The LUMINIDEPENDENS protein is a general repressor of transcription in Arabidopsis [RNA-Seq 2]

Genomic integrity is constantly challenged by transcription/replication conflicts, a major source of replication stress and instability across all life forms. While extensive studies have uncovered transcription/replication conflicts resolution mechanisms in animals, yeast, and prokaryotes, their counterparts in plants remain largely unexplored. Through a forward genetic screen, we identified the LUMINIDEPENDENS (LD) protein, previously known for regulating the flowering repressor FLC, as a key player in mitigating replication stress in plants. Strikingly, transcriptomic analyses reveal that loss of LD results in the upregulation of over 13,000 genes, establishing LD as a global transcriptional repressor. Consistent with this role, LD binds a substantial portion of the Arabidopsis genome and interacts with the MED18 subunit of the Mediator complex to modulate RNA polymerase II phosphorylation. These findings uncover a fundamental function of LD in fine-tuning transcription genome-wide, with an additional role in suppressing transcription/replication conflicts by locally dampening transcription and promoting replication fork progression. Our work highlights a previously unrecognized genome-protective strategy in plants, opening new avenues for understanding transcription/replication conflict management in eukaryotic systems. Overall design: The experimental design integrates two spike-in RNA-seq datasets (Dataset1: Arabidopsis thaliana 7-day-old plantlets of Col0, fld, and ld mutants; Dataset2: Col0, pol2a, ld, and ld pol2a mutants) and a classic RNA-seq dataset (shoot apices of Col0, ld, pol2a, and ld pol2a mutants), each with three biological replicates.