Combining chromatin immunoprecipitation and DNA footprinting: a novel method to analyze protein–DNA interactions in vivo
| Autor: | Jörg Bungert, Sung-Hae Lee Kang, Karen F. Vieira |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2002 |
| Předmět: |
Immunoprecipitation
Molecular Sequence Data DNA Footprinting DNA footprinting Biology chemistry.chemical_compound NF-E2 Transcription Factor Genetics Tumor Cells Cultured Animals Humans Promoter Regions Genetic NAR Methods Online Base Sequence Protein footprinting DNA Molecular biology Precipitin Tests Footprinting Chromatin Cell biology Globins DNA-Binding Proteins chemistry NF-E2 Transcription Factor p45 Subunit Erythroid-Specific DNA-Binding Factors Upstream Stimulatory Factors DNase footprinting assay Chromatin immunoprecipitation Protein Binding Transcription Factors |
| Popis: | A variety of methods are available to analyze protein-DNA interactions in vivo. Two of the most prominent of these methods are chromatin immunoprecipitation (ChIP) and in vivo footprinting. Both of these procedures have specific limitations. For example, the ChIP assay fails to document where exactly a protein binds in vivo. The precipitation of a specific segment of DNA with antibodies directed against DNA-binding proteins does not necessarily indicate that the protein directly interacts with a sequence in the precipitate but could rather reflect protein-protein interactions. Furthermore, the results of in vivo footprinting studies are inconclusive if a DNA sequence is analyzed that is bound by a specific protein in only a certain fraction of cells. Finally, in vivo footprinting does not indicate which protein is bound at a specific site. We have developed a new procedure that combines the ChIP assay and DMS footprinting techniques. Using this method we show here that antibodies specific for USF1 and NF-E2 precipitate the murine beta-globin promoter in MEL cells. DMS footprinting analysis of the DNA precipitated with NF-E2 antibodies revealed a protection over a partial NF-E2-binding site in the beta-globin downstream promoter region. We believe that this novel method will generally benefit investigators interested in analyzing protein-DNA interactions in vivo. |
| Databáze: | OpenAIRE |
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