Jessica Sook Yuin Ho's research while affiliated with Icahn School of Medicine at Mount Sinai and other places

... The rst step consists of translating both the reverse and forward strand in three reading frames, in order to account for every possible translation frame. Therefore, cases with overlapping genes, shifted translation starts and AUG-codon independent translation initiation 41 ...

... The method reveals the genome-wide transcription start sites (TSSs) of both stable and unstable transcripts and, thus, all active regulatory elements, including promoters and enhancers, which we will collectively refer to as transcription start regions (TSRs). Since changes in enhancer RNA transcription serve as one of the most reliable markers for nearby gene regulation (Mikhaylichenko et al., 2018), csRNA-seq profiles can provide critical information about the state of regulatory networks in the cell (Duttke et al., 2019;Lim et al., 2021). Furthermore, the single-nucleotide resolution of csRNA-seq data provides a high-resolution mapping of regulatory elements and can reveal spacing relationships between individual transcription start sites (TSS) and TF binding sites (Duttke et al., 2019). ...

... Several drugs suppressing or attenuating proinflammatory cytokine storms have been administered in the clinical treatment of severe or critical COVID-19 patients. 150,151 Siltuximab is a monoclonal antibody targeting IL-6R. 152 Numerous studies showed that various microbial metabolites inhibit inflammation. ...

... In another study, Ren et al. used single-cell RNA sequencing (scRNA-seq) analysis to evaluate the expression and distribution of angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine protease (TMPRSS) genes in kidney cell components. They found that podocytes and proximal straight tubule cells were potential host cells targeted by SARS-CoV-2, resulting in acute kidney injury (AKI) caused by the SARS-CoV-2-induced cytopathic effect [12]. Given the critical role of chromatin factors such as topoisomerase I in regulating the transcriptional response to SARS-CoV-2 infection, Ho et al. evaluated transcriptional and epigenetic changes in the human alveolar basal epithelial carcinoma (A549) cell line expressing the human SARS-CoV-2 entry receptor Ace2 (A549-ACE2) infected with SARS-CoV-2 followed by the depletion of topoisomerase I and discovered promising effects of epigenetic therapy in modifying aberrant genome restructuring and selective suppression of inflammatory and anti-viral genes involved in severe COVID-19 [13]. ...

... Considering its location in the anticodon loop, we suggest that it likely participates in regulating loop conformation, codon-anticodon base pairing and/or the biogenesis of tRNA-derived small regulatory RNAs. Loss of cytoplasmic tRNA Ser m 3 C formation was found to influence pluripotency and cancer cell growth (10). ...

... Computational and experimental studies demonstrated compelling evidence for an important regulatory role of uORF-mediated translational control in (patho-)physiology [3,[8][9][10], and several uORF-associated genetic variants have been linked to the development of disease [8,[10][11][12][13][14][15]. A recent study also demonstrated that virus-derived uORFs are translated during infection and contribute to virulence [16]. Upstream ORFs represent important relays of gene expression regulation, as translation of the downstream CDS from uORF-bearing transcripts requires leaky scanning across the uORF start site or reinitiation of ribosomes after translating the uORF [9,17,18]. ...