The apolipoprotein E gene (APOE) has three genetic variants (i.e., ε2, ε3, and ε4), and the ε4 variant of the APOE is the strongest genetic risk factor for Alzheimer's disease (AD). This means that APOE plays a major role in the development of AD. The expression levels of APOE gene products (mRNA and protein) are potential candidates that may partially explain APOE's effects in AD. But studies on APOE expression in AD have always yielded conflicting data, and there is no consensus on whether ε4 carriers produce higher or a lower APOE mRNA/protein. Such conflicting results have significantly obscured interpretation of APOE's expression role in AD. Clearly, gaps exist between APOE's expression, the ε2/ε3/ε4 alleles, and AD status. There is a need for better understanding their relationship. In our preliminary study, we have found that only a fraction of APOE mRNA extends the full length of the gene; that is, the majority of mRNAs are prematurely terminated and cannot produce functional apoE proteins. We have also detected the presence of novel circular RNAs in APOE RNA pools. These data suggest that APOE's RNA transcription is complex and may pose more biological consequences than previously thought; and that past APOE mRNA expression studies may have been flawed for not measuring the true functional full-length mRNA. Deciphering the interplay between various APOE RNA transcripts, the production of full-length mRNA, and the ε2/ε3/ε4 alleles will lead us to better understand the effects of APOE expression in AD. In this study, we hypothesize that only a fraction of APOE mRNA extend the full length of the gene to produce apoE protein; the ε2/ε3/ε4 alleles differentially modulate the production of these functional full-length mRNAs, thereby adding diverse effects to AD risk. Our long-term goal is to fully understand gene regulation of APOE and to use this knowledge to develop strategies for AD prevention and/or intervention. Our short-term goal is to clarify the relationship between APOE RNAs transcription, the ε2/ε3/ε4 variants, and AD risk and to understand the molecular mechanisms that regulate APOE RNAs production. We have designed three specific aims for the study. Aim 1 will investigate APOE RNAs and correlate their expression levels with the ε2/ε3/ε4 allele variants, and AD status in human postmortem brain. Aim 2 will characterize the epigenetic mechanisms that modulate the APOE RNAs transcription in human cell lines. Aim 3 will investigate the function, biogenesis, and distribution of the newly discovered APOE circular RNA in human cell lines and body fluid. Our work will not diminish the role of apoE protein; instead, it will dissect the contributions of APOE RNA from apoE protein to complement APOE gene's comprehensive effects in AD.