RNA-Seq of Col-0, dek3-2, dek4-2, and dek3-2 dek4-2 (dd-2) 7-day-old seedlings in Arabidopsis

Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing, and transcriptional regulation in eukaryotes. Here, we show that two DEK proteins, DEK3 and DEK4, redundantly control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression. The binding of DEK3 and DEK4 to histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression. Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis. Overall design: 7-day-old seedlings of Col-0, dek3-2, dek4-2, and dd-2 were examined with RNA-Seq to identify differentially expressed genes caused by DEK3 and DEK4 mutation in Arabidopsis. 8 samples from Col-0, dek3-2, dek4-2, and dd-2 7-day-old seedlings grown under long day condition with two biological replicates.