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Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)—a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5′ untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.

Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts while containing decipherable information about RNA base modifications and poly-A tail lengths. Although many published studies have been exploring and expanding the potential of dRNA-seq, the sequencing accuracy and error patterns remain understudied. We present the first comprehensive evaluation of accuracy and systematic errors in dRNA-seq data from diverse species, as well as synthetic RNA. Deletions significantly outnumbered mismatches/insertions, while the median read accuracy exhibited species-level variation. In addition to homopolymer errors, we observed systematic biases across nucleotides and heteropolymeric motifs in all species. In general, cytosine/uracil-rich regions were more likely to be erroneous than guanines/adenines. Moreover, the systematic errors were strongly dependent on local sequence contexts. By examining raw signal data, we identified underlying signal-level features potentially associated with the error patterns. While read quality scores approximated error rates at base and read levels, failure to detect DNA adapters may lead to data loss. By comparing distinct basecallers, we reason that some sequencing errors are attributable to signal insufficiency rather than algorithmic (base-calling) artefacts. Lastly, we discuss the implications of such error patterns for downstream applications of dRNA-seq data.

The arenavirus nucleoprotein (NP) plays an important role in the virus’ ability to block interferon (IFN) production, and its exonuclease function appears to contribute to this activity. However, efforts to analyze this contribution are complicated by the functional overlap between the exonuclease active site and a neighboring region involved in IKKε-binding and subsequent inhibition of IRF3 activation, which also plays an important role in IFN production. To circumvent this issue, we mutated a residue located away from the active site that is involved in binding of the dsRNA substrate being targeted for exonuclease digestion, i.e. H426A. We found that expression of Tacaribe virus (TCRV) NP containing this RNA-binding H426A mutation was still able to efficiently block IFN-β promoter activity in response to Sendai virus infection, despite being strongly impaired in its exonuclease activity. This was in contrast to a conventional exonuclease active site mutant (E388A), which was impaired with respect to both exonuclease activity and IFN antagonism. Importantly, growth of a recombinant virus encoding the RNA-binding mutation (rTCRV-H426A) was similar to wild-type in IFN-deficient cells, unlike the active site mutant (rTCRV-E388A), which was already markedly impaired in these cells. Further, in IFN-competent cells, the TCRV-H426A RNA-binding mutant showed more robust growth and delayed IFN-β mRNA upregulation compared to the TCRV-E388A active site mutant. Taken together, this novel mutational approach, which allows us to now dissect the different contributions of the NP exonuclease activity and IKKε-binding/IRF3 inhibition to IFN antagonism, clearly suggests that conventional exonuclease mutants targeting the active site overestimate the contribution of the exonuclease function, and that rather other IFN antagonistic functions of NP play the dominant role in IFN-antagonism.

Chemical probing experiments interrogate RNA structure by reacting with unpaired residues whose positions are typically read out by mutational profiling on short-read sequencing machines. Such experiments make rapid and genome-wide measurements of RNA structure, but short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, RNA structure information is acquired as a population average in common regions between transcripts. Here, we present nanopore dimethyl-sulfate mutational profiling (Nano-DMS-MaP-seq) for obtaining isoform resolved structural information of highly similar RNA molecules. We demonstrate the utility of Nano-DMS-MaP-seq by resolving the complex structural landscape of HIV-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures in the common 5’UTR explaining the specific packaging of only unspliced RNAs into viral particles. Thus, Nano-DMS-MaP-seq is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short read ensemble analyses.

RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5′ untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5′ UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS–SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.

