Epigenetic studies often use antibodies for immunoprecipitation, Western blot or immunolocalization experiments to analyze modified nucleic acids, transcription cofactor proteins and histones. DNA immunoprecipitation based experiments are often followed by microarray or next generation high-throughput sequencing.
Me-DIP enriches for methylated or hydroxymethylated DNA, and can be carried out in the presence of cofactors such as heterodimer partners, competitors or small molecule binding inhibitors (1).
Chromatin immunoprecipitation (ChIP), which uses modification specific histone antibodies, is the most commonly used method to analyze histone modifications associated with genes (2). The isolated DNA may be used for next-generation sequencing for genome wide studies.
Antibodies against chromatin modifying enzymes such as histone acetyltransferases/deacetylases, histone methyltransferases/demethylases, histone kinases/phosphatases, and ubiquitin ligases can be used to probe their functions and locations on chromatin.
RNA binding protein immmunoprecipitation (RIP) uses antibodies to pull down RNA binding proteins, which co-precipitate with their interacting RNA molecules for downstream analysis by RT-PCR (3) followed by sequencing.
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