ChIP was performed as described in Lee et al. Nat Protoc. 2006 (PMID 17406303) (MEF input 1, MEF POL-II_S2P, and MEF POL-II-S5P) and Takahashi et al. Science's STKE 2000 (PMID 11752617) (MEF input 2, MEF H3K4me3, and MEF H3K36me3). Paired-end Solexa ChIP libraries were prepared as described in the Illumina ChIP sequencing manual with minor modifications and using NEB Next DNA sample prep reagent Set 1 (E6000S) (NEB). Input DNA was used as a control and for normalization. Modifications to the Illumina protocol were: (1) 30 ng of ChIP products were used as template, (2) paired-end adapters were ligated to end-repaired and A-tailed DNA using T4 DNA ligase (NEB) for 2 hours at 16°C, and (3) Phusion polymerase in GC buffer (Finzyme) was used instead of Phusion polymerase in HF buffer. DNA products were purified with QIAquick spin columns (Qiagen). Concentration, size distribution (400-500bp), and purity of libraries were assessed on the DNA 1000 Bioanalyzer chip (Agilent). Genome Analyzer II (Illumina) was used to perform 2x36 cycles of paired-end sequencing.