Whether you work in Hollywood or the research labs close by at UCLA, it seems like a good set of Abs can solve most problems. Unfortunately there’s no airbrushing when it comes to ChIP.
Most ChIP antibodies are pretty good at recognizing the specific histone modification they were raised against, as a couple of recent papers have demonstrated (Jeltsch et al. and Lieb et al.). But when a particular modification isn’t the only one on a histone tail, will the antibody still be able to pick out its target from the crowd? This question was raised by Brian Strahl’s group at the University of North Carolina School of Medicine when they tested the abilities of over 20 widely used commercial antibodies to bind histone marks alone or in combination with other modifications.
The researchers used a new type of peptide array containing a library of combinatorially modified histone peptides. In addition to testing antibodies, the team looked at the binding of histone-interacting proteins to the various combinations of histone modifications.
The study demonstrated that antibody binding to a target modification was highly influenced by neighboring modifications. For example, binding of an antibody against H3K4me3 was perturbed by modification at H3R2. Similarly, histone-binding domains from three different proteins were sensitive to nearby modifications.
These results support the “histone code” hypothesis formulated by Strahl and his postdoctoral advisor, C. David Allis, a decade ago, which says that combinations of histone modifications work together to recruit chromatin-remodeling proteins. They also raise concerns about the abilities of current antibodies to crack this complex code.
See how your favorite antibody fared at Current Biology, December 16, 2010