Biology subjects

Fire, A.

Publications and source records attributed to Fire, A..

9 recordsLinked to original sources

bioRxiv2026

A host enzyme pseudouridylates an RNA bacteriophage genome and accelerates virus production

RNA modifications are prevalent and potent regulators of gene expression across all domains of life. However, whether they exist in bacteriophages and whether they impact phage-host interactions are largely unexplored. To address this, we leveraged the ssRNA bacteriophage MS2 and its E. coli host. Using quantitative nanopore direct RNA sequencing and pseudouridine profiling, we found that essentially all copies of MS2 genomic RNA are pseudouridylated at a single position within the maturation protein gene. Through analysis of the surrounding sequence context, analysis of predicted structure, and genetic assignment of the pseudouridine to its installing enzyme, we demonstrate that the bacterial host enzyme RluA is responsible for pseudouridylation of the phage genome. In the absence of host RluA, the latent and eclipse periods are extended, indicating that the enzyme is important to early stages of phage infectivity. We find that this pseudouridine is present at varying occupancies in additional ssRNA coliphages, also installed by host RluA, and that the conserved features of RluA substrates are present in diverse ssRNA phages with host species beyond E. coli. Altogether, our findings identify RNA modification as a feature of bacteriophage genomes and establish host RNA-modifying enzymes as a class of infection-modulating phage host factors.

molecular biology↗

bioRxiv2026

Prion-induced heritable states in Caenorhabditis elegans

Self-replicating protein conformations can encode persistent epigenetic states that underlie prion diseases and contribute to age-related neurodegenerative disorders in mammals. In fungi, such conformers are transmitted through mitosis and meiosis, enabling robust inheritance of diverse phenotypes. Whether analogous transgenerational protein-based inheritance extends beyond unicellular systems to metazoans remains unknown. Here, we address this question in C. elegans, a genetically tractable, short-lived animal well suited for tracking the transmission of heritable information across generations. We found that a yeast prion domain, when fused to a host protein, induced a heritable altered state that arose at elevated temperatures and persisted across generations at lower temperatures. The emergence of this state depended on known prionogenic yeast repeats, while the state itself was reversible and behaved semi-dominantly in crosses, consistent with a protein-based epigenetic mechanism. These findings provide direct evidence that protein domains capable of adopting self-replicating conformers can encode heritable information in an animal.

genetics↗

bioRxiv2025

A default silencing mechanism restrains stress-induced genes in C. elegans

Inducible gene expression programs require that target genes remain silent until the proper activation signal is received, a hallmark of stress-response pathways. This quiescence is typically assumed to be the default state of stress-inducible genes, maintained without active cellular intervention. Using a forward genetic screen for constitutive activation of inducible heat shock proteins (iHSPs) in C. elegans, we found that the multi-zinc-finger protein ZNF-236 is essential for maintaining iHSP quiescence under normal conditions. Loss of znf-236 causes constitutive iHSP expression throughout the genome, affecting both endogenous iHSP loci and iHSP sequences inserted at dispersed chromosomal sites. However, the effect is also chromosomal context-dependent: robustly heat-responsive iHSP transgenes integrated into the ribosomal DNA locus or extrachromosomal arrays are unaffected by znf-236 loss. This differential responsiveness suggests iHSP induction in znf-236 mutants results from a shift in genome organization, rather than from accumulated denatured proteins or engagement of the canonical heat shock response. Our findings demonstrate the existence of a potent ZNF-236-dependent default silencing mechanism that broadly restrains iHSP genes across the genome and helps ensure appropriate iHSP quiescence even at ectopic chromosomal locations. Contrary to prior assumptions, this suggests that quiescence of stress-inducible genes reflects an actively maintained genomic state rather than merely a passive absence of expression. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/683740v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@76b062org.highwire.dtl.DTLVardef@360ac9org.highwire.dtl.DTLVardef@1fe330eorg.highwire.dtl.DTLVardef@1c9ea7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Nucleosome-mediated conformational switches in micro-eccDNAs

Extrachromosomal-circular DNA (eccDNA) are circular-DNA elements that are implicated in cellular processes such as genomic diversification and instability, along with other genomic mechanisms. However, their structure and chromatinization state is poorly understood. Here we identified a 358-bp circular micro-eccDNA molecule derived from the human Titin gene, which was selected for this study based on its size and sequence characteristics, and used atomistic molecular dynamics simulations to study its interaction with nucleosomes and corresponding topological state. We show the presence or absence of bound nucleosomes provides a topological switch between intact and denatured DNA.

biophysics↗

bioRxiv2023

DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution

Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.

