ChIP-seq experiments were performed as described before (31). Briefly, nuclei were isolated from cells fixed with 1% formaldehyde. Next, using a Diagenode Bioruptor, chromatin was fragmented into ~250 bp. ChIP was performed with the antibodies listed below. Chromatin from Drosophila (1:100 ratio to the experimental chromatin) and Drosophila-specific H2Av antibody was used as spike-in control in each sample. For ChIP-seq, libraries were prepared as described in (43) using 1 to 30 ng of immunoprecipitated DNA.

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