ChIP-seq profiling in SWD2-like Arabidopsis mutant seedlings

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution in defining gene expression programs are poorly defined in plant systems. Differently from S. cerevisiae in which a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with SET1), this activity involves multiple histone methyltransferases (HMTs) in Arabidopsis thaliana, among which the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. Here we report that SDG2 co-regulates hundreds genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of the evolutionarily conserved COMPASS complex. Accordingly, S2Lb associates with the AtCOMPASS core subunit WDR5a within a high-molecular weight complex and is required for proper H3K4me3 enrichment over genes highly occupied by RNA Polymerase II. S2Lb knock-out plants display little transcriptomic defects, suggesting that H3K4me3 deposition is important for optimal gene induction rather than for determining on/off transcriptional states. We further report that S2Lb and H3K4me3 are accurately targeted over most genes in hub1 mutant plants lacking histone H2B monoubiquitination. Collectively, our study indicates that a plant-specific COMPASS-like complex acting mainly through an H2Bub-independent mechanism is a major determinant of H3K4me3 deposition in Arabidopsis. 6 ChIP-seq libraries were sequenced