Long noncoding RNA BACE1-AS modulates chromatin methylation and enhancer RNA expression: implications for heart failure pathogenesis

Abstract Background Beta-Secretase-1 (BACE1) contributes to β-amyloid accumulation in Alzheimer’s disease (AD) and is regulated by the long noncoding RNA BACE1-antisense RNA (BACE1-AS), transcribed from its opposite strand. Our previous research demonstrated that the BACE1-AS/BACE1/β-amyloid axis is also activated in ischemic heart failure (HF), promoting cardiomyocyte death. However, the mechanisms underlying BACE1-AS function remain unclear. Purpose To investigate the epigenetic and transcriptional effects of BACE1-AS in cardiomyocytes and its role in HF pathogenesis. Methods We evaluated chromatin accessibility using ATAC-sequencing and identified BACE1-AS-interacting RNAs through RNA-seq after BACE1-AS pull-down in AC16 cardiomyocytes. Loss- and gain-of-function studies were performed via Gapmer/ASOs transfection and lentiviral transduction, respectively. RRBS (Reduced Representation Bisulfite Sequencing) assessed DNA methylation, while CRISPR-Cas9 was used to generate BACE1-null AC16 cells. RNA-PolII ChIP enriched for active PolII RNA transcripts. Gene expression was quantified by RT-qPCR. In vivo, Myo2A-AAV-mediated Bace1-as cardiac homing and was performed in an ischemic HF mouse model obtained by ligation of the left anterior descending coronary artery, following ethical guidelines. Results BACE1-AS overexpression significantly altered chromatin accessibility, including the RNF214/BACE1/BACE1-AS locus, thereby influencing BACE1 transcription. BACE1-AS pull-down identified interacting RNAs transcribed from enhancer regions, some of which were hypomethylated in AD brains and annotated as eRNAs (enhancer RNAs). Among these there was lncSHC3, a 1,152-nt nuclear eRNA within the SEMA4D locus. Under hypoxia, BACE1-AS and lncSHC3 expression increased in AC16 cardiomyocytes, alongside lncSHC3-targets CHS2, SHC3, and SEMA4D. These effects were reversed by BACE1-AS silencing and persisted in BACE1-null cells, indicating that BACE1-AS exerts epigenetic regulation independent of BACE1. RNA-PolII ChIP revealed that BACE1-AS and lncSHC3 physically interacted with RNA PolII. Furthermore, BACE1-AS overexpression induced hypomethylation of lncSHC3 and its target genes, supporting its role in transcriptional regulation via chromatin remodeling. In the HF mouse model, Myo2A-AAV-Bace1-as injection did not affect overall cardiac function, but modulated the expression of cardiac remodeling markers (e.g., Col3a1, Myh10, and Ctgf), suggesting a regulatory role in HF. Conclusions BACE1-AS modulates gene expression independently of BACE1 by interacting with RNA-PolII and inducing hypomethylation. In hypoxic cardiomyocytes, it regulates lncSHC3 and SEMA4D pathways, while in HF mice, it influences cardiac remodeling markers. These findings highlight BACE1-AS as a potential epigenetic regulator in HF.