Infection.

Several host cell nuclear factors are known to restrict herpes simplex virus 1 (HSV-1) replication, but their mechanisms of action remain to be defined. Interferon-inducible protein 16 (IFI16) and the nuclear domain 10-associated proteins, such as promyelocytic leukemia (PML) protein, localize to input viral genomes, but they are also capable of restricting progeny viral transcription. In this study, we used structured illumination microscopy to show that after HSV DNA replication, IFI16 forms nuclear filamentous structures on DNA within a subset of nuclear replication compartments in HSV-1 ICP0-null mutant virus-infected human cells. The ability to form filaments in different cell types correlates with the efficiency of restriction, and the kinetics of filament formation and epigenetic changes are similar. Thus, both are consistent with the filamentous structures being involved in epigenetic silencing of viral progeny DNA. IFI16 filaments recruit other restriction factors, including PML, Sp100, and ATRX, to aid in the restriction. Although the filaments are only in a subset of the replication compartments, IFI16 reduces the levels of elongation-competent RNA polymerase II (Pol II) in all replication compartments. Therefore, we propose that IFI16 filaments with associated restriction factors that form in replication compartments constitute a "restrictosome" structure that signals in cis and trans to silence the progeny viral DNA throughout the infected cell nucleus. The IFI16 filamentous structure may constitute the first known nuclear supramolecular organizing center for signaling in the cell nucleus.IMPORTANCE Mammalian cells exhibit numerous strategies to recognize and contain viral infections. The best-characterized antiviral responses are those that are induced within the cytosol by receptors that activate interferon responses or shut down translation. Antiviral responses also occur in the nucleus, yet these intranuclear innate immune responses are poorly defined at the receptor-proximal level. In this study, we explored the ability of cells to restrict infection by assembling viral DNA into transcriptionally silent heterochromatin within the nucleus. We found that the IFI16 restriction factor forms filaments on DNA within infected cells. These filaments recruit antiviral restriction factors to prevent viral replication in various cell types. Mechanistically, IFI16 filaments inhibit the recruitment of RNA polymerase II to viral genes. We propose that IFI16 filaments with associated restriction factors constitute a "restrictosome" structure that can signal to other parts of the nucleus where foreign DNA is located that it should be silenced.

Ultrabroadband etalon-free detection of infrared transients by van-der-Waals contacted sub-10-µm GaSe detectors.

We demonstrate ultrabroadband electro-optic detection of multi-THz transients using mechanically exfoliated flakes of gallium selenide of a thickness of less than 10 µm, contacted to a diamond substrate by van-der-Waals bonding. While the low crystal thickness allows for extremely broadband phase matching, the excellent optical contact with the index-matched substrate suppresses multiple optical reflections. The high quality of our structure makes our scheme suitable for the undistorted and artifact-free observation of electromagnetic waveforms covering the entire THz spectral range up to the near-infrared regime without the need for correction for the electro-optic response function. With the current revolution of chemically inert quasi-two-dimensional layered materials, we anticipate that exfoliated van-der-Waals materials on index-matched substrates will open new flexible ways of ultrabroadband electro-optic detection at unprecedented frequencies.

Mechanisms of Host IFI16, PML, and Daxx Protein Restriction of Herpes Simplex Virus 1 Replication.

The initial events after DNA virus infection involve a race between epigenetic silencing of the incoming viral DNA by host cell factors and expression of viral genes. Several host gene products, including the nuclear domain 10 (ND10) components PML (promyelocytic leukemia) and Daxx (death domain-associated protein 6), as well as IFI16 (interferon-inducible protein 16), have been shown to restrict herpes simplex virus 1 (HSV-1) replication. Whether IFI16 and ND10 components work together or separately to restrict HSV-1 replication is not known. To determine the combinatorial effects of IFI16 and ND10 proteins on viral infection, we depleted Daxx or PML in primary human foreskin fibroblasts (HFFs) in the presence or absence of IFI16. Daxx or IFI16 depletion resulted in higher ICP0 mutant viral yields, and the effects were additive. Surprisingly, small interfering RNA (siRNA) depletion of PML in the HFF cells led to decreased ICP0-null virus replication, while short hairpin RNA (shRNA) depletion led to increased ICP0-null virus replication, arguing that different PML isoforms or PML-related proteins may have restrictive or proviral functions. In normal human cells, viral DNA replication increases expression of all classes of HSV-1 genes. We observed that IFI16 repressed transcription from both parental and progeny DNA genomes. Taken together, our results show that the mechanisms of action of IFI16 and ND10 proteins are independent, at least in part, and that IFI16 exerts restrictive effects on both input and replicated viral genomes. These results raise the potential for distinct mechanisms of action of IFI16 on parental and progeny viral DNA molecules.IMPORTANCE Many human DNA viruses transcribe their genomes and replicate in the nucleus of a host cell, where they exploit the host cell nuclear machinery for their own replication. Host factors attempt to restrict viral replication by blocking such events, and viruses have evolved mechanisms to neutralize the host restriction factors. In this study, we provide information about the mechanisms of action of three host cell factors that restrict replication of herpes simplex virus (HSV). We found that these factors function independently and that one acts to restrict viral transcription from parental and progeny viral DNA genomes. These results provide new information about how cells counter DNA virus replication in the nucleus and provide possible approaches to enhance the ability of human cells to resist HSV infection.

