A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1

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Sergey A. Shaposhnikov, Sergey B. Akopov, Igor P. Chernov, Preben Dybdahl Thomsen, Claus Bøttcher Jørgensen, Andrew R. Collins, Eirik Frengen, Lev G. Nikolaev

There is abundant evidence that the DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. To explore the DNA domain organization of the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1, we have identified a significant portion of the scaffold/matrix attachment regions (S/MARs) within this region. Forty independent putative S/MAR elements were assigned within the 16q22.1 locus. More than 90% of these S/MARs are AT rich, with GC contents as low as 27% in 2 cases. Thirty-nine (98%) of the S/MARs are located within genes and 36 (90%) in gene introns, of which 15 are in first introns of different genes. The clear tendency of S/MARs from this region to be located within the introns suggests their regulatory role. The S/MAR resource constructed may contribute to an understanding of how the genes in the region are regulated and of how the structural architecture and functional organization of the DNA are related.
Original languageEnglish
JournalGenomics
Volume89
Issue number3
Pages (from-to)354-361
Number of pages8
ISSN0888-7543
DOIs
Publication statusPublished - 2007

    Research areas

  • Former LIFE faculty - Functional genomics, Gene regulation, Physical mapping, Nuclear matrix, Scaffold/matrix attachment regions

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