Context dependent protein interpretation of the histone language

Throughout the past decade there have been a myriad of histone modification protein "readers" with varied specificity found in a wide array of proteins and complexes. Detailed structural and functional studies have helped uncover the way in which histone modifications are recognized by these specialized "readers" and translated into functional outputs. Distinct classes of protein readers have been assigned based on structural and sequence similarities and on binding specificities. Gaining a better understanding of the interaction between modifications and protein readers is an excellent springboard for eventually apprehending the functional response that may stem from this interaction. It may also provide a foundation for developing novel therapeutic strategies when module-modification interactions go awry in human disease.;An important remaining piece of the multifaceted epigenetic puzzle is the development of techniques and tools for studying the effect of histone modifications on modules that recognize neighboring modifications (for example, the effect of H3S10ph on H3K9me3 binders). Of no less importance is attacking the contextual complexity of combinatorial readout by paired histone binding modules through creative and well-directed biochemical experiments.;The work presented in the following chapters addresses some of the challenges when interpreting histone-binding module/modification interactions paying special attention to combinatorial complexity and context dependence. Chapter 2 highlights the development of a randomized, combinatorial peptide library based on the N-terminus of histone H3 that was utilized to interrogate multi-site specificity of six chromatin-binding modules, which read the methylation status of K4. The discovery of a new histone modification H3T6ph will be discussed in this chapter. Chapter 3 will investigate the ability of the tandem PHD-finger containing proteins CHD4 and CHD5 to read the histone language. This study lays the foundation for overcoming some of the challenges when investigating combinatorial readout by paired histone binding modules. Chapter 4 will highlight some recent and ongoing developments that were made with a spatially addressed histone library as well as provide some general conclusions and future directions from the preceding chapters.