Biology subjects

Nachmani, D.

Publications and source records attributed to Nachmani, D..

4 recordsLinked to original sources

bioRxiv2026

An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch

Epstein-Barr virus (EBV) establishes life-long latency in human B-cells yet the molecular strategies that balance its persistence with lytic replication remain incompletely understood. Here, we identify the EBV-encoded small nucleolar RNA, v-snoRNA1, as a bona fide 2'-O-methylation guide that directs methylation of host ribosomal RNAs at 18S-C621 and 28S-U1760, two conserved residues in the ribosomal A-site. V-snoRNA1-mediated hypermethylation impairs 18S rRNA maturation and compromises translational fidelity and output, resulting in slower cellular proliferation. Infection with a v-snoRNA1 deleted virus ({Delta}v-snoRNA1) leads to enhanced protein synthesis and increased proliferation, together with extensive rewiring of host and viral gene expression. This rewiring includes suppression of immune and interferon pathways and alterations in transcription factor activities important for B-cell differentiation. Importantly, we find that v-snoRNA1 is required to facilitate viral production. Our findings reveal a molecular strategy by which EBV directly controls translation to promote infection.

molecular biology↗

bioRxiv2025

A unified analysis of cell-type and trajectory-associated pathways in single-cell data using Phoenix

Single-cell RNA sequencing has transformed our ability to resolve complex cellular heterogeneity within biospecimens at the molecular level. However, identifying which biological pathways accurately reflect distinct cell types or continuous cellular trajectories remains a major challenge. Traditional methods often miss subtle or non-linear pathway activities, limiting biological interpretability and insights. To address this, we develop Phoenix, a pathway analysis framework that leverages random forest models and non-parametric significance testing to evaluate the relevance of functional gene sets for distinguishing between cell-types and organizing cells along pseudotemporal cellular trajectories. Phoenix reveals both up- and downregulated processes, including those shaped by complex non-linear gene interactions, and quantifies their effect sizes. Applied to human and mouse hematopoiesis as well as zebrafish embryogenesis, Phoenix identifies both cell-type-specific and trajectory-associated pathways, spanning housekeeping, developmental, and lineage-specific programs. It outperforms existing tools in capturing cell-type-specific activities of small pathways and reveals greater overlap in pathway activities across species. Ultimately, Phoenix provides a sensitive and interpretable framework for uncovering biologically meaningful pathways and eliciting the interactions between their components in complex single-cell datasets, opening new opportunities to explore dynamic gene regulation across biological systems.

bioinformatics↗

bioRxiv2025

Dynamic Ribosomal RNA Methylation Regulates Translation in the Hematopoietic System and is Essential for Stem Cell Fitness

Self-renewal and differentiation are at the basis of hematopoiesis. While it is known that tight regulation of translation is vital for hematopoietic stem cells (HSCs) biology, the mechanisms underlying translation regulation across the hematopoietic system remain obscure. Here we reveal a novel mechanism of translation regulation in the hematopoietic hierarchy, which is mediated by ribosomal RNA (rRNA) methylation dynamics. Using ultra-low input ribosome-profiling, we characterized cell-type-specific translation capacity during erythroid differentiation. We found that translation efficiency changes progressively with differentiation and can distinguish between discrete cell populations as well as to define differentiation trajectories. To reveal the underlying mechanism, we performed comprehensive mapping of the most abundant rRNA modification - 2-O-methyl (2OMe). We found that, like translation efficiency, 2OMe dynamics followed a distinct trajectory during erythroid differentiation. Genetic perturbation of individual 2OMe sites demonstrated their distinct roles in modulating proliferation and differentiation. By combining CRISPR screening, molecular and functional analyses, we identified a specific methylation site, 28S-Gm4588, which is progressively lost during differentiation, as a key regulator of HSC self-renewal. We showed that low methylation at this site led to translational skewing, mediated mainly by codon frequency, which promoted differentiation. Functionally, HSCs with diminished 28S-Gm4588 methylation exhibited impaired self-renewal capacity ex-vivo, and loss of fitness in-vivo in bone marrow transplantations. Extending our findings beyond the hematopoietic system, we also found distinct dynamics of 2OMe profiles during differentiation of non-hematopoietic stem cells. Our findings reveal rRNA methylation dynamics as a general mechanism for cell-type-specific translation, required for cell function and differentiation. KEY POINTSO_LIHematopoietic differentiation is associated with rRNA methylation dynamics to control cell-type-specific translation. C_LIO_LITranslation efficiency can distinguish discrete cell types and define differentiation trajectories. C_LIO_LIHSC fitness is regulated by a single rRNA methylation. C_LI

molecular biology↗

bioRxiv2020

Macrophage Function is Regulated by NPM1-Mediated 2'-O-Methylation

The NPM1 gene is frequently a target of genetic alteration in hematological tumors, particularly of the myeloid lineage. Complete inactivation of Npm1 in the mouse disrupts primitive hematopoiesis and results in embryonic lethality. Npm1 heterozygosity produces features similar to those of MDS that progress to overt leukemia, and specific point mutations of Npm1 lead to bone marrow failure due to loss of hematopoietic stem cells. However, little is known about NPM1s role in mature, differentiated cells. Here we generated a conditional mouse mutant to inactivate Npm1 across the myelomonocytic lineage, and investigated its ability to influence macrophage maturation and function. We found that Npm1 is not required to maintain macrophage viability, while its loss in mature macrophages reduces production of reactive oxygen species, chemotactic properties and phagocytic capacity. Taking advantage of our recently established Npm1D180del mouse model of ribosome dysfunction and hematological disease, we identify cellular translation and rRNA 2-O-methlyation as a crucial element in controlling macrophage function. These analyses demonstrate a role for Npm1 in adult immune cells, and reveal the importance of translation regulation in macrophage function. Statement of significanceMacrophages are a major component of the immune response to various insults including to cancer. Here we show that NPM1, the most frequently mutated gene in acute myeloid leukemia, displays a critical role in macrophage function, and we identify ribosome deregulation as one of the underlying mechanisms.

cell biology↗