DNase I- and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific.

Levy-Wilson, Beatriz; Fortier, Catherine; Blackhart, Brian D.; McCarthy, Brian J.

doi:10.1128/mcb.8.1.71

Cited by 57 publications

(45 citation statements)

References 42 publications

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“…Some of the identified AT islands have been experimentally shown to function as MARs. Examples include the c-Myc MAR (29) and the ApoB MAR (30). Our preliminary results confirm also that the Z79699/AF385609 AT island, the "hottest" identified region for bizelesin binding motifs, binds specifically to the isolated nuclear matrix, and hence functions as an in vitro MAR.…”

Section: Discussionsupporting

confidence: 68%

“…However, the AT islands in GenBank™ sequences X04682 and X00364 correspond precisely to the known AT-rich MAR domains in the apoB and c-myc genes, respectively (29,30). The potential bizelesin targets also include AT islands in the AT-rich fragile sites (31), FRA16D (in Gen- Bank™ AF217490, with a total of 60 bizelesin cross-linking sites, Table II) and FRA16B (see on-line supplement).…”

Section: Long Range Distribution Of Bizelesin Binding Motifsmentioning

confidence: 99%

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AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs

Woynarowski¹,

Treviño²,

Rodriguez³

et al. 2001

Journal of Biological Chemistry

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Interstrand cross-links at T(A/T) 4 A sites in cellular DNA are associated with hypercytotoxicity of an anticancer drug, bizelesin. Here we evaluated whether these lethal effects reflect targeting critical genomic regions. An in silico analysis of human sequences showed that T(A/T) 4 A motifs are on average scarce and scattered. However, significantly higher local motif densities were identified in distinct minisatellite regions (200 -1000 base pairs of ϳ85-100% AT), herein referred to as "AT islands." Experimentally detected bizelesin lesions agree with these in silico predictions. Actual bizelesin adducts clustered within the model AT island naked DNA, whereas motif-poor sequences were only sparsely adducted. In cancer cells, bizelesin produced high levels of lesions (ϳ4.7-7.1 lesions/kilobase pair/M drug) in several prominent AT islands, compared with markedly lower lesion levels in several motif-poor loci and in bulk cellular DNA (ϳ0.8 -1.3 and ϳ0.9 lesions/kilobase pair/M drug, respectively). The identified AT islands exhibit sequence attributes of matrix attachment regions (MARs), domains that organize DNA loops on the nuclear matrix. The computed "MAR potential" and propensity for supercoiling-induced duplex destabilization (both predictive of strong MARs) correlate with the total number of bizelesin binding sites. Hence, MAR-like ATrich non-coding domains can be regarded as a novel class of critical targets for anticancer drugs.

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Section: Discussionsupporting

confidence: 68%

Section: Long Range Distribution Of Bizelesin Binding Motifsmentioning

confidence: 99%

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs

Woynarowski¹,

Treviño²,

Rodriguez³

et al. 2001

Journal of Biological Chemistry

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“…Tissue Culture and Transient Transfection Assays-Human hepatoma cells (HepG2), Chinese hamster ovary (CHO) cells, and HeLa cells were grown as described previously (18). Transient transfections with the various plasmid constructs were performed by the calcium phosphate coprecipitation method as described previously (19) with 7 g of the CAT gene expression plasmid and 6 g of an internal reference plasmid (pRSV␤-gal).…”

Section: Methodsmentioning

confidence: 99%

“…DNase I Hypersensitivity-DNase I hypersensitivity studies were performed as described by Levy-Wilson et al (18).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Hepatic-specific Regulatory Elements in the Promoter Region of the Human Cholesterol 7α-Hydroxylase Gene

