Predicted PRE polycomb response element defined as a region of Rpd3 (HDAC1) or HDAC4 binding that overlaps sites of His3 H3K27me3 modification but not H3K4me3.

Genomic sequences identified as putative polycomb response elements (silencers): regions of Rpd3 (HDAC1) or HDAC4 binding that overlap regions of His3 modification H3K27me3 but not H3K4me3. A synthesis of ChIP data sets; DNA sequences identified by genomic tiling array.

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.