Peak calling for ChIP-chip experiments was performed using MAT (Johnson et al. 2006. Proc. Natl. Acad. Sci. U.S.A. 103(33): 12457-12462.). The union of Rpd3 (HDAC1) and HDAC4 peaks was filtered to remove those regions that overlap the His3 modification H3K4me3. The remaining HDAC1/HDAC4 sites that overlapped regions of H3K27me3 modification were taken to generate a list of 537 predicted polycomb response elements.