Open AccessA non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro
Author(s) -
EunAng Raiber,
Ramon Kranaster,
Enid Y.N. Lam,
Mehran Nikan,
Shankar Balasubramanian
Publication year - 2011
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkr882
Subject(s) - biology , sp1 transcription factor , transcription factor , dna , binding site , consensus sequence , genetics , dna binding protein , transcription (linguistics) , promoter , structural motif , microbiology and biotechnology , gene , biochemistry , gene expression , base sequence , linguistics , philosophy
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.