ChIP and sequence analysis

ChIP was performed essentially as previously described (Tamaru et al. 2003), except mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP or for 30 min in 1% formaldehyde for GFP ChIP. Tissue was disrupted by sonication for 30 pulses before chromatin was sheared using a bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. The following antibodies were used: anti-H3K27me2/3 (Active Motif, 39535), anti-H3K27me2 (Active Motif, 61435), anti-H3K27me3 (Millipore, 07-449), anti-H3K9me3 (Active Motif, 39161), and anti-GFP (Abcam, 6556). ChIP-qPCR was performed as previously described (Jamieson et al. 2013) using the SYBR FAST ABI Prism qPCR kit (KAPA, KK4605). For primers, see Supplemental Table S2. ChIP samples were normalized to antibody specific background levels at histone H4.

Sequence alignments were performed as previously described (Jamieson et al. 2013) except that reads were mapped to N. crassa OR74A (NC12) genome (Neurospora crassa Sequencing Project, Broad Institute of Harvard and MIT; http://www.broadinstitute.org/) and that read densities were averaged over 200-bp windows to generate all tiled data files with the exception of the tracks included in Figure 5B, in which read densities were averaged over 25 bp.