Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis.

The novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we analyzed public host and viral RNA sequencing data to better understand how SARS-CoV-2 interacts with human respiratory cells. We identified genes, isoforms and transposable element families that are specifically altered in SARS-CoV-2-infected respiratory cells. Well-known immunoregulatory genes including CSF2, IL32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were upregulated. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and eukaryotic initiation factor 4 (eIF4b). We also identified a viral sequence variant with a statistically significant skew associated with age of infection, that may contribute to intracellular host-pathogen interactions. These findings can help identify host mechanisms that can be targeted by prophylactics and/or therapeutics to reduce the severity of COVID-19.

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.

Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. Although single splicing events have been described for ≤200 single cells with statistical confidence, full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled. We developed a method that starts with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. Using single-cell isoform RNA-Seq (ScISOr-Seq), we identified RNA isoforms in neurons, astrocytes, microglia, and cell subtypes such as Purkinje and Granule cells, and cell-type-specific combination patterns of distant splice sites. We used ScISOr-Seq to improve genome annotation in mouse Gencode version 10 by determining the cell-type-specific expression of 18,173 known and 16,872 novel isoforms.

Characterization of calbindin D28k expressing interneurons in the ventral horn of the mouse spinal cord.

BACKGROUND: Expression of the calcium binding protein, calbindin (CB), is well established as a hallmark of Renshaw cells, a class of interneurons found in spatially restricted areas in the ventral spinal cord that directly modulate motor neuron activity. CB expression, however, is not restricted only to Renshaw cells in the ventral horn, and within this population other interneuron subtypes may be identifiable on the basis of cell position and the potential for coexpression of other calcium binding proteins. RESULTS: Here we have quantified the changing CB expression pattern in the ventral spinal cord across postnatal development in the mouse. Fewer neurons express CB as postnatal development progresses, and those neurons frequently coexpress other calcium binding proteins (calretinin and parvalbumin) in subpopulations with distinct spatial distributions. We also found a significant portion of CB-expressing interneurons receive putative synaptic contacts from primary sensory afferents. CONCLUSIONS: These findings suggest CB labels a heterogeneous group of interneurons in the ventral horn, some of which may process sensory information. Based on cellular position, CB expression may be a shared feature of subsets of interneurons arising from multiple ventral progenitor domains. Developmental Dynamics 247:185-193, 2018. © 2017 Wiley Periodicals, Inc.