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Vol. 10, Issue 6, 832-838, June 2000

LETTER
The 10q25 Neocentromere and its Inactive Progenitor Have Identical Primary Nucleotide Sequence: Further Evidence for Epigenetic Modification

Alyssa E. Barry, Melissa Bateman, Emily V. Howman, Michael R. Cancilla, Kellie M. Tainton, Danielle V. Irvine, Richard Saffery, and K.H. Andy Choo1

The Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville 3052, Australia

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.

[The sequences in this paper have been submitted to GenBank under accession nos. AF222855 (not yet available) for HC; AF042484 for NCI; AF222854 (not yet available) for NCII; and AF222856 (not yet available) for PnC.]

1 Corresponding author.

10:832-838 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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