A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system. This approach provides an unbiased view of proteins interacting with epitope-tagged TEFs. The second protocol (Subheading 3.2) depicts details about a chromatin immunoprecipitation (ChIP) procedure to characterize genomic binding sites of TEFs. These methods should be valuable tools for the analysis of a broad variety of nuclear proteins.
CITATION STYLE
Pfab, A., Antosz, W., Holzinger, P., Bruckmann, A., Griesenbeck, J., & Grasser, K. D. (2017). Analysis of in vivo chromatin and protein interactions of Arabidopsis transcript elongation factors. In Methods in Molecular Biology (Vol. 1629, pp. 105–122). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7125-1_8
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