mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation

Pseudouridine (psi) is one of the most abundant human mRNA modifications generated from the isomerization of uridine via psi synthases, including TRUB1 and PUS7 . Nanopore direct RNA sequencing combined with our recent tool, Mod- p ID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is highly efficient for detecting changes in positional psi occupancies across cell types, which can inform our understanding of the impact on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, among a list of highly conserved sites across cell types, most are TRUB1 substrates and fall within the coding sequence. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. We validate these sites by ruling out single-nucleotide variants, analyzing current traces, and performing enzymatic knockdowns of psi synthases. Finally, we characterize sites with multiple psi modifications on the same transcript (hypermodification type II) and found that these can be conserved or cell type-specific. Among these, we discovered examples of multiple psi modifications within the same k-mer for the first time and analyzed the effect on current distribution. Our data support the hypothesis that motif sequence and the presence of psi synthase are insufficient to drive modifications and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.

Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity

Chemical modifications in mRNAs such as pseudouridine (psi) can regulate gene expression, although our understanding of the functional impact of individual psi modifications, especially in neuronal cells, is limited. We apply nanopore direct RNA sequencing to investigate psi dynamics under cellular perturbations in SH-SY5Y cells. We assign sites to psi synthases using siRNA-based knockdown. A steady-state enzyme-substrate model reveals a strong correlation between psi synthase and mRNA substrate levels and psi modification frequencies. Next, we performed either differentiation or lead-exposure to SH-SY5Y cells and found that, upon lead exposure, not differentiation, the modification frequency is less dependent on enzyme levels suggesting translational control. Finally, we compared the plasticity of psi sites across cellular states and found that plastic sites can be condition-dependent or condition-independent; several of these sites fall within transcripts encoding proteins involved in neuronal processes. Our psi analysis and validation enable investigations into the dynamics and plasticity of RNA modifications.

Paired Capture and FISH Detection of Individual Virions Enable Cell-Free Determination of Infectious Titers

Early detection of viruses can prevent the uncontrolled spread of viral infections. Determination of viral infectivity is also critical for determining the dosage of gene therapies, including vector-based vaccines, CAR T-cell therapies, and CRISPR therapeutics. In both cases, for viral pathogens and viral vector delivery vehicles, fast and accurate measurement of infectious titers is desirable. The most common methods for virus detection are antigen-based (rapid but not sensitive) and polymerase chain reaction (PCR)-based (sensitive but not rapid). Current viral titration methods heavily rely on cultured cells, which introduces variability within labs and between labs. Thus, it is highly desirable to directly determine the infectious titer without using cells. Here, we report the development of a direct, fast, and sensitive assay for virus detection (dubbed rapid capture fluorescence in situ hybridization (FISH) or rapture FISH) and cell-free determination of infectious titers. Importantly, we demonstrate that the virions captured are "infectious," thus serving as a more consistent proxy of infectious titers. This assay is unique because it first captures viruses bearing an intact coat protein using an aptamer and then detects genomes directly in individual virions using fluorescence in situ hybridization (FISH); thus, it is selective for infectious particles (i.e., positive for coat proteins and positive for genomes).

Prolonged activation of EP3 receptor-expressing preoptic neurons underlies torpor responses

Many species use a temporary drop in body temperature and metabolic rate (torpor) as a strategy to survive food scarcity. A similar profound hypothermia is observed with activation of preoptic neurons that express the neuropeptides Pituitary Adenylate-Cyclase-Activating Polypeptide (PACAP)1, Brain Derived Neurotrophic Factor (BDNF)2, or Pyroglutamylated RFamide Peptide (QRFP)3, the vesicular glutamate transporter, Vglut24,5 or the leptin receptor6 (LepR), estrogen 1 receptor (Esr1)7 or prostaglandin E receptor 3 (EP3R) in mice8. However, most of these genetic markers are found on multiple populations of preoptic neurons and only partially overlap with one another. We report here that expression of the EP3R marks a unique population of median preoptic (MnPO) neurons that are required both for lipopolysaccharide (LPS)-induced fever9 and for torpor. These MnPOEP3R neurons produce persistent fever responses when inhibited and prolonged hypothermic responses when activated either chemo- or opto-genetically even for brief periods of time. The mechanism for these prolonged responses appears to involve increases in intracellular calcium in individual EP3R-expressing preoptic neurons that persist for many minutes up to hours beyond the termination of a brief stimulus. These properties endow MnPOEP3R neurons with the ability to act as a two-way master switch for thermoregulation.