Biology subjects

DeFalco, L.

Publications and source records attributed to DeFalco, L..

3 recordsLinked to original sources

bioRxiv2025

A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation

Long-range RNA-RNA pairing impacts the genome structure and function of SARS-CoV-2 variants. To understand the structure and function relationships of different SARS-CoV-2 variants that have emerged during the COVID-19 pandemic, we performed high-throughput structure probing and modelling of the genomic structures of the wildtype (WT), Alpha, Beta, Delta and Omicron variants of SARS-CoV-2. We observed that genomes of SARS-CoV-2 variants are generally structurally conserved, and that single-nucleotide variations and interactions with RNA binding proteins can impact RNA structures across the viruses. Importantly, using proximity ligation sequencing, we identified many conserved ultra-long-range RNA-RNA interactions, including one that spans more than 17 kb in both the WT virus and the Omicron variant. We showed that mutations that disrupt this 17 kb long-range interaction reduce viral fitness at later stages of its infection cycle, while compensatory mutations partially restore virus fitness. Additionally, we showed that this ultra-long-range RNA-RNA interaction structure binds directly to ADAR1 to alter the RNA editing levels on the viral genome. These studies deepen our understanding of RNA structures in the SARS-CoV-2 genome and their ability to interact with host factors to facilitate virus infectivity.

genomics↗

bioRxiv2025

Evaluating Molecular Docking Programs for RNA-Targeted Ligand Screening: Influence of Binding Modes and Ligand Types

Structured RNAs are critical regulators of gene expression and represent promising targets for drug discovery. Despite this potential, structure-based virtual screening approaches--in particular, molecular docking--have been underutilized for RNA targets, largely due to the intrinsic conformational flexibility of RNA and the limited docking methods specifically optimized for RNA. In our study, we evaluated the efficacy of three widely used docking programs for RNA-ligand docking screens. The performance of these programs -- Glide, Gold, and rDock, were evaluated with the dataset of 25 diverse RNA targets with 432 small molecule RNA binders. We found that the performance was similar across docking methods, but consistent differences emerged among RNA classes. We further explored consensus scoring across both receptor conformations and docking methods, finding that selecting the average scores across docking programs and RNA structures yielded stable performance when compared to individual methods. Finally, clustering analysis of RNA binders revealed distinct scoring function preferences for different chemotypes of RNA binders, underscoring the potential for tailored scoring strategies in RNA-targeted drug discovery. Together, this work provides a comprehensive evaluation of the performance of available docking methods in different cases of RNA-ligand docking and offers practical guidance for improving virtual screening against structured RNAs.

bioinformatics↗

bioRxiv2021

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant ({Delta}382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within the SARS-CoV-2 genome, observed that identical sequences can fold into divergent structures on different subgenomic RNAs, and that WT and {Delta}382 virus genomes can fold differently. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host RNAs. SARS-CoV-2 binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2-O-methylated. 2-O-methylation sites in the virus genome are enriched in the untranslated regions and are associated with increased pair-wise interactions. SARS-CoV-2 infection results in a global decrease of 2-O-methylation sites on host mRNAs, suggesting that binding to snoRNAs could be a pro-viral mechanism to sequester methylation machinery from host RNAs towards the virus genome. Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, cellular factors important during infection and provide a platform for targeted therapy.

genomics↗