A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro.
SP1 is a ubiquitous transcription factor that is involved in the regulation of various house-keeping genes. It is known that it acts by binding to a double-stranded consensus motif. Here, we have discovered that SP1 binds also to a non-canonical DNA structure, a G-quadruplex, with high affinity. In particular, we have studied the SP1 binding site within the promoter region of the c-KIT oncogene and found that this site can fold into an anti-parallel two-tetrad G-quadruplex. SP1 pull-down experiments from cellular extracts, together with biophysical binding assays revealed that SP1 has a comparable binding affinity for this G-quadruplex structure and the canonical SP1 duplex sequence. Using SP1 ChIP-on-chip data sets, we have also found that 87% of SP1 binding sites overlap with G-quadruplex forming sequences. Furthermore, while many of these immuoprecipitated sequences (36%) even lack the minimal SP1 consensus motif, 5'-GGGCGG-3', we have shown that 77% of them are putative G-quadruplexes. Collectively, these data suggest that SP1 is able to bind both, canonical SP1 duplex DNA as well as G-quadruplex structures in vitro and we hypothesize that both types of interactions may occur in cells.
Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Eun-Ang
EA
Raiber
Ramon
R
Kranaster
Enid
E
Lam
Mehran
M
Nikan
Shankar
S
Balasubramanian
D001665:Binding Sites; D054856:G-Quadruplexes; D016678:Genome; D006367:HeLa Cells; D006801:Humans; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics; D016329:Sp1 Transcription Factor / Q000378:metabolism*
D016329:Sp1 Transcription Factor; D019009:Proto-Oncogene Proteins c-kit