H3K4me3 ChIP-seq in S. cerevisiae and S. paradoxus
H3K9ac ChIPseq was performed on BY4743 (S. cerevisiae) and CBS432 (S. paradoxus) strains growing at mid-log phase, as described previously (Liu et al. 2005), with some modifications.  Samples were sonicated (using BioRuptor) for 60 min (30 sec intervals, and were precipitated with an anti-trimethyl-H3K4 antibody (Abcam ab8580) conjugated to protein A beads.  Samples for each strain were pooled before sequencing.  Library preparation and high throughput sequencing were performed using the Illumina GAII system at the Department of Biological Services, Weizmann Institute of Science, Israel.