Dielectric Engineering of Electronic Correlations in a van der Waals Heterostructure.

Heterostructures of van der Waals bonded layered materials offer unique means to tailor dielectric screening with atomic-layer precision, opening a fertile field of fundamental research. The optical analyses used so far have relied on interband spectroscopy. Here we demonstrate how a capping layer of hexagonal boron nitride (hBN) renormalizes the internal structure of excitons in a WSe2 monolayer using intraband transitions. Ultrabroadband terahertz probes sensitively map out the full complex-valued mid-infrared conductivity of the heterostructure after optical injection of 1s A excitons. This approach allows us to trace the energies and line widths of the atom-like 1s-2p transition of optically bright and dark excitons as well as the densities of these quasiparticles. The excitonic resonance red shifts and narrows in the WSe2/hBN heterostructure compared to the bare monolayer. Furthermore, the ultrafast temporal evolution of the mid-infrared response function evidences the formation of optically dark excitons from an initial bright population. Our results provide key insight into the effect of nonlocal screening on electron-hole correlations and open new possibilities of dielectric engineering of van der Waals heterostructures.

Phase-locked multi-terahertz electric fields exceeding 13 MV/cm at a 190 kHz repetition rate.

We demonstrate a compact source of energetic and phase-locked multi-terahertz pulses at a repetition rate of 190 kHz. Difference frequency mixing of the fundamental output of an Yb:KGW amplifier with the idler of an optical parametric amplifier in GaSe and LiGaS2 crystals yields a passively phase-locked train of waveforms tunable between 12 and 42 THz. The shortest multi-terahertz pulses contain 1.8 oscillation cycles within the intensity full width at half-maximum. Pulse energies of up to 0.16 µJ and peak electric fields of 13 MV/cm are achieved. Electro-optic sampling reveals a phase stability better than 0.1 π over multiple hours, combined with free carrier-envelope phase tunability. The scalable scheme opens the door to strong-field terahertz optics at unprecedented repetition rates.

Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases.

Thiolutin is a disulfide-containing antibiotic and anti-angiogenic compound produced by Streptomyces. Its biological targets are not known. We show that reduced thiolutin is a zinc chelator that inhibits the JAB1/MPN/Mov34 (JAMM) domain-containing metalloprotease Rpn11, a deubiquitinating enzyme of the 19S proteasome. Thiolutin also inhibits the JAMM metalloproteases Csn5, the deneddylase of the COP9 signalosome; AMSH, which regulates ubiquitin-dependent sorting of cell-surface receptors; and BRCC36, a K63-specific deubiquitinase of the BRCC36-containing isopeptidase complex and the BRCA1-BRCA2-containing complex. We provide evidence that other dithiolopyrrolones also function as inhibitors of JAMM metalloproteases.

Direct Observation of Ultrafast Exciton Formation in a Monolayer of WSe2.

Many of the fundamental optical and electronic properties of atomically thin transition metal dichalcogenides are dominated by strong Coulomb interactions between electrons and holes, forming tightly bound atom-like states called excitons. Here, we directly trace the ultrafast formation of excitons by monitoring the absolute densities of bound and unbound electron-hole pairs in single monolayers of WSe2 on a diamond substrate following femtosecond nonresonant optical excitation. To this end, phase-locked mid-infrared probe pulses and field-sensitive electro-optic sampling are used to map out the full complex-valued optical conductivity of the nonequilibrium system and to discern the hallmark low-energy responses of bound and unbound pairs. While the spectral shape of the infrared response immediately after above-bandgap injection is dominated by free charge carriers, up to 60% of the electron-hole pairs are bound into excitons already on a subpicosecond time scale, evidencing extremely fast and efficient exciton formation. During the subsequent recombination phase, we still find a large density of free carriers in addition to excitons, indicating a nonequilibrium state of the photoexcited electron-hole system.

Analysis of S. cerevisiae RNA Polymerase I Transcription In Vitro.

