Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2′-Deoxyguanosine

Abstract

Sequences of DNA typically adopt B-form duplexes in genomes, although noncanonical structures such as G-quadruplexes, imotifs, Z-DNA, and cruciform structures can occur. A challenge is to determine the functions of these various structures in cellular processes. We and others have hypothesized that G-rich G-quadruplex-forming sequences in human genome promoters serve to sense oxidative damage generated during oxidative stress impacting gene regulation. Herein, chemical tools and a cell-based assay were used to study the oxidation of guanine to 8-oxo-7,8-dihydroguanine (OG) in the context of a cruciformforming sequence in a gene promoter to determine the impact on transcription. We found that OG in the nontemplate strand in the loop of a cruciform-forming sequence could induce gene expression; conversely when OG was in the same sequence on the template strand, gene expression was inhibited. A model for the transcriptional changes observed is proposed in which OG focuses the DNA repair process on the promoter to impact expression. Our cellular and biophysical studies and literature sources support the idea that removal of OG from duplex DNA by OGG1 yields an abasic site (AP) that triggers a structural shift to the cruciform fold. The AP-bearing cruciform structure is presented to APE1, which functions as a conduit between DNA repair and gene regulation. The significance is enhanced by a bioinformatic study of all human gene promoters and transcription termination sites for inverted repeats (IRs). Comparison of the two regions showed that promoters have stable and G-rich IRs at a low frequency and termination sites have many AT-rich IRs with low stability.

Oxidative DNA Damage and Cisplatin Neurotoxicity Is Exacerbated by Inhibition of OGG1 Glycosylase Activity and APE1 Endonuclease Activity in Sensory Neurons

“…G-quadruplexes (G4) are secondary structures of guanine-rich nucleic acids that form a helical structure due to guanine: guanine interactions and are commonly seen in promoter regions, 5 and 3 untranslated regions, and within telomeric regions of DNA [54]. In addition to G-quadruplexes, oxidative DNA damage has also been shown to alter cruciform DNA sequences in the promoter elements of genes [55]. The formation of G4 and cruciform structures can enhance or repress the transcription of genes, depending on whether the secondary structure forms within the template or nontemplate strands [55,56], thus oxidation-induced increases in DNA secondary structures provide another means by which oxidative damage alters gene transcription.…”

“…In addition to G-quadruplexes, oxidative DNA damage has also been shown to alter cruciform DNA sequences in the promoter elements of genes [55]. The formation of G4 and cruciform structures can enhance or repress the transcription of genes, depending on whether the secondary structure forms within the template or nontemplate strands [55,56], thus oxidation-induced increases in DNA secondary structures provide another means by which oxidative damage alters gene transcription. Recent reports suggest that APE1 binding to AP sites within G4 sequences increases the folding of DNA into G4 structures and maintenance of APE1 binding, via APE1 acetylation, stabilizes the G4 and increases transcription factor recruitment to the promoter [29].…”

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

“…For example, a cruciform DNA nanostructure is used for targeted delivery of doxorubicin to cancer cells [ 121 ] and was used to treat colon cancer [ 122 ]. It has also been demonstrated that cruciforms in gene promoters impact transcription upon oxidative modification of 2’-Deoxyguanosine [ 123 ]. The association of cruciforms with the regulation of transcription [ 90 ], as discussed above, opens other therapeutic windows where the specific levels of gene expression are influenced by the their presence and stability in promoter regions.…”

Evolution of Diverse Strategies for Promoter Regulation

“…Also, it is now clear that non-B-DNA structures are powerful determinants of mutagenesis [106]. There are an abundance of non-B-DNA structures [36], but those that are particularly relevant to gene promoter regions are G-quadruplexes [46,47], i-motifs [65,66], cruciforms [69], triplexes [107], and Z-DNA [108], as illustrated in Figure I. These local non-B-DNA structures are often targets of protein binding, including various transcription factors [109][110][111].…”

“…Other non-B-DNA structures shown to be important in promoters are hairpins and the cruciforms, which can be formed by inverted repeat sequences that are abundant in many genomes [34,36,69]. Hairpins and cruciforms serve as effective targets for several regulatory proteins, including transcription factors such as p53 and p73 [70][71][72].…”