Biology subjects

Day, T. A.

Publications and source records attributed to Day, T. A..

6 recordsLinked to original sources

bioRxiv2026

G4 DNA structures induced by UV radiation: a multi-omic approach

DNA G quadruplexes (G4s) are secondary structures with critical roles in regulating genome function. G4s in regulatory regions like promoters and enhancers are important for controlling gene expression, while aberrant formation of G4s has been linked to genomic instability and human disease. Despite G4s importance and inherent danger, their dynamic formation remains incompletely understood. Here, we show that ultraviolet (UV) radiation uniquely induces widespread and persistent G4 formation in human cells, distinguishing it from other genotoxins. Through integrated genomic, transcriptomic, and proteomic analyses, we uncovered key features and functions of UV-induced G4s. Proteomic profiling identified RCOR3 as a factor associated with specific UV-induced G4s at late time points. Functional studies revealed that RCOR3 is essential for the formation and persistence of these structures. Furthermore, genes associated with UV G4s that are differentially expressed are enriched in pathways related to response to UV radiation, highlighting their biological relevance. These findings define the multi-omic landscape of UV-induced G4s and reveal new mechanistic insights into the interplay between genotoxic stress responses and the regulation of non-canonical DNA structures. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/738736v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@8c2e32org.highwire.dtl.DTLVardef@12d1379org.highwire.dtl.DTLVardef@5971a3org.highwire.dtl.DTLVardef@33bcee_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Tracking tau and cellular responses in human iPSC-microglia from uptake to seedable secretion in extracellular vesicles

The templated spread of tau aggregates in tauopathies has been attributed to neuron-to- neuron spread, but microglia have also been implicated through mouse studies. Here we examine in detail the uptake, processing, release and seeding of tau using human iPS- derived microglia (iMGL). We show that tau is taken up by iMGL via LRP1 and heparan sulfate proteoglycans, with a role for LRRK2 in LRP1 trafficking, and that phagocytosed fibrils can escape into the cytoplasm. Monomeric tau has minimal effects on iMGL, but recombinant or brain-derived tau fibrils induce a shift towards chemokine and interferon response subtypes, alongside downregulation of homeostatic and MHC genes. Endogenous tau protein is undetectable in iMGL, and monomeric internalised tau is digested to completion, but fibrillar tau is more resistant to degradation and becomes phosphorylated on two specific residues. Finally, fibrillar tau is released by iMGL, visualized within extracellular vesicles by cryo-EM, and can seed tau aggregation in downstream neurons.

cell biology↗

bioRxiv2024

The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability

DNA G-quadruplexes (G4s) are secondary structures with significant roles in regulating genome function and stability. Dysregulation of the dynamic formation of G4s is linked to genomic instability and disease, but the underlying mechanisms are not fully understood. In this study, we conducted a screen of chromatin-modifying enzymes and identified nine potential inhibitors of G4 formation, including seven that were not previously characterized. Among these, we highlight the role of BAZ2 chromatin remodelers as key suppressors of G4 DNA and G4-related genome instability. Depletion of BAZ2 subunits led to increased G4 formation, especially at transcriptional regulatory elements. BAZ2B was found to associate with G4 loci, suggesting that it plays a direct role in suppressing G4s. While BAZ2-deficient cells exhibited modest genomic instability, treatment with the G4-stabilizing ligand BRACO19 exacerbated double-strand breaks (DSBs), highlighting its utility as a tool to study G4-dependent genome instability. DSB profiling using INDUCE-seq uncovered distinct breakage patterns around G4s, further underscoring the impact of G4s on genome integrity. Notably, we found that within G4s, G repeats were more susceptible to DSBs than loops. These results establish BAZ2 chromatin remodeling complexes as direct regulators of G4 dynamics and provide new insights into G4-dependent genome instability.

molecular biology↗

bioRxiv2023

Biochemical and functional characterization of the p.A165T missense variant of mitochondrial amidoxime-reducing component 1 in HepG2 cells

Recent genome-wide association studies have identified a missense variant p.A165T in mitochondrial amidoxime-reducing component 1 (mARC1) that is strongly associated with protection from all-cause cirrhosis and improved prognosis in nonalcoholic steatohepatitis (NASH). The precise mechanism of this protective effect is unknown. Substitution of alanine 165 with threonine is predicted to affect mARC1 protein stability and to have deleterious effects on its function. To investigate the mechanism, we have generated a knock-in mutant mARC1 A165T in human hepatoma HepG2 cells, enabling characterization of protein subcellular distribution, stability, and biochemical functions of the mARC1 mutant protein expressed from its endogenous locus. Compared to wild-type (WT) mARC1, we found that the A165T mutant exhibits significant mislocalization outside of its traditional location anchored in the mitochondrial outer membrane and reduces protein stability, resulting in lower basal levels. We evaluated the involvement of the ubiquitin proteasome system in mARC1 A165T degradation and observed increased ubiquitination and faster degradation of the A165T variant. In addition, we have shown that HepG2 cells carrying the MTARC1 p.A165T variant exhibit lower N-reductive activity on exogenously-added amidoxime substrates in vitro. The data from these biochemical and functional assays suggest a mechanism by which the MTARC1 p.A165T variant abrogates enzyme function which may contribute to its protective effect in liver disease.

