Inhibition and enhancement of eukaryotic gene expression by potential non-B DNA sequences

Specialized DNA Structures Act as Genomic Beacons for Integration by Evolutionarily Diverse Retroviruses

Retroviral integration site targeting is not random and plays a critical role in expression and long-term survival of the integrated provirus. To better understand the genomic environment surrounding retroviral integration sites, we performed a meta-analysis of previously published integration site data from evolutionarily diverse retroviruses, including new experimental data from HIV-1 subtypes A, B, C and D. We show here that evolutionarily divergent retroviruses exhibit distinct integration site profiles with strong preferences for integration near non-canonical B-form DNA (non-B DNA). We also show that in vivo-derived HIV-1 integration sites are significantly more enriched in transcriptionally silent regions and transcription-silencing non-B DNA features of the genome compared to in vitro-derived HIV-1 integration sites. Integration sites from individuals infected with HIV-1 subtype A, B, C or D viruses exhibited different preferences for common genomic and non-B DNA features. In addition, we identified several integration site hotspots shared between different HIV-1 subtypes, all of which were located in the non-B DNA feature slipped DNA. Together, these data show that although evolutionarily divergent retroviruses exhibit distinct integration site profiles, they all target non-B DNA for integration. These findings provide new insight into how retroviruses integrate into genomes for long-term survival.

G-Quadruplex DNA and Other Non-Canonical B-Form DNA Motifs Influence Productive and Latent HIV-1 Integration and Reactivation Potential

The integration of the HIV-1 genome into the host genome is an essential step in the life cycle of the virus and it plays a critical role in the expression, long-term persistence, and reactivation of HIV expression. To better understand the local genomic environment surrounding HIV-1 proviruses, we assessed the influence of non-canonical B-form DNA (non-B DNA) on the HIV-1 integration site selection. We showed that productively and latently infected cells exhibit different integration site biases towards non-B DNA motifs. We identified a correlation between the integration sites of the latent proviruses and non-B DNA features known to potently influence gene expression (e.g., cruciform, guanine-quadruplex (G4), triplex, and Z-DNA). The reactivation potential of latent proviruses with latency reversal agents also correlated with their proximity to specific non-B DNA motifs. The perturbation of G4 structures in vitro using G4 structure-destabilizing or -stabilizing ligands resulted in a significant reduction in integration within 100 base pairs of G4 motifs. The stabilization of G4 structures increased the integration within 300-500 base pairs from G4 motifs, increased integration near transcription start sites, and increased the proportion of latently infected cells. Moreover, we showed that host lens epithelium-derived growth factor (LEDGF)/p75 and cleavage and polyadenylation specificity factor 6 (CPSF6) influenced the distribution of integration sites near several non-B DNA motifs, especially G4 DNA. Our findings identify non-B DNA motifs as important factors that influence productive and latent HIV-1 integration and the reactivation potential of latent proviruses.

Association of HO-1 (GT)n Promoter Polymorphism and Cardiovascular Disease: A Reanalysis of the Literature

BACKGROUND

Heme-oxygenase 1 (HO-1), an inducible heme-degrading enzyme, has antiatherogenic effects through its enzymatic end products. HO-1 gene expression is modulated by a guanidine thymidine dinucleotide ([GT]n) repeat polymorphism in the promoter region. Shorter repeats with (GT)n < 25 are associated with higher inducibility and activity of HO-1.

METHODS

We performed a systematic review of all literature from 1997 to 2013 on the association of the HO-1 (GT)n and cardiovascular disease (CVD). On the basis of predefined criteria (patient characteristics, genotype data format, allelic distribution, repeat length cutoff) 41 articles were selected. Patients were redistributed into 4 homogeneous subpopulations: patients with CVD (CVD group), patients without CVD (nonCVD), 'controls' with unknown cardiovascular status (unspecified) and children younger than 20 years of age (unselected). Genotype distributions (homozygous short [SS] or long [LL], and heterozygous) of the 4 patient categories were compared and odds ratios (ORs) for CVD were calculated using logistic regression analysis.

