Biology subjects

van Werven, F. J.

Publications and source records attributed to van Werven, F. J..

3 recordsLinked to original sources

bioRxiv2026

Cellular context restricts a promiscuous m6A reader IDR to a single functional effector interface for mRNA decay

N6-methyladenosine (m6A) is a conserved mRNA modification that regulates transcript stability, yet how m6A readers engage effectors remains unknown. We show that during yeast meiosis, the YTH-domain protein Pho92 promotes the decay of m6A-modified transcripts through an uncharacterised, promiscuous intrinsically disordered region (IDR). In vitro, the Pho92 IDR makes multiple contacts with the Ccr4-NOT deadenylase complex and drives tethered reporter decay in the absence of any single subunit. Yet in meiosis, turnover of endogenous m6A-modified transcripts strictly depends on a single interface: direct binding of the Pho92 IDR to Caf40. A single hydrophobic residue substitution is sufficient to abolish Caf40 binding and halt transcript decay. Human YTHDF proteins can functionally substitute for Pho92, but require multiple hydrophobic patches within the IDR for decay activity. Thus, on endogenous m6A-modified transcripts during meiosis, the promiscuous Pho92 IDR is restricted to a single functional interface, revealing unappreciated specificity in m6A-directed mRNA decay.

molecular biology↗

bioRxiv2023

Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast

Starvation of budding yeast diploid cells induces the cell-fate program that drives meiosis and spore formation. Transcription activation of early meiotic genes (EMGs) requires the transcription activator Ime1, its DNA-binding partner Ume6, and GSK-3{beta} kinase Rim11. Phosphorylation of Ume6 by Rim11 is key for EMG activation. We report that Rim11 integrates multiple input signals to control Ume6 phosphorylation and EMG transcription. Under nutrient-rich conditions PKA represses Rim11 to low levels while TORC1 keeps Rim11 localized to the cytoplasm. Inhibiting PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. Additionally, Ime1 is an essential anchor protein for phosphorylating Ume6. Subsequently, Ume6-Ime1 coactivator complexes form that drive EMG transcription. Our results demonstrate how varied signalling inputs (PKA/TORC1/Ime1) integrated by Rim11 determine EMG expression and entry into meiosis. We propose that the signalling-regulatory network described here generates robustness in cell-fate control.

molecular biology↗

bioRxiv2018

Repression of divergent noncoding transcription by a sequence-specific transcription factor

Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.

molecular biology↗