Biology subjects

Zhu, W.-Y.

Publications and source records attributed to Zhu, W.-Y..

2 recordsLinked to original sources

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↗

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↗