Biology subjects

Liu, R.-J.

Publications and source records attributed to Liu, R.-J..

5 recordsLinked to original sources

bioRxiv2026

m1A58 acts as a conformational checkpoint coupling human initiator tRNA maturation to translation initiation

tRNAs are characterized by extensive chemical modifications that influence tRNA fate. N1-methyladenosine at position 58 (m1A58) is a widespread core tRNA modification linked to physiological and pathological processes. However, how m1A58 coordinate tRNA folding and processing to ensure translational efficiency in mammalian cells remains largely unknown. Using acute dTAG-mediated degradation and CRISPR-Cas9 knockout, we identified initiator methionine tRNA (tRNAiMet) as selectively vulnerable to m1A58 loss, lacking the isodecoder buffering observed for most other tRNA isoacceptors. NMR analysis of the tRNAiMet showed that m1A58 stabilizes D/T-loop interactions, consistent with a maturation-competent conformation. In vitro processing assays further demonstrated that m1A58 promotes RNase P-mediated 5'-leader removal and RNase Z-mediated 3'-trailer cleavage, while La/SSB protects accumulated precursors. Disrupting this checkpoint impaired the assembly of the eIF2-containing 43S pre-initiation complex and global protein synthesis, which was substantially rescued by adding m1A58-modified tRNAiMet. Acute TRMT6 degradation elicited temporally coordinated gene-expression responses involving proteostasis, transport and signaling. Together, these findings establish m1A58 as a conformational checkpoint coupling human initiator-tRNA maturation to translation initiation and stress responses.

molecular biology↗

bioRxiv2026

Ultra-sensitive FLORA-seq links cell-type-specific tRNAome dynamics to differentiation trajectories guiding therapeutic suppressor tRNA candidate selection

Mammalian genomes encode hundreds of tRNA genes, but the role of individual tRNAs in development and cell identity remains unclear. Here, we introduce FLORA-seq, a method for simultaneous, low-input profiling of tRNAs, tRNA-derived RNAs (tdRs) and their modifications from as few as 5-20 cells. Applying FLORA-seq to mouse hematopoiesis revealed 50 high-variance isodecoders whose expression profiles recapitulate known hematopoietic cell types and correlate with differentiation trajectories. At the isoacceptor level, tRNA pools are largely stable within hematopoietic stem and progenitor cells (HSPCs), showing only subtle, specific variations, but become both distinct from HSPCs and internally stable within each terminally differentiated lineage. We further detected dynamic changes in tdR ratios and modification patterns, underscoring precise tRNA regulation during differentiation. Crucially, analysis of 54 endogenous tRNA isodecoders and their engineered suppressor counterparts showed that efficient premature termination codon readthrough preferentially arises from highly expressed cognate isodecoders. This correlation provides a rational framework for prioritizing suppressor tRNA candidates and implies non-redundant functions for individual isodecoders.

molecular biology↗

bioRxiv2024

Pyramidal cell types and 5-HT2A receptors are essential for psilocybin's lasting drug action

Psilocybin is a serotonergic psychedelic with therapeutic potential for treating mental illnesses1-4. At the cellular level, psychedelics induce structural neural plasticity5,6, exemplified by the drug-evoked growth and remodeling of dendritic spines in cortical pyramidal cells7-9. A key question is how these cellular modifications map onto cell type-specific circuits to produce psychedelics behavioral actions10. Here, we use in vivo optical imaging, chemogenetic perturbation, and cell type-specific electrophysiology to investigate the impact of psilocybin on the two main types of pyramidal cells in the mouse medial frontal cortex. We find that a single dose of psilocybin increased the density of dendritic spines in both the subcortical-projecting, pyramidal tract (PT) and intratelencephalic (IT) cell types. Behaviorally, silencing the PT neurons eliminates psilocybins ability to ameliorate stress-related phenotypes, whereas silencing IT neurons has no detectable effect. In PT neurons only, psilocybin boosts synaptic calcium transients and elevates firing rates acutely after administration. Targeted knockout of 5-HT2A receptors abolishes psilocybins effects on stress-related behavior and structural plasticity. Collectively these results identify a pyramidal cell type and the 5-HT2A receptor in the medial frontal cortex as playing essential roles for psilocybins long-term drug action.

neuroscience↗

bioRxiv2023

Frontal cortex norepinephrine, serotonin, and dopamine dynamics in an innate fear-reward behavioral model

Animals must survive by foraging for food in an uncertain and dangerous world. Neural circuits for naturalistic decision-making under these conditions must balance competing motivational demands for approaching reward and avoiding danger. To enable flexible switching between motivational states, neuromodulators are released and alter neural excitability and plasticity. The question of how neuromodulators encode motivational state is thus fundamental to systems neuroscience, yet the dynamics of neuromodulators during naturalistic decision making are not fully understood. Here, we developed a naturalistic approach/avoidance task in mice involving a tradeoff between seeking reward versus safety in the presence of looming predation risk. We utilized fiber photometry, computational behavior tracking, and local pharmacology in this task. Silencing medial prefrontal cortex (mPFC) reduced looming defensive behaviors. Moreover, by using fiber photometry combined with GPCR-based sensors, we found that cortical norepinephrine (NE) plays a more prominent role in encoding looming threats while dopamine (DA) represents reward and threat. In contrast, serotonin (5HT) dynamic negatively correlates to both emotional valences. To begin to understand neuromodulatory interactions, we used ex vivo slice physiology to understand 5HT impact on spontaneous firing of locus coeruleus NE neurons. In conclusion, monoamines such as NE, DA, 5HT can converge in their encoding of naturalistic motivated behaviors as well as dissociate from one another. By utilizing this novel innate reward-threat task, we can better understand neurochemical signaling events during natural behavior, and may contribute to the understanding of neural mechanisms underlying emotional decision-making and its implications for psychiatric disorders.

neuroscience↗

bioRxiv2023

THUMPD2 catalyzes N2-methylation on the spliceosome catalytic center of U6 snRNA and regulates pre-mRNA splicing

How the relatively evolutionarily conserved spliceosome is able to manage the enormously expanded number of splicing events that occur in humans ([~]200,000 vs. [~]400 reported for yeast) is not well understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G)-on the G72 nucleoside of U6 snRNA (known to function as the catalytic center of the spliceosome) results in profoundly increased pre-mRNA splicing activity in human cells. This U6 m2G72 modification is conserved among vertebrates. Further, we demonstrate that THUMPD2 is the methyltransferase responsible for U6 m2G72 and show that it interacts with an auxiliary protein (TRMT112) to specifically recognize both sequence and structural elements of U6. THUMPD2 KO blocks U6 m2G72 and down-regulates the pre-mRNA splicing activity of major spliceosome, yielding thousands of changed alternative splicing events of endogenous pre-mRNAs. Notably, the aberrantly spliced pre-mRNA population of the THUMPD2 KO cells elicits the nonsense-mediated mRNA decay (NMD) pathway and restricts cell proliferation. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome differentially regulates global pre-mRNA splicing.

biochemistry↗