cell biology↗

bioRxiv2020

Ivermectin inhibits extracellular vesicle secretion from parasitic nematodes

Lymphatic filariasis (LF) is a disease caused by parasitic filarial nematodes that is endemic in 49 countries and affects or threatens over 890 million people. Strategies to control LF rely heavily on mass administration of anthelmintic drugs including ivermectin (IVM), a macrocyclic lactone drug considered an Essential Medicine by the WHO. However, despite its widespread use the therapeutic mode of action of IVM against filarial nematodes is not clear. We have previously reported that filarial nematodes secrete extracellular vesicles (EVs) and that their cargo has immunomodulatory properties. Here we investigate the effects of IVM and other anti-filarial drugs on parasitic nematode EV secretion, motility, and protein secretion. We show that inhibition of EV secretion was a specific property of IVM, which had consistent and significant inhibitory effects across nematode life stages and species (with the exception of male parasites). IVM inhibited EV secretion, but not parasite motility, at therapeutically relevant concentrations. Protein secretion was inhibited by IVM in the microfilariae stage, but not in any other stage tested. Our data provides evidence that inhibiting the secretion of immunomodulatory EVs by parasitic nematodes could explain, at least in part, IVM mode of action and provides a phenotype for novel drug discovery.

molecular biology↗

bioRxiv2020

Identification of Bovine Genotypes Conferring Diminished Susceptibility to Salmonellosis and Colonization by Salmonella and E. coli O157:H7

ABSTRACTSalmonella and E. coli O157:H7 are two of the most important problems for the beef industry. Cattle can develop salmonellosis and persistently harbor Salmonella, or they can asymptomatically shed Salmonella and/or E. coli O157:H7 resulting in contamination of the hide and carcass surfaces during processing. Additionally, Salmonella infiltrates lymph nodes that get incorporated into ground beef. In this study, we investigated the possibility of identifying cattle with reduced susceptibility to one or both of these infections. Empirical observations from previous studies suggested that a diminished susceptibility was possible in amelanotic cattle, i.e., cattle bearing the mcr1/mcr1 genotype and lacking overt black pigmentation. By searching for single nucleotide polymorphisms (SNP) present in the 34 genes encoding the Salmonella interactome, we identified a SNP that was consistently present in amelanotic cattle with diminished susceptibility to Salmonella. Specifically, we used an ex vivo assay to screen 500 cattle blood samples for the diminished ability of Salmonella to penetrate peripheral leukocytes. Diminished Salmonella penetration was observed in 150 of these blood samples and 147 of these samples harbored two alleles bearing a SNP that introduces a miRNA cleavage site (bta-let-7b) in the 3’UTR of the bsynJ1 gene, which we designate as the SYNJ1/SNYJ1 genotype. Further ex vivo studies revealed a decreased expression of SYNJ1 in leukocytes bearing the SYNJ1/SNYJ1 genotype. In vivo experimental challenge studies revealed a diminished susceptibility to salmonellosis in cattle with the SYNJ1/SNYJ1::mcr1/mcr1 genotype. Additional in vivo challenge studies revealed that SYNJ1/SNYJ1::mcr1/mcr1 cattle have a decreased susceptibility to lymph node infiltration by two Salmonella serotypes (S. Anatum and S. Montevideo) implicated in this lymph node problem, and a decreased susceptibility to E. coli O157:H7 colonization of the recto-anal junction. A field study revealed that the SYNJ1/SNYJ1::mcr1/mcr1 genotype was five times more prevalent, when compared to the SYNJ1/synj1::mcr1/mcr1 and synj1/ synj1::mcr1/mcr1 genotypes, in Salmonella-free lymph nodes. Small-scale genetic surveys revealed that the SYNJ1/SNYJ1 genotype was present in the following mcr1/mcr1 breeds: Akaushi, Barzona, Braunvieh, Hereford, Piedmontese, Red and White Holsteins, Red Angus, Red Poll, Shorthorn, Simmental (Red), and Tarentaise. Studies using the aforementioned ex vivo penetration assay, which putatively predicts the diminished susceptibility phenotype, revealed that the penetrance of the diminished susceptibility is >99% in SYNJ1/SNYJ1::mcr1/mcr1 cattle but only ∼1% in SYNJ1/SNYJ1 cattle with at least one MCR1 allele. Further studies with the ex vivo assay revealed that three additional SNPs are part of a genotype conferring diminished susceptibility to a broad array of Salmonella serotypes commonly associated with cattle. In summary, the studies presented herein reveal a bovine genotype associated with decreased susceptibility to Salmonella and E. coli O157:H7. PSR Genetics LLC holds a U.S. patent on testing for the SYNJ1/SNYJ1 genotype (patent number 9,049,848) while the three complementary SNPs are under further investigation.Competing Interest StatementThis study was funded by PSR Genetics LLC which included a rental agreement for laboratory space at Iowa State UniversityView Full Text

genetics↗