Sanges Ametlle, M. | bioRxiv Science

bioRxiv2025

PUMILIOs and m6A-ECT2/ECT3 share mRNA targets and exert opposing control over organogenesis

PUMILIO/Fem-3 Binding Factor (PUF) proteins are conserved eukaryotic mRNA-binding proteins. Higher plants encode an expanded family of PUF proteins with 26 members in Arabidopsis thaliana of which 6 (PUM1-PUM6) have a domain organization equivalent to metazoan PUF proteins implicated in mRNA regulation. Here, we show that the PUF proteins PUM2 and PUM6 are expressed in mitotically active cells of root and shoot meristems, while PUM5 is mostly expressed in the differentiation zone of root meristems exiting from active division. Increased PUM2 dosage in proliferating cells causes growth repression and developmental delay reminiscent of mutants with defects in cytoplasmic YTHDF proteins that bind to N6-methyladenosine (m6A) in mRNA. Remarkably, even weak defects in the m6A-YTHDF system enhance the effect of increased PUM2 dosage. In line with this genetic interaction, mRNA targets overlap significantly between PUFs and the major YTHDF proteins ECT2 and ECT3. Furthermore, the enrichment of the core PUF recognition motif URUAY around m6A sites is largely explained by PUF targeting, not by direct URUAY methylation as previously suggested. Our results indicate that the balance between the reciprocal activities of the deeply conserved cytoplasmic RNA binding protein families PUF and YTHDF is an important element of growth control in plants.

plant biology↗

bioRxiv2025

Multivariate analysis of glycogenes reveals coordinated regulation of immunoglobulin glycosylation in an immortalized human B cell system

While neutralizing ability has traditionally been considered the most important antibody function, appreciation has grown for Fc-mediated extra-neutralizing functions, which are shaped by IgG glycosylation. However, there remain fundamental questions as to how B lymphocytes induce and regulate antibody glycosylation and thus functional capability. Understanding how transcriptional and cell state regulation shape glycosylation could reveal levers to tune protective humoral profiles in a disease- and antigen-specific manner. Prior studies have explored a limited panel of glycogenes and measured bulk glycosylation changes. Here, employing an in vitro antigen-specific B cell culture system, we systematically characterize transcriptional and humoral responses to cytokine perturbations. After exposure to a broad panel of cytokines (IL-4, IL-6, IL-10, IL-17, TNFa, IFNg, APRIL, and BAFF) across multiple concentrations and timepoints, transcriptomic profiling and lectin-based IgG glycome assays are employed to associate cytokine stimuli with both glycogene expression and IgG glycosylation. Supervised and unsupervised machine learning models identify cytokine-specific glycogene "signatures" as well as distinct immunoglobulin glycosylation profiles. We find that cytokines induce rapid transcriptional responses, with glycogene signatures outperforming single-gene changes in distinguishing stimulation conditions. We further demonstrate the ability to induce both pro- and anti-inflammatory IgG glycosylation profiles, particularly in terms of IgG galactosylation. This work demonstrates the utility of this system to parse the cytokine-driven regulation of B lymphocyte glycogenes, establishing a framework for dissecting how environmental cues shape antibody glycosylation, with relevance for autoimmune disease, infection, and vaccine responses.

systems biology↗