Cooper

Chen

Botelho-Yetkinler

et al. 1997

Journal of Biological Chemistry

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Cholesterol 7␣-hydroxylase is the rate-limiting enzyme in the degradation of cholesterol to bile salts and plays a central role in regulating cholesterol homeostasis. The mechanisms involved in the transcriptional control of the human gene are largely unknown. HepG2 cells represent an appropriate model system for the study of the regulation of the gene. To identify liverspecific DNA sequences in the promoter of the human CYP7 gene, we first examined the DNase I hypersensitivity in the 5 -region of the gene. An area of hypersensitivity was observed in the region from ؊50 to ؊200 of the human gene in nuclei from transcriptionally active HepG2 cells, but was absent in transcriptionally inactive HeLa cell nuclei or in free DNA. Various 5 -promoter deletion constructs were made and transfected into HepG2 cells. About 300 base pairs of upstream sequence are required for high level promoter activity of the human CYP7 gene in HepG2 cells. DNase I footprinting of the hypersensitive region revealed nine protected sequences. Gel retardation experiments demonstrated binding of HNF-3 to the segment from ؊80 to ؊70 and of hepatocyte nuclear factor HNF-4 (and ARP-1) to the segment from ؊148 to ؊127 of the human CYP7 promoter. Deletion of either of these sites depressed promoter activity in HepG2 cells. A third region from ؊313 to ؊285 is bound by members of the HNF-3 family and acts as an enhancer. Additionally, the segment from ؊197 to ؊173 binds a negative regulatory protein that is present in Chinese hamster ovary cell extracts and in HepG2 cell extracts. These experiments define the key control elements responsible for basal transcription of the human CYP7 gene in HepG2 cells.Cholesterol 7␣-hydroxylase catalyzes the rate-limiting step in the pathway that leads to the catabolism of cholesterol to bile acids (for review, see Ref. 1). Cholesterol 7␣-hydroxylase is a microsomal enzyme member of the cytochrome P-450 family. In human and rat, the major products of this metabolic pathway are cholic acid and chenodeoxycholic acid. Bile acids have an important role in cholesterol homeostasis; their synthesis and excretion cause a decrease in hepatic cholesterol levels, while their presence in the intestine facilitates the solubilization of dietary fats and is required for the absorption of cholesterol and fat-soluble vitamins. Because of the importance of these functions, bile acid synthesis in the liver is carefully regulated to maintain cholesterol homeostasis (1). To date, little is known about the molecular mechanisms that control cholesterol catabolism and bile acid synthesis.The cDNAs and genes for cholesterol 7␣-hydroxylase have been isolated from rat (2-4), human (5, 6), hamster (7), and mouse (8). CYP7 mRNA is found exclusively in the liver (9), making this gene a target for the study of the molecular mechanisms implicated in hepatic-specific gene expression. Work by several groups has demonstrated that CYP7 mRNA levels are modulated in cultured cells by a number of effectors. For example, in cultured rat hepatocytes (10) ...

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“…DNA was extracted from soluble chromatin fractions [11] and analysed on 1.5% agamse gel. It was then Southern transferred and processed for hybridization.…”

Section: Methodsmentioning

confidence: 99%

Age‐related analysis of EcoRI generated satellite DNA‐containing chromatin of rat liver

1996

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SummaryEcoRI digestion of nuclei and their subsequent lysis with EDTA solubilizes 45% and 36% of chromatin DNA from the liver of young (18+2 weeks) and old (100+5 weeks) rats, respectively. After hybridization with 185 bp rat satellite I DNA, these soluble fractions are found to be enriched in specific DNA sequences such as satellite DNA. Besides regular repeat pattern, a major portion of the satellite chromatin forms higher order organization Digestion kinetics confirms condensation of satellite DNAcontaining chromatin similar to that of bulk chromatin in old age. Furthermore, densitometric scanning of the slot-blot of soluble chromatin fractions reveals loss of satellite DNA in the okL However, an increase in the linker histone HI and its subfraction HI ° in the satellite DNA-emiched fraction of chromatin from old rats suggests greater compaction. These results provide the first evidence that the satellite DNAcontaining chromatin differs in the liver of young and old rats.

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DNase I- and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific.

Cited by 57 publications

References 42 publications

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs

Characterization of Hepatic-specific Regulatory Elements in the Promoter Region of the Human Cholesterol 7α-Hydroxylase Gene

Age‐related analysis of EcoRI generated satellite DNA‐containing chromatin of rat liver

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