Expression of the brain-derived neurotrophic factor (BDNF) is under tight regulation to accommodate its intricate roles in controlling brain function. Transcription of BDNF initiates from multiple promoters in response to distinct stimulation cues. However, regardless which promoter is used, all BDNF transcripts are processed at two alternative polyadenylation sites, generating two pools of mRNAs that carry either a long or a short 3′UTR, both encoding the same BDNF protein. Whether and how the two distinct 3′UTRs may differentially regulate BDNF translation in response to neuronal activity changes is an intriguing and challenging question. We report here that the long BDNF 3′UTR is a bona fide cis-acting translation suppressor at rest whereas the short 3′UTR mediates active translation to maintain basal levels of BDNF protein production. Upon neuronal activation, the long BDNF 3′UTR, but not the short 3′UTR, imparts rapid and robust activation of translation from a reporter. Importantly, the endogenous long 3′UTR BDNF mRNA specifically undergoes markedly enhanced polyribosome association in the hippocampus in response to pilocarpine induced-seizure before transcriptional up-regulation of BDNF. Furthermore, BDNF protein level is quickly increased in the hippocampus upon seizure-induced neuronal activation, accompanied by a robust activation of the tropomyosin-related receptor tyrosine kinase B. These observations reveal a mechanism for activity-dependent control of BDNF translation and tropomyosin-related receptor tyrosine kinase B signaling in brain neurons.alternative 3′UTR | tropomyosin-related kinase receptor B | hippocampal mossy fiber | epilepsy B rain-derived neurotrophic factor (BDNF) is known to elicit a plethora of functions in the brain via activation of the tropomyosin-related receptor tyrosine kinase B (TrkB), ranging from neuronal survival and differentiation to circuit development and synaptic plasticity (1-3). Abnormalities in BDNF function have been implicated in both neurological and psychiatric disorders (4-6). To accommodate such diverse functions, a variety of mechanisms have evolved that tightly control BDNF expression. Transcription of the BDNF gene can be initiated from nine distinct promoters in mammals, allowing for sophisticated regulation by divergent extracellular and developmental cues (7-9). Moreover, the primary BDNF transcript can be processed at two alternative polyadenylation sites in all tissues examined, giving rise to two pools of BDNF mRNAs that harbor either a short or a long 3′UTR of 0.35 kb and 2.85 kb in length, respectively (8, 9). Each BDNF mRNA isoform encodes for the same BDNF protein. However, the relative abundance of the short and long 3′UTR BDNF mRNAs differ in various brain regions (10). The different 3′UTRs in BDNF mRNAs presumably interact with distinct trans-acting factors, thus offering a mechanism to increase the capacity and complexity for regulation of BDNF expression at posttranscriptional levels, such as translation and subcellular localization, which ...