BACKGROUND: Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays 
(Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide 
identification of binding sites of chromatin associated proteins. However, the 
highly variable quality of antibodies and the availability of epitopes in 
crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have 
often been used as more reliable alternatives. In addition, we have employed 
protein in vivo biotinylation tagging as a very high affinity alternative to 
antibodies. In this paper we describe the optimization of biotinylation tagging 
for ChIP and its coupling to a known epitope tag in providing a reliable and 
efficient alternative to antibodies.
RESULTS: Using the biotin tagged erythroid transcription factor GATA-1 as 
example, we describe several optimization steps for the application of the high 
affinity biotin streptavidin system in ChIP. We find that the omission of SDS 
during sonication, the use of fish skin gelatin as blocking agent and choice of 
streptavidin beads can lead to significantly improved ChIP enrichments and lower 
background compared to antibodies. We also show that the V5 epitope tag performs 
equally well under the conditions worked out for streptavidin ChIP and that it 
may suffer less from the effects of formaldehyde crosslinking.
CONCLUSION: The combined use of the very high affinity biotin tag with the less 
sensitive to crosslinking V5 tag provides for a flexible ChIP platform with 
potential implications in ChIP sequencing outcomes.