RESULTS

Overall, the proportion of the SS genotype was lower in CVD compared with nonCVD and unspecified. The ORs for CVD was highest in patients carrying the LL genotype (OR LL vs SS, 1.769 [95% confidence interval, 1.594-1.963]). Furthermore, genotype distribution differed between Caucasian and Asian individuals, the latter having a much higher proportion of the SS genotype (22% vs 11%).

CONCLUSIONS

This review of the available literature on the epidemiological association between the HO-1 (GT)n repeat polymorphism and CVD supports the presumed protective effects of HO-1. The second but probably even more relevant finding of our review is that racial disparities in HO-1 (GT)n repeat length distribution exist and might influence the associations of the genotype with CVD status.

Mapping of intrinsic bent DNA sites in the upstream region of DNA puff BhC4-1 amplified gene

We have identified bent DNA sites in the distal and proximal DNA puff BhC4-1 amplified gene promoter region of Bradysia hygida. The 2D modeling of the 3D DNA path and the ENDS ratio values calculated in this promoter region resulted in the identification of ten pronounced bent sites named BhC4B - 9 to + 1. The 1847 bp fragment (- 3697 to - 1850) in relation to the transcription start site shows multiple bending sites, BhC4B - 9 to BhC4B - 4, with periodicity approximately 300 bp. The analysis of the other identified bent region, starting at position - 957, reveals that the BhC4B + 1 bent site colocalizes with the putative BhC4-1 minimal promoter. The sequence analysis of bent site BhC4B - 4 shows a distribution of dA*dT at approximately 10 bp intervals between the middle of each tract, but intervals with more than one turn, approximately 20 bp, two helix turns, were detected in the other bent sites described here. The bent sites BhC4B - 6 and BhC4B - 4, contain two consensus sequences, with 60 bp each. The apparent molecular weight of fragments in the BhC4-1 promoter region were estimated in agarose gels and compared with the data obtained in polyacrylamide gels without and with ethidium bromide. The mobility reduction ratios (R-values) were determined, and a high R-value, 1.80, for a 1215 bp fragment in the distal promoter region and a 1.23 significant R-value for a 662 bp fragment in the proximal segment were found. To further analyze the predicted bent DNA sites in these fragments, the 2D trajectories of the 3D DNA path and other parameters, AT percentage, roll angle, ENDS ratio and DeltaG, were determined. The role of these bent sites in the BhC4-1 transcription regulation is discussed.

Polyamine-induced Z-DNA conformation in plasmids containing (dA-dC)n.(dG-dT)n inserts and increased binding of lupus autoantibodies to the Z-DNA form of plasmids

Blocks of potential Z-DNA-forming (dA-dC)n.(dG-dT)n sequences are ubiquitous in eukaryotic genomes. We examined whether naturally occurring polyamines, putrescine, spermidine and spermine, could provoke the Z-DNA conformation in plasmids pDHf2 and pDHf14 with 23 and 60 bp inserts respectively of (dA-dC)n.(dG-dT)n sequences using an e.l.i.s.a. Spermidine and spermine could provoke Z-DNA conformation in these plasmids, but putrescine was ineffective. For pDHf2 and pDHf14, the concentration of spermidine at the midpoint of B-DNA to Z-DNA transition was 25 microM, whereas that of spermine was 16 microM. Polyamine structural specificity was evident in the ability of spermidine homologues to induce Z-DNA. Inorganic cations, Co(NH3)6(3+) and Ru(NH3)6(3+), were ineffective. Our experiments also showed increased binding of anti-DNA autoantibodies from lupus patients as well as autoimmune MRL-lpr/lpr mice to pDHf2 and pDHf14 in the presence of polyamines. These data demonstrate that small blocks of (dA-dC)n.(dG-dT)n sequences could assume the Z-DNA conformation in the presence of natural polyamines. Increased concentrations of polyamines in the sera of lupus patients might facilitate immune complex-formation involving circulating DNA and anti-Z-DNA antibodies.

