ChIP and input sequencing reads from all LCL datasets were aligned using Bowtie 0.12.7 with the parameters O-n 2 -m 3 -k 1 -best to the following genome assemblies: human GRCh37, chimpanzee CHIMP2.1, gorilla gorGor3, orangutan PPYG2, macaque Mmul 1, and marmoset C. jaccus 3.2.1.
Scanning was carried out according to manufacturer's specifications.
nucleic acid library construction protocol
Protein-bound DNA was immunoprecipitated with antibodies against CTCF (Millipore, 07-729), or YY1 (Santa Cruz, sc-281).
Immunoprecipitated DNA was end-repaired, A-tailed and single-end Illumina sequencing adapters ligated before 18 cycles of PCR amplification. 200-300 bp DNA fragments were selected and 36 bp reads sequenced on an Illumina Genome Analyser II according to manufacturer's instructions.
1x10^8 cells were cross-linked with 1% formaldehyde as previously described (Schmidt, Methods,2009). ChIP-seq assays were performed as previously described (Schmidt, 2009).
Lymphoblast cell lines were obtained for seven primate species. All cell lines were transformed by the Epstein Barr virus except for the macaque cell lines that were transformed by a herpesvirus. Cells were grown in suspension at a confluency of 200 000-1 x106 cells/ml in RPMI1640 media supplemented with 10% Fetal Bovine Serum and 2 mM L-glutamine. C57BL/6J mice were housed in the Biological Resources Unit under UK Home Office licensing. Tissue was obtained from at least two independent males and cross-linked as described in (Schmidt, Methods,2009). Male and female human tissue samples were obtained from biopsied tissue collected at Addenbrooke's Hospital, Cambridge, and were provided by the Biobank under human tissue license 08/H0308/117. Liver tissue was also obtained from the Liver Tissue Distribution Program (NIDDK contract number N01-DK-9-2310) at the University of Pittsburgh.