Optimal use of tandem biotin and V5 tags in ChIP assays. Export

@article{citeulike:4020529, abstract = {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.}, author = {Kolodziej, Katarzyna E. and Pourfarzad, Farzin and de Boer, Ernie and Krpic, Sanja and Grosveld, Frank and Strouboulis, John}, citeulike-article-id = {4020529}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2199-10-6}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19196479}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19196479}, day = {05}, doi = {10.1186/1471-2199-10-6}, issn = {1471-2199}, journal = {BMC molecular biology}, keywords = {chip-chip, chip-seq, methods}, month = {February}, pages = {6+}, posted-at = {2009-03-22 14:16:53}, priority = {2}, title = {Optimal use of tandem biotin and V5 tags in ChIP assays.}, url = {http://dx.doi.org/10.1186/1471-2199-10-6}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:4020529 L3 - citeulike-article-id:4020529 N2 - 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. JF - BMC molecular biology SN - 1471-2199 TI - Optimal use of tandem biotin and V5 tags in ChIP assays. VL - 10 SP - 6 KW - chip-chip KW - chip-seq KW - methods AU - Kolodziej, Katarzyna AU - Pourfarzad, Farzin AU - de Boer, Ernie AU - Krpic, Sanja AU - Grosveld, Frank AU - Strouboulis, John PY - 2009/02/05/ UR - http://dx.doi.org/10.1186/1471-2199-10-6 ER -