title: The 10q25 neocentromere and its inactive progenitor have identical primary nucleotide sequence: further evidence for epigenetic modification.
abstract: We have previously localized the core centromere protein-binding domain of a 10q25.2-derived neocentromere to an 80-kb genomic region. Detailed analysis has indicated that the 80-kb neocentromere (NC) DNA has a similar overall organization to the corresponding region on a normal chromosome 10 (HC) DNA, derived from a genetically unrelated CEPH individual. Here we report sequencing of the HC DNA and its comparison to the NC sequence. Single-base differences were observed at a maximum rate of 4.6 per kb; however, no deletions, insertions, or other structural rearrangements were detected. To investigate 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 which the NC DNA descended, was cloned and sequenced. Direct comparison of the PnC and NC sequences revealed 100% identity, suggesting that the differences between NC and HC DNA are single nucleotide polymorphisms (SNPs) and that 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 which a cloned NC DNA has been compared directly with its inactive progenitor DNA at the primary sequence level. The results form the basis for future sequence comparison outside the core protein-binding domain, and provide direct support for the involvement of an epigenetic mechanism in neocentromerization.
authors.affiliation: The Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville 3052, Australia.
authors.forename: A E
authors.initials: AE
authors.lastname: Barry
authors.forename: M
authors.initials: M
authors.lastname: Bateman
authors.forename: E V
authors.initials: EV
authors.lastname: Howman
authors.forename: M R
authors.initials: MR
authors.lastname: Cancilla
authors.forename: K M
authors.initials: KM
authors.lastname: Tainton
authors.forename: D V
authors.initials: DV
authors.lastname: Irvine
authors.forename: R
authors.initials: R
authors.lastname: Saffery
authors.forename: K H
authors.initials: KH
authors.lastname: Choo
mesh_terms: D000483:Alleles; D001483:Base Sequence / Q000235:genetics*; D002460:Cell Line; D002503:Centromere / Q000235:genetics*; D002879:Chromosomes, Human, Pair 10 / Q000737:chemistry / Q000235:genetics*; D003001:Cloning, Molecular; D005786:Gene Expression Regulation / Q000235:genetics; D006801:Humans; D018386:Kinetochores; D008297:Male; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA