Catalytic activity of KMT5B promotes ciliogenesis without affecting global chromatin accessibility

Multiciliated cells (MCCs) are specialized cells found in the brain, reproductive and respiratory tracts of mammals, and the epidermis of tadpole-stage Xenopus embryos. KMT5B and KMT5C are histone methyltransferases that deposit the dimethyl mark on histone 4 lysine 20 (H4K20). We previously showed that KMT5B/C double knockdown down-regulates H4K20me2 levels in bulk chromatin, as well as transcription of ciliary genes. MCCs of embryos lacking both enzymes, or only KMT5B, have depleted cilia. Here, we separate the function of KMT5B in multiciliogenesis and show that single knockdown of KMT5B, not KMT5C, leads to aberrant transcription and down-regulation of ciliary genes. This phenotype is rescued by catalytically active PHF8, an H4K20me1 demethylase, whereas hormone-inducible multicilin (MCI), master regulator of cilia, has no effect. Notably, the expression of key transcription factors of ciliogenesis is unaffected by KMT5B depletion, which dominates the transcriptional response to ectopic multicilin. Finally, ATAC-seq in animal caps shows KMT5B knockdown results in few differentially accessible peaks and does not compact chromatin at ciliary genes. This suggests KMT5B regulates MCCs via an alternative pathway to the canonical MCI-driven programme.