Biology subjects

SHAO, Y.

Publications and source records attributed to SHAO, Y..

3 recordsLinked to original sources

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

The acute sleep-inducing effects of light require histamine neurotransmission in mice

Sleep regulation depends on the complex interplay between homeostatic and circadian processes synchronized by the light/dark cycle. Sleep is also directly regulated by light via the retinal inputs to the preoptic area (POA). Although the light-responsive POA neurons project to several wake-promoting structures, including histaminergic neurons in the tuberomammillary nucleus (TMn), there is no functional evidence for their involvement in light-induced sleep. To bridge this gap, we used histidine decarboxylase (HDC, the histamine-synthetizing enzyme) knockout mice (HDC-/-, n=7) and hM4Di-HDC-cre mice (HDC+/+, n=8) subjected to an ultradian light/dark protocol (LD 1h:1h over 24h), and another group of hM4Di-HDC-cre mice (n=8) exposed to a 1-h light pulse. We found that light pulses during the biological night enhanced slow wave sleep and increased cortical EEG power in the delta range (0.5-3Hz), and that these effects were significantly attenuated both in HDC-/- (83 vs 23 min/6h, p=0.005) under LD 1h:1h condition and in hM4Di-HDC-cre mice after acute chemogenetic silencing of histamine neurons by the DREADD ligand deschloroclozapine (15 vs 6 min/h, p=0.0016) under a 1-h light pulse. In addition, the sleep-inducing effect of light was circadian dependent, with the strongest effect at the beginning and end of the night but no effect at all during the biological day in HDC+/+mice. Our study provides functional evidence that the acute sleep-inducing effects of light on sleep require histamine neurotransmission in mice.

neuroscience↗

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↗