Biology subjects

GUO, Z.

Publications and source records attributed to GUO, Z..

4 recordsLinked to original sources

bioRxiv2026

When CycloneSEQ meets Oxford Nanopore Technologies: a performance comparison of contemporary nanopore DNA sequencing platforms

Nanopore sequencing enables direct analysis of native DNA modifications, but these modifications can also introduce systematic basecalling errors. Here, we investigated how bacterial DNA methylation contributes to nanopore substitution errors using matched native whole-genome sequencing (WGS) and methylation-depleted whole-genome amplification (WGA) datasets from six bacterial species across CycloneSEQ (CS) and Oxford Nanopore Technologies platforms (ONT). Adenine-to-guanine (A2G) and guanine-to-adenine (G2A) substitutions were consistently enriched across species, nanopore platforms, sequencing configurations, and basecalling models, indicating a shared nanopore-associated substitution bias. This enrichment remained detectable in WGA reads, whereas native WGS reads showed a further increase. Using independent PacBio methylation profiling, we found that the WGS-associated substitution excess was strongly concentrated around bacterial methylation motifs and was minimal in non-motif regions. The magnitude and substitution pattern of these errors varied among motifs and sequencing platforms. At a subset of motif-associated positions, alternative-base fractions exceeded 50%, producing SNP-like signals. In ONT data, 28 WGS-specific calls survived the applied SNP-calling filters, all within PacBio-supported methylation contexts, and most showed significant strand imbalance. Together, these results identify a shared A2G/G2A substitution bias in all nanopore datasets and support a methylation-associated increase in these errors near bacterial methylation motifs, with some loci producing SNP-like artifacts.

bioinformatics↗

bioRxiv2025

Nanopore direct-RNA sequencing reveals TGEV epitranscriptomic and transcriptomic landscapes modulated by gene 7

Viral non-structural proteins have gained increasing attention for their roles in regulating host-virus interplay and reported to act as a key mediator of host and virus RNA modification dynamics. Transmissible gastroenteritis virus (TGEV) gene 7 has been implicated in virulence, but its other molecular functions remain unclear. Here, we compared wild-type TGEV (TGEV-wt) with a recombinant strain lacking gene 7 (TGEV-{Delta}7) in swine testis cells using Oxford Nanopore direct RNA sequencing. High-coverage datasets enabled simultaneous profiling of the full-length transcriptome, N6-methyladenosine (m6A) modifications, and polyA tail length. Deletion of TGEV gene 7 halved viral RNA replication yet increased m6A modification by [~]32 % across the viral genome, and elevated host m6A levels by [~]17 %, accompanied by reciprocal shifts in the m6A regulators FTO (eraser) and RBM15 (writer). Despite bulk transcriptome changes were comparable between strains, gene 7 deletion introduced additional DEGs beyond WT infection, showing stronger enrichment of antiviral and chemokine pathways, indicating heightened innate immunity. PolyA analysis uncovered the polyA features of TGEV gRNA and sgRNAs, and revealed a gene 7 dependent extension of viral by 7 nt, but not host polyA tails. These findings highlight RNA-modification machinery as a potential target for coronavirus control and provide a framework for vaccine strategies exploiting gene 7 attenuation.

microbiology↗

bioRxiv2025

Architecture and mechanism of a dual-enzyme retron system in prokaryotic immunity

Retrons are bacterial genetic retroelements encoding a reverse transcriptase (RT) and a non-coding RNA (ncRNA)-multi-copy single-stranded DNA (msDNA) hybrid. Diverse effector proteins or domains are found to associate with retrons, typically forming tripartite toxin-antitoxin systems involved in anti-phage defense. Although retrons have attracted growing interest in genome editing technologies, the mechanisms underlying most retron-mediated immune systems remain poorly understood. Here, we characterized a distinct quaternary retron system, Ec78, harboring a dual-enzymatic effector complex, in which the PtuA ATPase and PtuB nuclease act in concert to mediate phage clearance. The cryo-EM structure of the Ec78 complex adopts a flower-basket-like architecture, with two Ec78 retrons engaging the PtuAB effector complexes through a unique msDNA-insertion assembly mechanism. Interestingly, a sensing loop on the RT protein tightly monitors the length of the msDNA, which is likely responsible for phage detection and the subsequent release of the toxic effector complex. We further determined the cryo-EM structure of the retron-unbound effector complex, revealing an arginine-lysine finger loop on the PtuB nuclease that undergoes an ordered-to-disordered transition for enzymatic activation. Together, our work not only delineates the molecular basis underlying the Ec78 system in antiviral defense but also highlights the mechanistic diversity of retron systems in prokaryotic immunity.

biochemistry↗

bioRxiv2025

Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Nanopore RNA004 Technology

RNA modifications are critical regulators of diverse cellular processes, yet their roles in prokaryotic mRNAs remain poorly understood. Recent advances in Oxford Nanopore sequencing--especially the RNA004 kit--have enabled higher yields, reduced signal-to-noise ratio, and improved read accuracy, making them promising tools for investigating bacterial epitranscriptomes. Here, we presented a comprehensive walkthrough for Escherichia coli RNA modification analysis based on RNA004. Using both native (WT) and in vitro-transcribed (IVT) RNA samples, we first evaluated the Dorado modification detection models ({Psi}, mA, mC, and A-to-I). While each model successfully identified known rRNA modification sites, it also generated many false positives, emphasizing the need for careful data interpretation. To address these limitations, we introduced nanoSundial (https://github.com/lrslab/nanoSundial), a new comparative method that leveraged raw current features from WT and IVT samples to detect multiple types of RNA modifications in prokaryotes. We optimized nanoSundial on well-studied rRNA sites and validated its effectiveness with tRNA modifications. Through technical and biological replicate analyses, nanoSundial demonstrated reproducibility exceeding 95% in tRNA, rRNA, and ncRNA regions, albeit with lower reproducibility ([~]61%) in mRNA. We further found enrichment of mRNA modifications at the start or end of coding sequences. In total, 190 stably modified CDS regions were identified in E. coli, many of which cluster near the end of highly expressed transcriptional units (TUs) in each operon. Overall, this study highlighted the strengths and limitations of current nanopore-based modification detection methods on bacterial RNA, introduced a robust new comparative tool, and elucidated previously uncharacterized mRNA modification landscapes. Our findings open new avenues for understanding the functional impacts of bacterial RNA modifications and advancing epitranscriptomic research in prokaryotes.

bioinformatics↗