Localization of a site for interaction with hepatic male-specific proteins in two rat estrogen sulfotransferase genes

Using electromobility shift assay the interaction of fragments of two paralogous rat estrogen sulfotransferase (Ste) genes with proteins of nuclear extracts from male and female rat liver was studied. Male-specific DNA–protein complexes were revealed with labeled oligonucleotides corresponding to fragments +1150/+1449, +1358/+1449, +1397/+1449, and +1417/+1449 of intron 1 of the Ste1 gene. The removal of a 20 bp region corresponding to the sequence +1430/+1449, or even either 5"- or 3"-terminal 5 bp of this region abolished the selective interaction of the oligonucleotides with the malespecific protein(s). According to the results of the experiments on mutual competition of the oligonucleotides, the fragment of the Ste2 gene corresponding to the sequence +1397/+1449 of the Ste1 gene formed complexes with the same male-specific protein(s) as the fragment of the Ste1 gene did. The data suggest the mapped element to participate in gender differentiation of the expression of the Ste1 and Ste2 genes.     

Characteristics of DNA sequences in the sites of permanent attachment to the nuclear matrix located in the vicinity of replication initiation site

The permanent DNA attachment sites to the nuclear matrix in the domain of chicken alpha-globin genes originally found in erythrocyte nuclei are shown to exist in sperm and cultured fibroblast cells too. Short fragments of permanently attached to the nuclear matrix DNA have been cloned and sequenced. A primary structure of a 1.7 k.b. fragment from 5'-region of chicken alpha-globin gene domain containing both replication origin and permanent attachment site has been determined. A region possessing homologies with papovaviral replication origins and putative mammalian ARS elements has been found on the 1.7 k.b. fragment. A region containing short internal repeats and GC-rich motifs has also been found. Similar motifs were observed in several of the cloned short fragments of DNA permanently attached to the nuclear matrix.     

Stimulation of transcriptional expression of human UDP-glucuronosyltransferase 1A1 by dexamethasone

Human UDP-glucuronosyltransferase (UGT) 1A1 is only enzyme in the conjugation of bilirubin for prevention of hyperbilirubinemia and jaundice. Deletion or mutation of the UGT1A1 gene causes Crigler-Najjar syndrome or Gilbert's syndrome. We previously reported the functional promoter region for expression of UGT1A1 [Hepatology Research 9, 152-163 (1997)]. We investigated the influence of some drugs on the transient transfection assay of the luciferase reporter gene containing the 5'-promoter region -3174/+14 of UGT1A1 in HepG2 cells. Among drugs investigated, dexamethasone was the most effective at the range of concentration of 10-100 microM, whereas stimulation by beta-estradiol was not found. We also could not find stimulation by bilirubin of the endogenous main substrate for UGT1A1. Stimulation by dexamethasone was continued for 48 hr. The luciferase reporter gene containing the 5'-region of -97/+14 was induced by dexamethasone but the gene of the 5'-region -53/+14 was not. The region -97/-53 is essential for induction by dexamethasone. This region contains HNF1 element, therefore, we speculated that dexamethasone directly and/or indirectly stimulates UGT1A1 expression through this HNF1 region in the promoter region of UGT1A1. Thus, we clarified that UGT1A1 was induced by dexamethasone and the key position was the region (-97/-53) in UGT1A1 promoter.     

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

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.     

Characterization of DNA pattern in the site of permanent attachment to the nuclear matrix located in the vicinity of replication origin

The permanent sites of DNA attachment to the nuclear matrix in the domain of chicken alpha-globin genes originally found in erythrocyte nuclei have also been shown to exist in sperm and cultured fibroblast cells. A primary structure of a 1.7 kb fragment located in 5'-upstream region of chicken alpha-globin gene domain and containing both replication origin and permanent nuclear matrix attachment site has been determined. It was found to possess homologies with papovaviral replication origins and contain short internal repeats and GC-rich motifs.     

Binding of 5-bromouracil-containing S/MAR DNA to the nuclear matrix.

Substitution of thymine with 5-bromouracil in DNA is known to change interaction between DNA and proteins, thereby inducing various biological phenomena. We hypothesize that A/T-rich scaffold/nuclear matrix attachment region (S/MAR) sequences are involved in the effects of 5-bromodeoxyuridine. We examined an interaction between DNA containing an intronic S/MAR sequence of the immunoglobulin heavy chain gene and nuclear halos prepared from HeLa cells. Upon substitution with 5-bromouracil, the S/MAR DNA bound more tightly to the nuclear halos. The multi-functional nuclear matrix protein YY1 was also found to bind more strongly to 5-bromouracil-substituted DNA containing its recognition motif. These results are consistent with the above hypothesis.     

Specific interactions of histone H1 and a 45 kilodalton nuclear protein with a putative matrix attachment site in the distal promoter region of a cell cycle-regulated human histone gene

Protein-DNA interactions within the promoter of a cell cycle-regulated human H4 histone gene were examined by binding of 5'-end-labeled DNA segments to Western blots of nuclear protein fractions. Specific protein interactions were observed with DNA segments located between -500 bp and -1,070 bp upstream of the ATG initiation codon and included a histone H1 binding segment flanked on both sides by binding sites for a 45 kD nuclear protein. This region of the gene contains a DNase I-sensitive site in the center (-720 to -820 bp), and sequence analysis revealed the presence of scaffold attachment sequences in the two flanking segments. Topoisomerase II consensus sequences and in vitro topoisomerase II cleavage sites were also detected in the two flanking segments. Our results suggest that the 45 kd nuclear protein may preferentially interact with these two segments of the H4 histone gene to mediate association with the nuclear matrix. The presence of negative regulatory elements in this putative matrix attachment region provides a basis for the speculation that such nuclear proteins are associated with alterations in gene-matrix interaction that are functionally related to gene expression.