A rapid method of genomic array analysis of scaffold/matrix attachment regions (S/MARs) identifies a 2.5-Mb region of enhanced scaffold/matrix attachment at a human neocentromere.
Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome.
Sumer
Huseyin
H
Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia.
Craig
Jeffrey M
JM
Sibson
Mandy
M
Choo
K H Andy
KH
D002461:Cell Line, Transformed; D002503:Centromere / Q000235:genetics*; D002869:Chromosome Aberrations; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D027042:Chromosomes, Artificial, P1 Bacteriophage / Q000235:genetics; D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D020451:Contig Mapping / Q000379:methods; D004247:DNA / Q000235:genetics; D005347:Fibroblasts / Q000821:virology; D020869:Gene Expression Profiling / Q000379:methods*; D004854:Herpesvirus 4, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D036961:Matrix Attachment Region Binding Proteins / Q000235:genetics*; D008677:Metaphase / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods
D036961:Matrix Attachment Region Binding Proteins; D004247:DNA