Cells were fixed in 1% formaldehyde and
resuspended in lysis buffer. Chromatin was sheared to
200-700bp using a Diagenode Bioruptor. Solubilized
chromatin was immunoprecipitated with antibodies against
each of the histone antibodies listed above.
Antibody-chromatin complexes were pulled-down using protein
A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II),
washed and then eluted. After cross-link reversal and proteinase K
treatment, immunoprecipitated DNA was extracted with
phenol-chloroform, ethanol precipitated, treated
with RNAse and purified. One to ten nanograms of DNA were
end-repaired, adapter-ligated and sequenced by Illumina Genome
Analyzers as recommended by the manufacturer.

Sequence reads from each IP experiment were aligned to the human
reference genome (hg18) using MAQ with default parameters, except
C=10 (maximum number of alignments/read <= 10).
Fragment densities were computed by counting the number of reads
overlapping each position in the genome (counted as 1 from the start
of each alignment to 200 bp downstream and by 0.25 from 200 to 300 bp,
and displayed at 25bp resolution). Discrete intervals of ChIP-seq
fragment enrichment were identified using a scan statistics approach,
under the assumption of uniform background signal.