Recent transcriptomics efforts have revealed that numerous protein-coding messenger RNAs have natural antisense transcript partners, most of which seem to be noncoding RNAs. Here we identify a conserved noncoding antisense transcript for β-secretase-1 (BACE1), a crucial enzyme in Alzheimer's disease pathophysiology. The BACE1-antisense transcript (BACE1-AS) regulates BACE1 mRNA and subsequently BACE1 protein expression in vitro and in vivo. It seems that the argument for concordant regulation can only be made in the experiments with the siRNA against BACE1-AS. This convention has been followed throughout the manuscript. Please check carefully.]. Upon exposure to various cell stressors including amyloid-β 1-42 (Aβ 1-42), expression of BACE1-AS becomes elevated, increasing BACE1 mRNA stability and generating additional Aβ 1-42 through a post-transcriptional feed-forward mechanism. BACE1-AS concentrations were elevated in subjects with Alzheimer's disease as well as in amyloid precursor protein transgenic mice. These data show that BACE1 mRNA expression is under the control of a regulatory noncoding RNA that may drive Alzheimer's disease-associated pathophysiology. In summary, we report that a long noncoding RNA is directly implicated in the increased abundance of Aβ 1-42 in Alzheimer's disease.Sequential cleavage of amyloid precursor protein (APP) by BACE1, the β-site cleaving enzyme essential for Aβ 1-42 and amyloid-β 1-40 (Aβ 1-40) biosynthesis 1 , and γ-secretase NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscriptinitiates the 'amyloid cascade' that is central to Alzheimer's disease pathophysiology2 , 3. Oligomers of Aβ 1-42 produced by BACE1 influence key aspects of Alzheimer's disease4 -9 . Studies have revealed elevated brain BACE1 concentrations in subjects with Alzheimer's disease compared with normal controls [10][11][12][13][14][15] . However, controversy exists concerning the extent of BACE1 upregulation and whether this upregulation involves BACE1 mRNA or protein [16][17][18] .Loss of BACE1 results in numerous behavioral and physiological deficits, including memory loss 19 , emotional deficits 20 , myelination defects in peripheral nerves 21,22 and loss of synaptic plasticity 20 . Thus, the subtle but crucial boundaries between BACE1 physiology and pathology indicate that BACE1 expression must be tightly regulated, allowing the enzyme to perform its physiological functions while avoiding the serious consequences of over-or underexpression.Here we report that BACE1-AS, a natural antisense transcript, plays a part in determining BACE1 expression. BACE1-AS rapidly and reversibly upregulates BACE1 levels in response to a variety of stresses, including Aβ 1-42 exposure. Furthermore, we show elevated BACE1-AS in several brain regions of individuals with Alzheimer's disease. These data suggest that this previously unexamined noncoding RNA has a role in regulating BACE1 and in driving Alzheimer's disease pathology. RESULTS Identification of BACE1 natural antisense transcriptBACE1...

Advances in the depth and quality of transcriptome sequencing have revealed many new classes of long non-coding RNAs (lncRNAs). lncRNA classification has mushroomed to accommodate these new findings, even though the real dimensions and complexity of the non-coding transcriptome remain unknown. Although evidence of functionality of specific lncRNAs continues to accumulate, conflicting, confusing, and overlapping terminology has fostered ambiguity and lack of clarity in the field in general. The lack of fundamental conceptual un-ambiguous classification framework results in a number of challenges in the annotation and interpretation of non-coding transcriptome data. It also might undermine integration of the new genomic methods and datasets in an effort to unravel function of lncRNA. Here, we review existing lncRNA classifications, nomenclature, and terminology. Then we describe the conceptual guidelines that have emerged for their classification and functional annotation based on expanding and more comprehensive use of large systems biology-based datasets.