gDNA from RAD55myc strain
Myc/HA-ChIP experiments were performed as described above. For genome-wide sequencing DNA was treated according to manufacturers instructions (Next ChIP-seq Library Prep Master Mix Set for Illumina, NEB) and submitted to deep sequencing (HiSeq 2500 sequencer). Obtained sequence reads were aligned to the yeast reference genome (sacCer3) with bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome.). Binding regions were identified by using MACS 2.0 with default settings for narrow peaks (Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS)). Supplementary Data X contains all obtained Csm2 and RAD55 peaks. The ChIP input was used as a control data set. Overlap of binding sites with other genomic features and binding regions were determined using a PERL script based on a permutation analysis between the query and subject features.