Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks
Chromatin immunoprecipitation (ChIP) provides a versatile tool to investigate the in vivo location of DNA-binding proteins on genomic DNA. ChIP approaches are gaining significance in plants, in cases when entire genome sequences are available (e.g., Arabidopsis), for which several high-density oligo arrays have been or are being developed. Nevertheless, plant ChIP and ChIP-chip still present some technical challenges. Here, we describe general methods for ChIP and ChIP-chip, which have been successfully applied to maize and Arabidopsis.
Methods to identify protein–DNA interactions include experimental and computational approaches, or combinations thereof (1). Experimental approaches involve investigating the formation of protein–DNA complexes for example by electrophoretic mobility shift assays (EMSA) or by exploring the specific DNA sequence recognized by a TF on a given fragment of DNA using chemical or nuclease footprinting techniques. These techniques, however,...
KeywordsWhole Genome Amplification Tiling Array ChIP Experiment Disuccinimidyl Suberate Dimethyl Suberimidate
We thank Herbert Auer for helping us develop the ChIP-chip method for Arabidopsis and for comments on this manuscript, Manli Davis for helping us grow and collect plant materials, and Marko Djordjevic for assistance with the analysis of ChIP-chip data. This research was supported by National Science Foundation (NSF) grant MCB-0418891 and by NRI grant 2007-35318-17805 from the USDA-CSREES to E.G.
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