evolutionary biology↗

bioRxiv2023

Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis

Replication of genetic material involves the creation of characteristic termini. Determining these termini is important to refine our understanding of the mechanisms involved in maintaining the genomes of cellular organisms and viruses. Here we describe a computational approach combining direct and indirect readouts to detect termini from next-generation short-read sequencing. While a direct inference of termini can come from mapping the most prominent start positions of captured DNA fragments, this approach is insufficient in cases where the DNA termini are not captured, whether for biological or technical reasons. Thus, a complementary (indirect) approach to terminus detection can be applied, taking advantage of the imbalance in coverage between forward and reverse sequence reads near termini. A resulting metric ("strand bias") can be used to detect termini even where termini are naturally blocked from capture or ends are not captured during library preparation (e.g., in tagmentation-based protocols). Applying this analysis to datasets where known DNA termini are present, such as from linear double-stranded viral genomes, yielded distinct strand bias signals corresponding to these termini. To evaluate the potential to analyze a more complex situation, we applied the analysis to examine DNA termini present early after HIV infection in a cell culture model. We observed both the known termini expected based on standard models of HIV reverse transcription (the U5-right-end and U3-left-end termini) as well as a signal corresponding to a previously described additional initiation site for plus-strand synthesis (cPPT [central polypurine tract]). Interestingly, we also detected putative terminus signals at additional sites. The strongest of these are a set that share several characteristics with the previously characterized plus-strand initiation sites (the cPPT and 3 PPT [polypurine tract] sites): (i) an observed spike in directly captured cDNA ends, an indirect terminus signal evident in localized strand bias, (iii) a preference for location on the plus-strand, (iv) an upstream purine-rich motif, and (v) a decrease in terminus signal at late time points after infection. These characteristics are consistent in duplicate samples in two different genotypes (wild type and integrase-lacking HIV). The observation of distinct internal termini associated with multiple purine-rich regions raises a possibility that multiple internal initiations of plus-strand synthesis might contribute to HIV replication.

genomics↗

bioRxiv2021

Heterologous reporter expression in the planarian Schmidtea mediterranea through somatic mRNA transfection

Planarians have long been studied for their regenerative abilities. Moving forward, tools for ectopic expression of non-native proteins will be of substantial value. Using a luminescent reporter to overcome the strong autofluorescence background of planarian tissues, we demonstrate heterologous protein expression in planarian cells and live animals. Our approach is based on the introduction of mRNA through several nanotechnological and chemical transfection methods. We improve reporter expression by altering untranslated region (UTR) sequences and codon bias, facilitating measurement of expression kinetics both in isolated cells and in whole planarians using luminescence imaging. We also examine protein expression as a function of variations in the UTRs of delivered mRNA, demonstrating a framework to investigate gene regulation at the post-transcriptional level. Together, these advances expand the toolbox for the mechanistic analysis of planarian biology and establish a strong foundation for the development and expansion of transgenic techniques in this unique model system. MotivationThe study of planarians has contributed to advances in our understanding of regeneration, stem cell dynamics, and many other fundamental biological processes. However, the persistent challenge of expressing transgenes in planarians has led to the speculation that they may be resistant to transfection. In this work, we develop methods to express exogenous mRNAs in both isolated planarian cells and whole animals by optimizing delivery techniques, genetic constructs, and detection methods. These methods allow us to study transfection kinetics and post-transcriptional regulation of gene expression in a quantitative manner. Beyond planarian research, this work should also provide a broadly applicable strategy to develop similar tools for animals that are also challenging to modify genetically.

bioengineering↗

bioRxiv2019

Deconvolution of Nucleic-acid Length Distributions: A Gel Electrophoresis Analysis Tool and Applications

Next-generation DNA-sequencing (NGS) technologies, which are designed to streamline the acquisition of massive amounts of sequencing data, are nonetheless dependent on various preparative steps to generate DNA fragments of required concentration, purity, and average size (molecular weight). Current automated electrophoresis systems for DNA- and RNA-sample quality control, such as Agilents Bioanalyzer (R)and TapeStation (R) products, are costly to acquire and use; they also provide limited information for samples having broad size distributions. Here we describe a software tool that helps determine the size distribution of DNA fragments in an NGS library, or other DNA sample, based on gel-electrophoretic line profiles. The software, developed as an ImageJ plug-in, allows for straightforward processing of gel images, including lane selection and fitting of univariate functions to intensity distributions. The user selects the option of fitting either discrete profiles in cases where discrete gel bands are visible, or continuous profiles, having multiple bands buried under a single broad peak. The method requires only modest imaging capabilities and is a cost-effective, rigorous alternative characterization method to augment existing techniques for library quality control.

genomics↗

bioRxiv2017

Beyond The Linear Genome: Comprehensive Determination Of The Endogenous Circular Elements In C. elegans And Human Genomes Via An Unbiased Genomic-Biophysical Method

Investigations aimed at defining the 3-D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. High-throughput sequencing has only recently made extensive genomic mapping of eccDNA sequences possible and had yet to be applied using a rigorous approach that distinguishes ascertainment bias from true enrichment. Here, we define eccDNA distribution, utilizing a set of unbiased topology-dependent approaches for enrichment and characterization. We use parallel biophysical, enzymatic, and informatic approaches to obtain a comprehensive profiling of eccDNA in C. elegans and in three human cell types, where eccDNAs were previously uncharacterized. We also provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture in which endogenous genomic DNA circles are present in normal physiological DNA metabolism, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.

genomics↗