Catalytic activity of KMT5B promotes cilia tuft formation without affecting chromatin accessibility of ciliary genes

Abstract

Multiciliated cells are a specialized cell type found in the brain, reproductive tract and respiratory tract of mammals. Multiciliated cells resembling those of the mammalian lung can also be found on the surface of the epidermis of tadpole stage Xenopus embryos, making the frog an ideal model organism to study this cell type. KMT5B/suv4-20h1 is a histone methyltransferase that writes the dimethyl mark on histone 4, lysine 20 (H4K20). We have previously shown that the multiciliated cells of embryos lacking KMT5B have depleted cilia and a reduced actin cap, and that knockdown of both KMT5B and KMT5C/suv4-20h2 leads to downregulation of ciliogenic genes. Here we further tease out the independent function of KMT5B in multiciliogenesis, and show that single knockdown of KMT5B, but not KMT5C leads to aberrant transcription and the downregulation of cilia genes. This phenotype is ameliorated by overexpression of catalytically active PHF8, an H4K20me1 demethylase, while a hormone inducible variant of multicilin (MCI), the master regulator of cilia tuft formation, has no effect. Notably, the expression of key transcription factors of ciliogenesis is unaffected by KMT5B depletion, and the transcriptional effect of KMT5B depletion dominates the response to ectopic multicilin. Finally, ATAC seq analysis in animal caps reveals that knockdown of KMT5B results globally in very few peaks with differential activity and does not compact chromatin at ciliary genes. Taken together, this suggests that KMT5B regulates multiciliated cells through an alternative pathway to the canonical MCI-driven multiciliogenic program.