Definition and prediction of the full range of transcription factor binding sites--the hepatocyte nuclear factor 1 dimeric site.

ABSTRACT: In animals, transcription factor binding sites are hard to recognize because of their extensive variation. We therefore characterized the general relationship between a specific protein-binding site and its DNA sequence and used this relationship to generate a predictive algorithm for searching other DNA sequences. The experimental process was defined by studying hepatocyte nuclear factor 1 (HNF1), which binds DNA as a dimer on two inverted-repeat 7-bp half sites separated by one base. The binding model was based on the equivalence of the two half sites, which was confirmed in examples where specific modified sites were compared. Binding competition analysis was used to determine the effects of substitution of all four bases at each position in the half site. From these data, a weighted ha

SUBMITTER: Locker J 

PROVIDER: S-EPMC137408 | biostudies-literature | 2002 Sep

REPOSITORIES: biostudies-literature