Biology subjects

Andrews, R. J.

Publications and source records attributed to Andrews, R. J..

6 recordsLinked to original sources

bioRxiv2026

ScanFold3: a robust and rapid approach for identifying structured RNA targets in genomes and transcriptomes

Background. The rapid expansion of high-throughput transcriptomic datasets has created a critical need for scalable tools to identify functional RNA secondary structures. While thermodynamics-based folding is a well-established method, most algorithms lack the scalability required for genomic-scale datasets due to O(n3) time complexity. Methods. We present ScanFold3, an enhanced version of the ScanFold pipeline that optimizes the "Fold" step for modern computing needs. This version models consensus structure generation as a minimum perfect weighted matching problem on a graph. To ensure maximum scalability, we implemented a Greedy Approximation Algorithm and optimized performance-critical components in C++. Results. Benchmarking on sequences up to 128 kb demonstrates that ScanFold3 achieves a 38-fold to 129-fold increase in speed over ScanFold2. Validation against annotated human RNAs shows that ScanFold3 offers improved positive predictive value (PPV). Most significantly, when ScanFold3 outputs are used as structural constraints for global refolding, it outperforms previous versions across all metrics, including the F1 score. Conclusions. ScanFold3 provides a robust, speedy, and user-friendly method for characterizing the thermodynamics of novel RNA and DNA sequences. It is designed as an efficient first step for high throughput bioinformatic pipelines, capable of paring down chromosome-scale transcriptomic data into stable structures amenable to advanced analysis.

bioinformatics↗

bioRxiv2025

Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions

The human transcriptome contains millions of A-to-I editing sites arising from an unclear number of poorly characterized dsRNAs. Editing sites are often used to infer presence of dsRNA, but this method is limited by transcription levels, read depth, ADAR expression and cannot identify unedited dsRNA. To address these limitations, we developed dsRNAscan. Applying dsRNAscan to the human genome predicted 5 million dsRNAs. Genomic distribution of dsRNAs encompassing repetitive elements was widespread, but non-repetitive dsRNAs were sparse and enriched at chromosomal tips. dsRNAscan predicted hundreds of long, highly paired dsRNAs suspected to be immunogenic, but only one was in a 3'UTR, and thus likely to challenge cytoplasmic immune sensors. We observed several thousand editing enriched regions suspected to arise from intermolecular structures, and dozens of neuronally enriched dsRNAs conserved across vertebrates. This study offers the first comprehensive set of dsRNA annotations for the human genome, available as a resource at https://dsrna.chpc.utah.edu/.

genomics↗

bioRxiv2024

ANALYSIS OF RESPIRATORY SYNCYTIAL VIRUS REVEALS CONSERVED RNA SECONDARY STRUCTURAL MOTIFS AND IMPACT VIRAL LIFECYCLE

An analysis that combined bioinformatics, comparative sequence/structural analysis, and experimental assays has been completed on respiratory syncytial virus (RSV). Both the genomic RNA and its reverse complement were studied using the novel bioinformatics pipeline ScanFold, which predicted 49 regions on RSV RNAs that appear to encode functional secondary structures (based on their unusually stable sequence order). Multiple motifs appear to be conserved between RSV and related virus strains, including one region within the F gene, which had a highly favorable overall prediction metric of a paired secondary structure. This motif was subjected to additional experimental analyses using SHAPE analysis to confirm ScanFold predicted secondary structure. In subsequent analysis, RSV F mRNA transcripts were made by in vitro transcription using T7 polymerase and transcripts which relaxed the predicted secondary structure yielded slightly higher mRNA transcripts and protein expression levels as wildtype F. However, using reverse genetics for comparison of viruses containing wildtype or relaxed F suggested that the predicted secondary structures may be critical for RSV replication in cells. To our knowledge, this is the first study to examine conserved RNA structures across multiple RSV strains and may help identify potential therapeutic targets to inhibit.

microbiology↗

bioRxiv2020

An in silico map of the SARS-CoV-2 RNA Structurome

SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis.

bioinformatics↗

bioRxiv2019

Crowder-induced Conformational Ensemble Shift in Escherichia Coli Prolyl-tRNA Synthetase

The effect of macromolecular crowding on the structure and function of Escherichia coli prolyl-tRNA synthetase (Ec ProRS) has been investigated using a combined experimental and theoretical method. Ec ProRS is a multi-domain enzyme; coupled-domain dynamics is essential for efficient catalysis. To gain an insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the \"soft-interactions\" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a significant shift in the conformational ensemble, which is consistent with the \"soft-interactions\" model of the crowding effect and explained the observed alteration in kinetic parameters. Collectively, the present study demonstrated that the effects of molecular crowding on both conformational dynamics and catalytic function, are correlated. This is the first report where molecular crowding has been found to impact the conformational ensemble in the multi-domain Ec ProRS, a member of aminoacyl-tRNA synthetase family, which is central to protein synthesis in all living cells. The present study affirmed that the effect of crowders should be considered while investigating the structure-dynamics-function relationship in modular enzymes.

biophysics↗

bioRxiv2018

PolyA tracks and poly-lysine repeats are the Achilles heel of Plasmodium falciparum

Plasmodium falciparum, the causative agent of human malaria, is an apicomplexan parasite with a complex, multi-host life cycle. Sixty percent of transcripts from its extreme AT-rich (81%) genome possess coding polyadenosine (polyA) runs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate that transcripts with polyA runs encoding poly-lysine are hot spots for ribosome stalling and frameshifting, eliciting mRNA surveillance pathways and attenuating protein synthesis in the majority of prokaryotic and eukaryotic organisms. Here, we show that the P. falciparum translational machinery is paradigm-breaking. Using bioinformatic and biochemical approaches, we demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately transcribed and translated in P. falciparum cells. Translation of polyA tracks in the parasite does not elicit any response from mRNA surveillance pathways usually seen in host human cells or organisms with similar AT content. The translation efficiency and accuracy of the parasite protein synthesis machinery reveals a unique role of ribosomes in the evolution and adaptation of P. falciparum to an AU-rich transcriptome and polybasic amino sequences. Finally, we show that the ability of P. falciparum to synthesize long poly-lysine repeats has given this parasite a unique protein exportome and an advantage in infectivity that can be suppressed by addition of exogenous poly-basic polymers.

microbiology↗