TY - JOUR T1 - Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq JF - bioRxiv DO - 10.1101/054387 SP - 054387 AU - Michele Busby AU - Catherine Xue AU - Catherine Li AU - Yossi Farjoun AU - Elizabeth Gienger AU - Ido Yofe AU - Adrianne Gladden AU - Charles B. Epstein AU - Evan M. Cornett AU - Scott B. Rothbart AU - Chad Nusbaum AU - Alon Goren Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/10/17/054387.abstract N2 - Background The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: they are non-renewable, vary in performance between lots, and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts in both human and mouse cells.Results Overall performance was highly similar for four monoclonal/polyclonal pairs, including when we used two distinct lots of the same monoclonal antibody. In contrast, the binding patterns for H3K27ac differed substantially between polyclonal and monoclonal antibodies. However, this was most likely due to the distinct immunogen used rather than the clonality of the antibody.Conclusions Altogether, we found that monoclonal antibodies as a class perform as well as polyclonal antibodies for the detection of histone post-translational modifications in both human and mouse. Accordingly, we recommend the use of monoclonal antibodies in ChIP-seq experiments.AbbreviationsChIP-seqChromatin immunoprecipitation followed by sequencingCSTCell Signaling TechnologyWCEwhole cell extract ER -