Fig. 4.

Chromatin contacts on the human and chimpanzee Y chromosomes, as evaluated from iPSCs. (A) Human Y chromosome contacts with palindromes (highlighted in light blue), pseudoautosomal regions (green), and centromere (red). The schematic representation of the sequencing classes on the Y chromosome is adapted from ref. 6. (B) Chimpanzee Y chromosome contacts with palindromes (highlighted in light blue). The schematic representation of the sequencing classes on the Y chromosome is adapted from ref. 7. (C) Chromatin interactions for the three largest palindromes on the human Y (the next three largest palindromes are displayed in SI Appendix, Fig. S10). To resolve ambiguity due to multimapping reads, each interaction was assigned a probability based on the fraction of reads supporting it (see SI Appendix, Supplemental Methods, for details). Palindrome arms are shown as blue arrows, and the spacer is shown as white space between them.