RNA polymerase I (Pol I) activity is crucial to provide cells with sufficient amounts of ribosomal RNA (rRNA). Synthesis of rRNA takes place in the nucleolus, is tightly regulated and is coordinated with synthesis and assembly of ribosomal proteins, finally resulting in the formation of mature ribosomes. Many studies on Pol I mechanisms and regulation in the model organism S. cerevisiae were performed using either complex in vitro systems reconstituted from more or less purified fractions or genetic analyses. While providing many valuable insights these strategies did not always discriminate between direct and indirect effects in transcription initiation and termination, when mutated forms of Pol I subunits or transcription factors were investigated. Therefore, a well-defined minimal system was developed which allows to reconstitute highly efficient promoter-dependent Pol I initiation and termination of transcription. Transcription can be initiated at a minimal promoter only in the presence of recombinant core factor and extensively purified initiation competent Pol I. Addition of recombinant termination factors triggers transcriptional pausing and release of the ternary transcription complex. This minimal system represents a valuable tool to investigate the direct impact of (lethal) mutations in components of the initiation and termination complexes on the mechanism and regulation of rRNA synthesis.

Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo.

Different models have been proposed explaining how eukaryotic gene transcription is terminated. Recently, Nsi1, a factor involved in silencing of ribosomal DNA (rDNA), was shown to be required for efficient termination of rDNA transcription by RNA polymerase I (Pol I) in the yeast Saccharomyces cerevisiae. Nsi1 contains Myb-like DNA binding domains and associates in vivo near the 3' end of rRNA genes to rDNA, but information about which and how DNA sequences might influence Nsi1-dependent termination is lacking. Here, we show that binding of Nsi1 to a stretch of 11 nucleotides in the correct orientation was sufficient to pause elongating Pol I shortly upstream of the Nsi1 binding site and to release the transcripts in vitro. The same minimal DNA element triggered Nsi1-dependent termination of pre-rRNA synthesis using an in vivo reporter assay. Termination efficiency in the in vivo system could be enhanced by inclusion of specific DNA sequences downstream of the Nsi1 binding site. These data and the finding that Nsi1 blocks efficiently only Pol I-dependent RNA synthesis in an in vitro transcription system improve our understanding of a unique mechanism of transcription termination.

Oleic acid is a precursor of linoleic acid and the male sex pheromone in Nasonia vitripennis.

Linoleic acid (C18:2(Δ9,12), LA) is crucial for many cell functions in organisms. It has long been a paradigm that animals are unable to synthesize LA from oleic acid (C18:1(Δ9), OA) because they were thought to miss Δ(12)-desaturases for inserting a double bound at the Δ(12)-position. Today it is clear that this is not true for all animals because some insects and other invertebrates have been demonstrated to synthesize LA. However, the ability to synthesize LA is known in only five insect orders and no examples have been reported so far in the Hymenoptera. LA plays a particular role in the parasitic wasp Nasonia vitripennis, because it is the precursor of the male sex pheromone consisting of (4R,5R)- and (4R,5S)-5-hydroxy-4-decanolides. Here we demonstrate by stable isotope labeling that N. vitripennis is able to incorporate externally applied fully (13)C-labeled OA into the male sex pheromone suggesting that they convert initially OA into LA. To verify this assumption, we produced fly hosts (Lucilia caesar) which were experimentally enriched in (13)C-labeled OA and reared male parasitoids on these hosts. Chemical analysis of transesterified lipid raw extracts from hosts and parasitoids revealed that N. vitripennis but not L. caesar contained (13)C-labeled LA methyl ester. Furthermore, male wasps from the manipulated hosts produced significant amounts of (13)C-labeled sex pheromone. These results suggest that N. vitripennis possesses a Δ(12)-desaturase. The additional fitness relevant function as pheromone precursor might have favored the evolution of LA biosynthesis in N. vitripennis to make the wasps independent of the formerly essential nutrient.

RNA polymerase I termination: Where is the end?

The synthesis of ribosomal RNA (rRNA) precursor molecules by RNA polymerase I (Pol I) terminates with the dissociation of the protein-DNA-RNA ternary complex. Based on in vitro results the mechanism of Pol I termination appeared initially to be rather conserved and simple until this process was more thoroughly re-investigated in vivo. A picture emerged that Pol I termination seems to be connected to co-transcriptional processing, re-initiation of transcription and, possibly, other processes downstream of Pol I transcription units. In this article, our current understanding of the mechanism of Pol I termination and how this process might be implicated in other biological processes in yeast and mammals is summarized and discussed. This article is part of a Special Issue entitled: Transcription by Odd Pols.