Structural specificity of polyamines in modulating the binding of estrogen receptor to potential Z-DNA forming sequences

Estrogen receptor (ER) is a gene-regulatory protein that mediates the action of estradiol. In order to examine the role of conformational dynamics of DNA in estrogenic regulation of gene expression, we studied the binding of ER to poly(dA-dC).poly(dG-dT) which undergoes transition to a left-handed Z-DNA form. This type of dinucleotide repeats are widely distributed in mammalian genome and are present in estrogen response elements. Binding affinity of ER for the polynucleotide was assessed by its ability to release ER bound to DNA-cellulose. ER binding by poly(dA-dC).poly(dG-dT) was enhanced in the presence of an endogenous polyamine, spermidine, H2N(CH2)4NH(CH2)3NH2. The concentration of spermidine required for facilitating 50% elution of ER (EC50) was 75 microM. This EC50 increased to 500 microM for a spermidine homolog, H2N(CH2)8NH(CH2)3NH2, demonstrating polyamine structural specificity. Spectroscopic measurements showed that the presence of 100-200 microM spermidine initiated changes in the conformation of the polynucleotide indicative of Z-DNA form, but a major alteration to Z-DNA spectrum occurred only at 300 microM concentration. These data suggest that ER favors DNA sequences poised for Z-DNA transition. The efficacy of spermidine homologs in facilitating ER-DNA interaction may be important in predicting their efficiency to replace cellular functions of spermidine.

Preferential alteration of inducible gene expression in vivo by carcinogens that induce bulky DNA lesions

Our laboratory is interested in whether chemical carcinogen-induced DNA damage is nonrandomly distributed in the genome, i.e., "targeted," at the level of individual genes. To examine this, we have been investigating whether carcinogen treatment in vivo differentially alters the expression of specific genes. In this study, we examined the effects of four model carcinogens that induce bulky lesions in DNA--benzo[a]pyrene (B[a]P), aflatoxin B1 (AFB1), 7,12-dimethylbenz[a]anthracene (DMBA), and 2-acetylaminofluorene (AAF)--on the steady-state mRNA expression of several constitutive and drug-inducible genes in vivo. We specifically tested the hypothesis that carcinogen-induced DNA damage is preferentially targeted to inducible genes relative to constitutively expressed genes using the chick embryo as a simple in vivo test system. In summary, the four carcinogens had no effect on the steady-state mRNA expression of constitutively expressed beta-actin, transferrin, or albumin genes over a 24-h period after a single dose of each carcinogen. In contrast, each of these same treatments significantly altered the mRNA expression of two glutethimide-inducible genes, ALA synthase and CYP2H1. Both the basal expression of these genes and their drug-inducible expression was altered. B[a]P and AFB1 had similar effects on expression of the two inducible genes and caused similar levels of covalent adducts in total DNA, even though the administered doses differed by 30-fold. B[a]P binding to DNA, and the basal expression of CYP2H1 were similar in liver and lung. However, B[a]P significantly altered basal CYP2H1 mRNA expression in liver, a tissue in which this gene is highly inducible by glutethimide, and had no effect on basal CYP2H1 mRNA expression in lung, a tissue in which this gene is not drug-inducible. These data support the hypothesis that inducible gene expression is a target for carcinogen-induced DNA damage in vivo.

Cloning and 5'-flanking sequence of a rat cholesterol 7 alpha-hydroxylase gene

A cholesterol 7 alpha-hydroxylase gene containing 8 kb of the 5'-flanking region and 5 kb of the transcription region which covers exons 1 to 5 was isolated from a rat genomic library. The 2015 bp nucleotide sequence 5'-upstream from the start codon was determined. This promotor region contains many liver-enriched or -specific elements (TGT3, HNF/LF-B1), putative hormone responsive elements (TRE, GRE, RRE or RARE) and ubiquitous transcription factor binding sites (NF-1, OCT-1). In addition, 21 CA repeats which have potential to form the Z-DNA structure were found in this region. These putative regulatory elements and repetitive motifs may play roles in the regulation of cholesterol 7 alpha-hydroxylase gene in the liver. The sequence identity of the rat gene to the human gene in this region is low. Only liver-enriched elements are conserved in the cholesterol 7 alpha-hydroxylase genes.