The anterior interpositus nucleus (AIN) is the proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remain unknown. To elucidate the molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delay eyeblink conditioning using microarray, quantitative real-time RT-PCR, and in situ hybridization techniques. Microarray analyses suggested that transcriptionally up-regulated gene sets were largely different between early (3-d training) and late (7-d) stages. Quantitative real-time RT-PCR aided by laser microdissection indicated that the expression of representative EARLY genes (Sgk, IkBa, and Plekhf1) peaked at 1-d training in both the paired and unpaired conditioning groups, and was maintained at a higher level in the paired group than in the unpaired group after 3-d training. In situ hybridization revealed increased expression of these genes in broad cerebellar areas, including the AIN, with no hemispheric preferences. In contrast, the expression of representative LATE genes (Vamp1, Camk2d, and Prkcd) was selectively increased in the AIN of the 7-d paired group, with dominance in the ipsilateral AIN. Increased Vamp1 mRNA expression was restricted to the ipsilateral dorsolateral hump, a subregion of the AIN. These expression patterns of two distinct subsets of genes fit well with the twostage learning theory, which proposes emotional and motor learning phases, and support the notion that AIN has a crucial role in memory formation of eyeblink conditioning.gene expression ͉ interpositus nucleus C lassical eyeblink conditioning is conserved among various species. Although the neuronal circuitries are well defined and the cerebellum is considered to be the site of memory formation of the classically conditioned response (CR, i.e., eyeblink) (1), evidence is still conflicting regarding the neural substrate for the memory trace of eyeblink conditioning in the cerebellum.In contrast to the suggestion that the basic memory trace of the CR is formed in the cerebellar cortex (2), accumulating evidence suggests that the anterior interpositus nucleus (AIN) in the deep cerebellar nuclei (DCN) is the site of memory for the association between the conditioned stimulus (CS) and the unconditioned stimulus (US) formed in eyeblink conditioning. This hypothesis has been examined repeatedly with lesions (3-7) and inactivation of the AIN (8, 9), and in mutant mice with Purkinje cell degeneration (10). Recent observations made using electron microscopy (11) or functional magnetic resonance imaging (12) further support the notion that the basic memory trace is formed in the AIN. On the other hand, the cerebellar cortex is implicated as a site of storage for the memory trace of CR timing (13).Although the existence of a Purkinje cell-specific promoter like L7/pcp-2 made it possible to test the relevance of some molecules to cortical function in eyeblink conditioning in vivo (14,15), mechanistic studies at the molecular level of the AIN, which is ...