Gonzalez, M. N. | Search bioRxiv

bioRxiv2025

Alternative splicing of PIF4 regulates plant development under heat stress

The Phytochrome-Interacting Factor 4 (PIF4) is a key player in the integration of multiple internal and external stimuli to optimize different aspects of plant development. While both the DNA encoding this transcription factor and its protein are known to be under tight control, no regulation at the RNA level has been previously reported. Our genomic analysis revealed that the exon/intron structure of the basic Helix-Loop-Helix (bHLH) DNA binding domain of PIF4 is conserved and pointed to skipping of an exon in this region specifically in response to heat stress. We then showed that this alternative splicing event downregulates PIF4 function under heat, which in etiolated seedlings induces photomorphogenic-related traits. Our results disclose a role for PIFs in plant responses to heat and reveal a new regulatory layer for the control of PIF4 function, underscoring the critical role of posttranscriptional regulatory processes in the molecular integration of environmental cues.

plant biology↗

bioRxiv2025

Systems-level feedback loops maintain gene expression homeostasis following RNA polymerase II dosage perturbation

Transcription is regulated by sequence-specific transcription factors and enzymes allowing access to genes in chromatin. However, recent data indicate that the abundance of RNA polymerase II (RNAPII) itself may under certain circumstances represent an additional, crucial determinant of transcription regulation. Here, we used the dTAG system to titrate the cellular dosage of human RPB1, the largest RNAPII subunit, to more generally assess the importance of RNAPII levels. Unexpectedly, cells are extremely sensitive to RPB1 dosage, with a mere 30% reduction sufficient to perturb cell proliferation, cell cycle progression, and global transcription. Importantly, alterations in RPB1 abundance trigger hierarchical gene expression changes that are highly organized rather than stochastic. Using a combination of sequencing and proteomic approaches, we uncover the existence of multiple feedback loops between transcriptional initiation, promotor-proximal pause release, transcript elongation, splicing, and mRNA half-life, which together establish RNAPII abundance as a crucial systems-level regulator of transcriptional homeostasis.

systems biology↗