The 10q25 neocentromere and its inactive progenitor have identical primarynucleotide sequence: Further evidence for epigenetic modification

We have previously localized the core centromere protein-binding domain of a 10q25.2-derived neocentromere to an 80-kb genomic region. Detailed analys is has indicated that the 80-kb neocentromere (NC) DNA has a similar overal l organization to the corresponding region on a normal chromosome 10 (HC) D NA, derived from a genetically unrelated CEPH individual. Here we report se quencing of the HC DNA and its comparison to the NC sequence. Single-base d ifferences were observed at a maximum rate of 4.6 per kb; however, no delet ions, insertions, or other structural rearrangements were detected. To inve stigate whether the observed changes, or subsets of these, might be de novo mutations involved in neocentromerization (i.e., in committing a region of a chromosome to neocentromere formation), the progenitor DNA (PnC) From wh ich the NC DNA descended, was cloned and sequenced. Direct comparison of th e PnC and NC sequences revealed 100% identity, suggesting that the differen ces between NC and HC DNA are single nucleotide polymorphisms (SNPs) and th at formation of the 10q25.2 NC did not involve a change in DNA sequence in the core centromere protein-binding NC region. This is the first study in w hich a cloned NC DNA has been compared directly with its inactive progenito r DNA at the primary sequence level. The results Form the basis for future sequence comparison outside the core protein-binding domain, and provide di rect support for the involvement of an epigenetic mechanism in neocentromer ization.