Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach.
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.
Rivera-Mulia
Juan Carlos
JC
Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, Toluca, Edo. Méx., México.
Aranda-Anzaldo
Armando
A
D000418:Albumins / Q000235:genetics*; D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D007700:Kinetics; D008297:Male; D045170:Matrix Attachment Regions / Q000235:genetics; D009690:Nucleic Acid Conformation; D020161:Physical Chromosome Mapping; D051381:Rats; D017208:Rats, Wistar
D000418:Albumins; D004247:DNA