Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach

Juan Carlos Rivera-Mulia, Armando Aranda-Anzaldo

Research output: Contribution to journalArticle

14 Scopus citations

Abstract

Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family.

Original languageEnglish (US)
Pages (from-to)23-35
Number of pages13
JournalDNA Research
Volume17
Issue number1
DOIs
StatePublished - Feb 1 2010
Externally publishedYes

Keywords

  • DNA topology
  • loop attachment regions
  • matrix attachment regions
  • nuclear matrix
  • nucleotype

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