Table 1.

Comparison of ChIP-chip, DamID, and PBM technologies.

Technology	Advantages	Disadvantages
ChIP-chip	in vivo provides a snapshot of DNA interactions in a given cell type, under the examined cellular conditions use of modification-specific antibodies permits the identification of genomic sites associated with a protein of a particular post-translational modification identifies genomic sites associated either directly or indirectly (via protein-protein interactions) with the protein	typically requires a gene-specific antibody, which may be a challenge to obtain to obtain enrichment of bound fragments, experiments must be performed in cellular conditions under which the protein of interest is expressed, nuclear, and regulating its target genes might require potentially limiting tissue source even with the use of densely tiled oligonucleotide arrays, difficulties in reducing size of immunoprecipitated DNA fragments limit resolution of DNA binding site identification
DamID	in vivo provides a snapshot of DNA interactions in a given cell type, under the examined cellular conditions does not require a gene-specific antibody could identify genomic sites associated either directly or indirectly (via protein-protein interactions) with the protein	requires slight over-expression of the protein because of expression of the fusion protein fusion protein might not exhibit same binding properties as endogenous protein to obtain enrichment of bound fragments, experiments must be performed in cellular conditions under which the protein of interest is expressed, nuclear, and regulating its target genes currently does not permit direct identification of genomic sites associated with a protein of a particular post-translational modification might require potentially limiting tissue source resolution has been limited so far to ∼1 kb due to methylation spreading
PBM	does not require a gene-specific antibody highly rapid provides a comprehensive survey of DNA binding site sequence variants, including data on non-binding sequences can have very high binding site resolution, down to the exact binding site sequence variant	in vitro experiments are performed typically at arbitrary protein concentrations, in an arbitrary buffer requires analyses of additional data types, such as phylogenetic sequence conservation and gene expression data, in order to identify which sites are likely to be utilized in vivo binding may not correspond to endogenous binding because of missing cofactors or chromatin context