Post-translational modifications (PTMs) of histone tails are major marks for transcription activation and silencing. Accordingly, detecting and capturing post-translationally modified histones represent a critical step in epigenetic research. A major technological bottleneck in this area of research is a paucity of high-quality affinity reagents. Polyclonal and monoclonal antibodies are the only widely available affinity reagents for histone tails, but they have fundamental limitations in reproducibility, scalability, storage and production throughput and expenses. The long-term goals of this project are to develop an innovative and powerful technology platform for facile production of high-quality affinity reagents for histone tails containing PTMs and to make a standard set of such affinity reagents broadly available to the epigenetics research community. This project is built on an innovative protein-engineering concept that our group has recently established. The concept, termed Affinity Clamping, harnesses the inherent specificity present in the so-called interaction domains and dramatically enhances their affinity and specificity by attaching an """"""""enhancer domain"""""""" and subsequently optimizing its interaction interface by directed evolution of combinatorial libraries. The resulting affinity reagents with clamshell architecture, collectively termed """"""""Affinity Clamps"""""""" thus """"""""clamp"""""""" the target, leading to orders-of-magnitude higher affinity and specificity. Protein libraries made in this manner are predisposed to binding to a specific class of peptide motifs (e.g. histone tails with a methylated lysine), and they virtually guarantee successful engineering of high-performance affinity reagents for a predefined peptide motif. Affinity Clamping represents a paradigm shift in affinity reagent generation. Because Affinity Clamps are fully recombinant reagents produced in E. coli, they can be easily produced in large quantities and distributed. Also they can be reformatted into a variety of fusion proteins suitable for in vitro and in vivo applications. Our proof-of-concept experiments have successfully demonstrated the general feasibility of the Affinity Clamping concept and suggest its enormous potential. Because there exist a number of interaction domains that weakly bind to post-translationally modified histone tails, we are confident that we can apply the Affinity Clamping strategy to produce high-quality affinity reagents to a variety of histone motifs. The proposed project will critically evaluate the feasibility and potential of applying the Affinity Clamping technology to epigenetic histone marks.
The specific aims of the initial project period are (i) to produce """"""""Histone Clamps"""""""" for well-characterized histone lysine methylation sites and benchmark them against commercially available monoclonal antibodies for their performance in commonly used assays;and (ii) to produce Histone Clamps for histone methylation sites for which no high-quality antibodies exist. Such Histone Clamps will be provided to the epigenetic community, which will have a major impact on the quality, scale and types of epigenetics research.
Accurately measuring the type and amounts of chemically modified forms of histones and capturing them for downstream analysis are major technological challenges in epigenetic research. This project will establish a totally new approach to facile generation of high-performance reagents for these purposes. This innovative and powerful technology will fill a major void in the currently epigenetic research, and products from this project, termed """"""""Histone Clamps"""""""", will make it feasible to establish a standard set of epigenetic capture reagents that can be distributed broadly to the community and open new avenues of epigenetics research.
