Ubiquitination of misfolded proteins, a common feature of many neurodegenerative diseases, is mediated by different lysine (K) residues in ubiquitin and alters the levels of toxic proteins. In Huntington disease, polyglutamine expansion causes N-terminal huntingtin (Htt) to misfold, inducing neurodegeneration. Here we report that shorter N-terminal Htt fragments are more stable than longer fragments and find differential ubiquitination via K63 of ubiquitin. Aging decreases proteasome-mediated Htt degradation, at the same time increasing K63-mediated ubiquitination and subsequent Htt aggregation in HD knock-in mice. The association of Htt with the K48-specific E3 ligase, Ube3a, is decreased in aged mouse brain. Overexpression of Ube3a in HD mouse brain reduces K63-mediated ubiquitination and Htt aggregation, enhancing its degradation via the K48 ubiquitin-proteasome system. Our findings suggest that aging-dependent Ube3a levels result in differential ubiquitination and degradation of Htt fragments, thereby contributing to the age-related neurotoxicity of mutant Htt.misfolding | proteolysis H untington disease (HD) is caused by an autosomal-dominant mutation in the HD gene that results in an expansion of CAG triplets (n > 35), leading to an expansion of polyglutamine (polyQ) repeats in the N-terminal region of huntingtin (Htt), as well as protein misfolding and aggregation (1, 2). Although Htt is ubiquitously expressed in the brain and body, mutant Htt (mHtt) causes selective neurodegeneration that preferentially occurs in the striatum and extends to other brain regions as disease progresses (1,3,4). The selective neurodegeneration in HD is apparently associated with the age-dependent accumulation of misfolded Htt in neuronal cells, which results in the formation of aggregates in the brain. Brains from patients with HD show Htt aggregates in neuronal nuclei and processes, which are formed by N-terminal fragments of mHtt (5, 6). The N-terminal fragments of mHtt in the nucleus can dysregulate gene transcription, and mHtt in neuronal processes can affect intracellular trafficking and neuron transmitter release (7-10). Similarly, most age-dependent neurodegenerative diseases, including Alzheimer's disease and Parkinson disease, show increased accumulation of misfolded proteins in neuronal cells with age (11, 12). Thus, understanding how mHtt accumulates in the brain will shed light on the mechanisms for several age-dependent neurodegenerative diseases.The accumulation of misfolded proteins is caused largely by impaired clearance of these proteins in aged neurons (13). Previous studies showed that the ubiquitin-proteasome system (UPS) and the autophagic pathway can degrade mHtt (14-20). Indeed, the neuronal aggregates seen in HD and other neurodegenerative diseases are found to contain ubiquitinated proteins (5, 6). Although these ubiquitin-enriched aggregates are a hallmark of HD and other neurodegenerative diseases, how they are linked to the development of neurodegeneration remains unclear.Previous studies revealed ...