KIT promoter: Structure, function and targeting

Ceschi, Silvia; Sissi, Claudia

doi:10.1016/bs.armc.2020.04.006

Cited by 6 publications

(9 citation statements)

References 89 publications

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“…These results suggest that whether the binding of SP1 at kit* appears to be required for the enhancement of gene expression observed in the absence of G-quadruplex folding, it is dispensable for the onset of gene expression. This picture fits with the confirmed presence of multiple transcription factor binding sites along the WT KIT promoter domain inserted in the plasmid that can support the basal expression of the protein [ 12 , 20 , 22 ].…”

Section: Resultssupporting

confidence: 76%

“…Accumulating evidence suggests that these higher order arrangements might work as regulatory elements to control gene transcription [ 9 , 10 ]. In the case of KIT , the G4s formation at the promoter has been associated with a reduction in the corresponding coded protein expression [ 11 , 12 ]. The high-resolution structures of kit1, kit2 and kit* G4 have been solved [ 6 , 7 , 13 , 14 , 15 , 16 ], thus paving the way to a rational design of new ligands able to stabilize them and, ultimately, to silence the gene in the cell.…”

Section: Introductionmentioning

confidence: 99%

“…This approach optimally prevented G4 formation, thus allowing the identification of sites where the DNA conformational shift from double strand to G4 can maximally impair the gene transcription. However, according to the proposed design, a suppression of gene expression can also derive from the concurrent modification of consensus sequences for the multiple transcription factors that bind this promoter region [ 12 ]. An interesting example is represented by SP1, a transcription factor that can drive KIT transcription either alone or in complex with other regulator factors (i.e., GATA-2) [ 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

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

Ros

Nicoletto

Rigo

et al. 2020

IJMS

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The regulation of conformational arrangements of gene promoters is a physiological mechanism that has been associated with the fine control of gene expression. Indeed, it can drive the time and the location for the selective recruitment of proteins of the transcriptional machinery. Here, we address this issue at the KIT proximal promoter where three G-quadruplex forming sites are present (kit1, kit2 and kit*). On this model, we focused on the interplay between G-quadruplex (G4) formation and SP1 recruitment. By site directed mutagenesis, we prepared a library of plasmids containing mutated sequences of the WT KIT promoter that systematically exploited different G4 formation attitudes and SP1 binding properties. Our transfection data showed that the three different G4 sites of the KIT promoter impact on SP1 binding and protein expression at different levels. Notably, kit2 and kit* structural features represent an on-off system for KIT expression through the recruitment of transcription factors. The use of two G4 binders further helps to address kit2-kit* as a reliable target for pharmacological intervention.

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Section: Resultssupporting

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Ros

Nicoletto

Rigo

et al. 2020

IJMS

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“…An increase in the expression of this gene is frequently associated with many forms of cancer, such as mastocytosis, gastrointestinal stromal tumours, lung cancer and leukemia ( 34 ). The regulation of KIT transcription levels appears to be largely dependent on the formation of three distinct G4 structures within the proximal promoter of the gene: kit2, kit* and kit1 ( 35 , 36 ). Accumulating evidence indicates that there is a reduction in KIT expression upon G4 formation at these sites ( 37 , 38 ).…”

Section: Introductionmentioning

confidence: 99%

Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene

Buglione

Salerno

Marrano

et al. 2021

Nucleic Acids Research

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G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.

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“…The promoter of the KIT proto-oncogene is among the most characterized to this regard ( 24 ). Upstream the transcription initiation site (TIS), it contains three distinct sites capable of folding into G4 structures, namely the sequence between bases −87 and −108, usually referred to as c-kit1 ( 25 , 26 ), the one comprised between bases −138 and −158, called c-kit2 ( 26–30 ), and that delimited by bases −115 and −136, named c-kit* ( 31 , 32 ).…”

Section: Introductionmentioning

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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KIT promoter: Structure, function and targeting

Cited by 6 publications

References 89 publications

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

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

Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene

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

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