G-Quadruplex Modulation of SP1 Functional Binding Sites at the KIT Proximal Promoter

Ros, Silvia Da; Nicoletto, Giulia; Rigo, Riccardo; Ceschi, Silvia; Zorzan, Eleonora; Dacasto, Mauro; Giantin, Mery; Sissi, Claudia

doi:10.3390/ijms22010329

Cited by 31 publications

(20 citation statements)

References 30 publications

(43 reference statements)

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“…We showed that CTCF binds folded G4s and consensus duplexes with comparable affinities (Figure 4). This is hardly surprising, because G4 recognition has been reported previously for other zinc-finger transcription factors with G-rich binding motifs, such as Sp1 [38,39] and MAZ [40]. The latter is functionally rather similar to CTCF, and the two work together as insulators to shape topologically associating domains (TAD) and sub-TAD domains.…”

Section: Discussionmentioning

confidence: 78%

DNA G-Quadruplexes Contribute to CTCF Recruitment

Tikhonova

Pavlova

Isaakova

et al. 2021

IJMS

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G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.

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Section: Discussionmentioning

confidence: 78%

DNA G-Quadruplexes Contribute to CTCF Recruitment

Tikhonova

Pavlova

Isaakova

et al. 2021

IJMS

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“…four ∼60 base-long oligonucleotides different in their central part (red in Figure 1 ) where the G4-forming sequences c-kit2 and c-kit* (c-kit2_TEMP and c-kit*_TEMP in Figure 1 , respectively), or their non G4-forming mutated counterparts (Blank2_TEMP and Blank*_TEMP, respectively) where inserted. The inability of the mutated sequences to form G4 is demonstrated in ( 42 ) for Blank2 and in ( 31 ) for Blank*.…”

Section: Methodsmentioning

confidence: 99%

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Vesco

Lamperti

Salerno

et al. 2021

Nucleic Acids Research

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G-quadruplexes embedded within promoters play a crucial role in regulating the gene expression. KIT is a widely studied oncogene, whose promoter contains three G-quadruplex forming sequences, c-kit1, c-kit2 and c-kit*. For these sequences available studies cover ensemble and single-molecule analyses, although for kit* the latter were limited to a study on a promoter domain comprising all of them. Recently, c-kit2 has been reported to fold according to a multi-step process involving folding intermediates. Here, by exploiting fluorescence resonance energy transfer, both in ensemble and at the single molecule level, we investigated the folding of expressly designed constructs in which, alike in the physiological context, either c-kit2 or c-kit* are flanked by double stranded DNA segments. To assess whether the presence of flanking ends at the borders of the G-quadruplex affects the folding, we studied under the same protocols oligonucleotides corresponding to the minimal G-quadruplex forming sequences. Data suggest that addition of flanking ends results in biasing both the final equilibrium state and the folding kinetics. A previously unconsidered aspect is thereby unravelled, which ought to be taken into account to achieve a deeper insight of the complex relationships underlying the fine tuning of the gene-regulatory properties of these fascinating DNA structures.

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“…Interestingly, G4s are often located in promoter sequences as shown for many human genes [69][70][71], including P53 targets; in fact, the presence of G4 prone sequences has been found around P53 RE in the promoter of the P53-induced apoptotic PUMA protein [34]. Therefore, the presence and the formation of a G4 structure could be an important transcriptional regulatory element, as previously observed in various organisms including humans [72][73][74].…”

Section: Discussionmentioning

confidence: 63%

Evaluating the Influence of a G-Quadruplex Prone Sequence on the Transactivation Potential by Wild-Type and/or Mutant P53 Family Proteins through a Yeast-Based Functional Assay

Monti

Brázda

Bohálová

et al. 2021

Genes

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P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at C-terminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and N-terminal truncated P53 family α isoforms (wild-type and mutant). Our results show that the presence of a G4 prone sequence upstream or downstream of the P53 RE leads to significant changes in the relative activity of P53 family proteins, emphasizing the potential role of structural DNA features as modifiers of P53 family functions at target promoter sites.

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G-Quadruplex Modulation of SP1 Functional Binding Sites at the KIT Proximal Promoter

Cited by 31 publications

References 30 publications

DNA G-Quadruplexes Contribute to CTCF Recruitment

DNA G-Quadruplexes Contribute to CTCF Recruitment

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Evaluating the Influence of a G-Quadruplex Prone Sequence on the Transactivation Potential by Wild-Type and/or Mutant P53 Family Proteins through a Yeast-Based Functional Assay

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