A Database for Nuclear Receptor DNA Binding Sites

Abstract

A database has been developed for nuclear receptor DNA binding sites and the corresponding nuclear receptor DNA binding domain (DBD) amino acid sequences. This database contains three main tables nuclear receptor DNA footprints, nuclear receptor DNA binding sites and the corresponding nuclear receptor DBD. The ultimate goal of this database is to provide a repository for all experimentally derived nuclear receptor DNA binding sites. Finite DNA binding sites and footprints are obtained from original peer reviewed research that used selected experimental methods to identify nuclear receptor DNA binding sites. Acceptable methods for the identification of DNA binding sites and/or footprints include reporter genes and DNA deletion analysis, DNAase I footprinting, exonuclease III footprinting, methylation protection, methylation interference, nuclear receptor protein mutagenesis and the electrophoretic mobility shift assay. With respect to this database, a nuclear receptor footprint is a DNA sequence less than 50 nucleotides in length identified by one of the methods listed above. A binding site is a DNA sequence identified within one of the footprints that is less than 15 nucleotides in length and corresponds to a previously identified half site, response element or consensus sequence. The five prime and three prime location of each footprint with respect to the transcription initiation site is noted in the database. The corresponding nuclear receptor DBD amino acid sequence is obtained from the Swiss-Prot database. The nuclear receptor data is annotated with the literature reference, DNA source, DNA binding site identification method, the nuclear receptor Swiss-Prot primary accession number, and inter halfsite spacing if specified. The tables are related by the literature reference, DNA source, experimental method and nuclear receptor ID. Sixty one publications have been identified from 1983 through 1994 that contain nuclear receptor binding sequences identified with one of the methods listed above. These publications were identified by selected review articles, cited references, citation index and PubMed searches. Currently, the database contains 21 DNA binding sites and 30 DNA footprints from 14 publications between 1983 and 1987. As the database expands, the literature citations will be used to design new search strategies for the nuclear receptor literature. After the current literature has been surveyed and the database is up to date, submissions will be accepted from past and future research. This database will eventually become publicly accessible. In order to interpret the experimentally derived DNA footprints, the specific DNA base - NR protein interactions are summarized from six X ray crystallographic studies.