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. 2018 Jan 22;35(4):949–962. doi: 10.1093/molbev/msy010

Fig. 5.

Fig. 5.

The human Y centromere and vertebrate neocentromeres are associated with dyad symmetries and non-B-form DNA. (A) Predicted ensemble free energies for DYZ3 and non-DYZ3 alphoid satellites classified based on CENP-A ChIP enrichment and centromere activity in artificial chromosome assays (Hayden et al. 2013; Henikoff et al. 2015). (B) Examples of minimum free energy structures for DYZ3 and D5Z2 alphoid fragments. A human chromosome 13 neocentromere (C) and a chicken chrZ neocentromere (D) with profiles from CENP-A ChIP-seq and SIST-predicted DNA melting and cruciform extrusion probabilities (left panels). Dyad symmetry and SIST DNA melting and cruciform extrusion scores for neocentromeres (“neo”) and composition-matched noncentromeric background genomic intervals (right panels). Data from genome-wide analysis of palindrome formation with sequencing (GAP-seq), which was performed in human cell lines, is also included in (A). Asterisks indicate two-sample Kolmogorov–Smirnov P < 0.05.