In eukaryotic cells, proper transcriptional regulation depends upon transcription factors (TFs) that bind to specific DNA-binding sites (Kadonaga, 2004).
NF-κB complexes are then translocated into the nucleus, bind to specific DNA-binding sites and regulate the transcription of target genes [ 15] including various anti-apoptotic proteins, but also several pro-apoptotic molecules, consistent with reports that NF-κB can promote apoptosis under certain circumstances [ 16, 17].
In the absence of NICD, RBP-J is bound to specific DNA binding sites ((C/T GTGGAA) and is thought to act as a transcriptional repressor due to its ability to bind transcriptional corepressors (NCoRs) and histone deacetylases (HDACs).
Histone proteins, for example, serve as structural DNA elements, binding ubiquitously throughout the genome with little sequence-based discrimination, while transcription factors, another class of DNA-binding proteins, selectively bind to specific DNA sequences within the genome where they help to control the expression of target loci.
As a result of ligand binding these receptors bind to specific DNA sequences, either ERE 3 or androgen response element, in their target genes, and recruit transcription factors, resulting in hormone-stimulated transcription (Fig. 2a).
Both HIF-1 subunits contain a basic helix-loop-helix domain, enabling them to recognize and bind to specific DNA sequences, called HIF-1 DNA binding sites (HBSs), within the regulatory regions of hypoxia-inducible genes.
DNA methylation and histone modifications affect gene expression by changing the profiles of proteins that bind to specific DNA regions; for example, the binding profiles of transcription factors to promoter regions.
To capture the capability of a protein to bind to specific DNA sequences, a GO MF term that describes 'sequence-specific DNA binding' (e.g. GO 0043565 'sequence-specific DNA binding') should be used.
According to the simplified model, upon ligand binding PPAR/RXR heterodimers recognize and bind to specific DNA sequences, called PPAR response elements (PPRE) [40].
Furthermore, such compounds that bind to specific DNA sequences may not only control the expression of specific genes but also exert other mechanisms in the anti-cancer effect than those of classical DNA binding drugs.
FOXG1 contains a highly conserved DNA-binding domain, which binds to specific DNA sequences and regulates gene expression (Yao et al, 2001).
