title: The limits of the DNase I-sensitive domain of the human apolipoprotein B gene coincide with the locations of chromosomal anchorage loops and define the 5' and 3' boundaries of the gene.
abstract: In eukaryotic cells, chromatin is organized as domains or loops that are generated by periodic attachment of the chromatin fiber to protein components of a nuclear matrix, or scaffold. These chromosomal loops may have a function in gene regulation. The length of the chromatin domain encompassing the human apolipoprotein B gene was studied by determining the locations of nuclear matrix attachment sites as well as the boundaries of the DNase I-sensitive domain in cells that express the gene (such as HepG2 and CaCo-2 cells) and in those that do not (HeLa cells). Three nuclear matrix attachment regions (MARs) of the human apolipoprotein B gene have been localized: a 3' -proximal MAR, between nucleotides +43,186 and +43,850; a 5' -proximal MAR, between nucleotides -2,765 and -1,801; and a 5' -distal MAR, between nucleotides -5,262 and -4,048. Both the 3' -proximal and the 5' -distal MARS were present in cells that express the gene (HepG2 and CaCo-2 cells) as well as in cells that do not (HeLa cells), whereas the 5' -proximal MAR was detected only in HepG2 cells. These MARs were located at the bases of chromosomal loops in histone-extracted nuclei in all three cell lines. Various classes of A/T-rich sequences resembling the recognition site for topoisomerase II were present within the MAR-containing fragments. The boundaries of the DNase I-sensitive domain coincide with the positions of the 3' -proximal and 5' -distal matrix attachment sites. These results suggest the existence of a 47.5-kilobase domain that represents a topologically sequestered functional unit containing the coding region and all known cis-acting regulatory elements of the human apolipoprotein B gene.
authors.affiliation: Gladstone Foundation Laboratories for Cardiovascular Disease, University of California, San Francisco 94140-0608.
authors.forename: B
authors.initials: B
authors.lastname: Levy-Wilson
authors.forename: C
authors.initials: C
authors.lastname: Fortier
mesh_terms: D001055:Apolipoproteins B / Q000235:genetics*; D001483:Base Sequence; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism; D002874:Chromosome Mapping; D004273:DNA, Neoplasm / Q000235:genetics; D003850:Deoxyribonuclease I / Q000378:metabolism*; D015870:Gene Expression; D005796:Genes; D006801:Humans; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000378:metabolism; D015183:Restriction Mapping
chemical_list: D001055:Apolipoproteins B; D004273:DNA, Neoplasm; D003850:Deoxyribonuclease I