UCSF

The H3K4me3 chromatin modification, a hallmark of promoters of actively transcribed genes, is dynamically removed by the KDM5 family of histone demethylases. The KDM5 demethylases have several accessory domains, two of which, ARID and PHD1, lie between the segments of the catalytic domain. KDM5C, which has a unique role in neural development, harbors a number of mutations adjacent to its accessory domains that cause X-linked intellectual disability (XLID). The roles of these accessory domains remain unknown, limiting an understanding of how XLID mutations affect KDM5C activity. Work in this thesis focuses on a mechanistic understanding of functional roles of accessory domains within KDM5C and dysregulation by select XLID mutations. Through in vitro binding and kinetic studies using nucleosomes, we find that while the ARID domain is required for efficient nucleosome demethylation, the PHD1 domain alone has an inhibitory role in KDM5C catalysis. In addition, the unstructured linker region between the ARID and PHD1 domains is necessary for nucleosome binding. Our data suggests a model in which the PHD1 domain regulates DNA recognition by KDM5C based on available H3K4me3 substrate cues. Importantly, we find that XLID mutations adjacent to the ARID and PHD1 domains break this regulation by enhancing DNA binding, resulting in the loss of specificity of substrate chromatin recognition and rendering demethylase activity sensitive to inhibition by linker DNA. Our findings suggest a unifying model by which XLID mutations could alter chromatin recognition and enable euchromatin-specific dysregulation of demethylation by KDM5C.