Stamidis, N. | Search bioRxiv

bioRxiv2025

SCAF1 driven polyadenylation site usage regulates mRNA isoform expression and neuronal differentiation

Accurate co-transcriptional processing is required for correct gene expression of mRNA transcript isoforms under unperturbed conditions, but particularly during development, to ensure tissue-specific mRNA isoform expression. Here we show that the poorly studied SR-related CTD-associated factors SCAF1 protein regulates polyadenylation site usage towards the end of genes. SCAF1 interacts directly with the phosphorylated C-terminal domain (CTD) of RNA polymerase II (RNAPII), in a complex enriched with elongation and 3 end processing factors. While SCAF1 knockout in HEK293 cells is innocuous, it leads to a shift towards expression of shorter mRNA transcripts by co-transcriptional usage of early polyadenylation sites. SCAF1 deficiency induced via auxin-dependent degradation in neuron differentiating mouse embryonic stem cells (mESCs) results in neuronal commitment defects, mediated by altered mRNA isoform usage that impacts expression of key neuronal genes. These findings highlight the importance of mRNA isoform usage and underscores the key role for SCAF proteins in its regulation though polyadenylation site selection.

molecular biology↗

bioRxiv2025

HDAC3 prevents enhancer hyperactivation to enable developmental transitions

Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate transcript dosage. However, the molecular mechanisms that ensure developmental genes are transcribed at specific levels remain largely unknown. Here, we discover that the epigenetic repressor histone deacetylase 3 (HDAC3), together with co-activators, binds a subset of the most active putative enhancer elements. Using a tunable mouse embryonic stem cell degron system, we uncover that HDAC3 directly prevents enhancer--and consequently gene--overactivation, effectively establishing a molecular "speed limit" for many naive pluripotency and housekeeping genes. Interestingly, we find that both the catalytic and non-catalytic functions of HDAC3 contribute to establishing this physiological transcript dose. Specifically during early development, HDAC3 rather than functioning as a canonical repressor, constrains the activity of highly transcribed genes of the implanting epiblast and ensures timely exit from naive pluripotency in vitro. Altogether, this indicates that a dynamic equilibrium between activators and repressors coexists at highly active enhancer elements in pluripotent stem cells, establishing appropriate transcriptional dosage and rendering them responsive to signaling cues, thereby enabling timely and coordinated developmental progression.

developmental biology↗