Arenaviruses cause several viral hemorrhagic fevers endemic to Africa and South America. The respective causative agents are classified as biosafety level (BSL) 4 pathogens. Unlike for most other BSL4 agents, for the New World arenavirus Junín virus (JUNV) both a highly effective vaccination (Candid#1) and a post-exposure treatment, based on convalescent plasma transfer, are available. In particular, neutralizing antibodies (nAbs) represent a key protective determinant in JUNV infection, which is supported by the correlation between successful passive antibody therapy and the levels of nAbs administered. Unfortunately, comparable resources for the management of other closely related arenavirus infections are not available. Given the significant challenges inherent in studying BSL4 pathogens, our goal was to first assess the suitability of a JUNV transcription and replication-competent virus-like particle (trVLP) system for measuring virus neutralization under BSL1/2 conditions. Indeed, we could show that infection with JUNV trVLPs is glycoprotein (GP) dependent, that trVLP input has a direct correlation to reporter readout, and that these trVLPs can be neutralized by human serum with kinetics similar to those obtained using authentic virus. These properties make trVLPs suitable for use as a proxy for virus in neutralization assays. Using this platform we then evaluated the potential of JUNV nAbs to cross-neutralize entry mediated by GPs from other arenaviruses using JUNV (strain Romero)-based trVLPs bearing GPs either from other JUNV strains, other closely related New World arenaviruses (e.g. Tacaribe, Machupo, Sabiá), or the distantly related Lassa virus. While nAbs against the JUNV vaccine strain are also active against a range of other JUNV strains, they appear to have little or no capacity to neutralize other arenavirus species, suggesting that therapy with whole plasma directed against another species is unlikely to be successful and that the targeted development of cross-specific monoclonal antibody-based resources is likely needed. Such efforts will be supported by the availability of this BSL1/2 screening platform which provides a rapid and easy means to characterize the potency and reactivity of anti-arenavirus neutralizing antibodies against a range of arenavirus species. Fil: Leske, Anne. Friedrich Loeffler Institut; Alemania Fil: Waßmann, Irke. Friedrich Loeffler Institut; Alemania Fil: Schnepel, Kevin. Friedrich Loeffler Institut; Alemania Fil: Shifflett, Kyle. National Institutes of Health; Estados Unidos Fil: Holzerland, Julia. Friedrich Loeffler Institut; Alemania Fil: Bostedt, Linus. Friedrich Loeffler Institut; Alemania Fil: Bohn, Patrick. Friedrich Loeffler Institut; Alemania Fil: Mettenleiter, Thomas C.. Friedrich Loeffler Institut; Alemania Fil: Briggiler, Ana Maria. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Brignone, Julia. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Enria, Delia. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Cordo, Sandra Myriam. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Hoenen, Thomas. Friedrich Loeffler Institut; Alemania. National Institutes of Health; Estados Unidos Fil: Groseth, Allison. Friedrich Loeffler Institut; Alemania. National Institutes of Health; Estados Unidos

Epidemiological studies have linked the high prevalence rates of IgE-mediated allergic diseases to an increase in exposure to traffic-related air pollutants such as diesel exhaust particles (DEPs). There is growing experimental evidence that organic compounds of DEPs, predominantly polycyclic aromatic hydrocarbons (PAHs), participate in the development and maintenance of allergic airway diseases. In this study we investigated the impact of organic extracts of urban aerosol (AERex) containing various PAH concentrations on the activation of human basophils. Whole blood samples from six birch pollen-allergic and five control subjects were repeatedly incubated in the presence of AERex with or without recombinant Bet v 1 (rBet v 1). Basophils were analyzed for CD63 expression as a measure of basophil activation by using multiparameter flow cytometry. Basophils, when exposed in vitro to AERex and rBet v 1, expressed CD63 significantly more than with antigen activation alone. AERex synergized with rBet v 1 in a dose-dependent manner, but did not activate basophils from nonallergic donors. AERex effect on CD63 upregulation was found in blood samples of all patients and did not occur in the absence of rBet v 1. Strongest basophil activation was monitored upon stimulation with AERex comprising the highest PAH content. The capability of AERex to increase activation of basophils from birch pollen-allergic subjects at ambient concentrations suggests an important role of organic compounds of airborne particles in the aggravation of IgE-mediated allergic diseases. This could be a new aspect of regulation of unspecific promoting stimuli in clinical manifestation of allergic inflammation.

Animal models to study the process of TB pathogenesis and vaccine development are of importance. NHP models, especially Rhesus macaques, are attractive because of available resources to evaluate their immunogenetic backgrounds and the aerosol model closely mimics the human infection route. In this study, we characterized the MHC immunogenetic background of a cohort of animals that have been vaccinated and/or infected with Mtb, defining 54 new immunodominant CD4 T cell epitopes using IFNγ ELISPOTs with antigens utilized in human clinical trials. Antigens which are immunodominant in humans are also immunodominant in rhesus macaques, including Rv3875 (ESAT-6) and Rv3874 (CFP10). Interestingly, the shared responses were not due to common ancestry or inbreeding upon identifying MHC alleles. Instead, the results indicate promiscuous binding, which is the first account of this phenomenon in the rhesus macaque TB model of infection. These results suggest that while the CD4 response of NHPs to TB is broad and heterogeneous, epitope sets can be defined to broadly follow and characterize these responses in genetically heterogeneous NHP animal cohorts. To our knowledge, this is the first comprehensive epitope identification effort for non-human primates. We reveal a profound repertoire overlap between epitopes recognized in NHPs and in humans. These findings have important implications for the evaluation of new vaccines and diagnostics in the setting of non-human primate model of TB.