Proneural basic helix-loop-helix transcription factor, Atoh1, plays a key role in the development of sensory hair cells. We show here that the level of Atoh1 must be accurately controlled by degradation of the protein in addition to the regulation of Atoh1 gene expression to achieve normal cellular patterning during development of the cochlear sensory epithelium. The stability of Atoh1 was regulated by the ubiquitin proteasome system through the action of Huwe1, a HECT-domain, E3 ubiquitin ligase. An interaction between Huwe1 and Atoh1 could be visualized by a proximity ligation assay and was confirmed by co-immunoprecipitation and mass spectrometry. Transfer of a lysine 48-linked polyubiquitin chain to Atoh1 by Huwe1 could be demonstrated both in intact cells and in a cell-free system, and proteasome inhibition or Huwe1 silencing increased Atoh1 levels. The interaction with Huwe1 and polyubiquitylation were blocked by disruption of casein kinase 1 (CK1) activity, and mass spectrometry and mutational analysis identified serine 334 as an important phosphorylation site for Atoh1 ubiquitylation and subsequent degradation. Phosphorylation by CK1 thus targeted the protein for degradation. Development of an extra row of inner hair cells in the cochlea and an approximate doubling in the number of afferent synapses was observed after embryonic or early postnatal deletion of Huwe1 in cochlear-supporting cells, and hair cells died in the early postnatal period when Huwe1 was knocked out in the developing cochlea. These data indicate that the regulation of Atoh1 by the ubiquitin proteasome pathway is necessary for hair cell fate determination and survival.Loss of mammalian cochlear hair cells, caused by genetic mutations, autoimmune disease, ototoxic medications, exposure to noise, and aging, is usually permanent. Mammals show limited ability to regenerate hair cells (1, 2). Hair cell differentiation is dependent on basic helix-loop-helix (bHLH; transcription factor, Atoh1 (3, 4). Overexpression of Atoh1 via gene transfer results in the generation of new hair cells from inner ear progenitors in the organ of Corti (5).Increasing information about the transcriptional regulation of the Atoh1 gene has shown that expression of Atoh1 is regulated strictly by overlapping pathways (6 -10). We were interested in the downstream regulation of Atoh1 because of the importance of Atoh1 levels for its function in cells of the ear. Posttranslational control of Atoh1 is largely unknown. The ubiquitin-proteasome pathway plays an important role in posttranslational regulation of proteins in eukaryotic cells (11). The system not only degrades misfolded or damaged proteins but is also essential for the regulation of cell-signaling pathways, determining the half-lives of proteins (12). Cells utilize spatial distribution of ubiquitin conjugation to regulate local abundance of proteins and compartmentalization of different subcellular domains.E3 ubiquitin ligases transfer ubiquitin to internal lysine residues of specific proteins to form mono-or ...