Sequence characterization of the HSA12/22/12 evolutionary breakpoint region on SSC5q21

The HSA12/22/12 evolutionary breakpoint region on SSC5q21 has been sequenced, further localized, and preliminarily characterized. The existence and location of the breakpoint regions were originally determined in the human-porcine comparative map constructed by Meyers and colleagues. Bacterial artificial chromosome (BAC) fingerprint analysis and radiation hybrid mapping of BAC-end sequences was used to construct a minimum tiling path (MTP) encompassing each breakpoint region. The MTP clones were sequenced. The MTP sequences were then evaluated for similarity to human sequences using the NCBI cross-species megaBLAST program on Build 37.3 of the human genome. The more centromeric HSA12/22 breakpoint region displays sequence similarity to megabase (Mb) positions 2.593-2.807 on HSA12 and 17.583-17.672 on HSA22, and the more telomeric HSA22/12 breakpoint region displays sequence similarity to Mb positions 18.566-18.660 on HSA22 and 34.252-49.523 on HSA12. The human genome coordinates corresponding to the HSA12/22 breakpoint region also suggest an alternative marker order to the marker order proposed by Meyers and colleagues, although additional research is necessary to finalize the true marker order. The sequence evidence indicates the presence of transposable elements and AT-rich sequence composition in the areas surrounding each of the breakpoint regions. The sequence characterization results are in agreement with several previous studies of evolutionary breakpoint regions and therefore suggest potential involvement of such factors in evolutionary breakpoint generation, although underlying molecular mechanisms remain poorly understood at this point in time