A common transcriptional mechanism involving R-loop, m6A and RNA abasic sites regulates an enhancer RNA of APOE.

RNA confers cell identity and responds to cellular and environmental signals. RNA is modified by hundreds of chemical reactions, and folds into innumerable shapes. But the regulatory role of RNA sequence and structure, and how dysregulation leads to diseases remain largely unknown. Here, we uncovered a mechanism where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. We uncovered an enhancer RNA, AANCR, that regulates the transcription and expression of APOE. In some human cells such as fibroblasts, AANCR is folded into an R-loop and modified by N6-adenine methylation and N-glycosidic cleavage; in this form, AANCR is a partially transcribed nonfunctional enhancer and APOE is not expressed. In contrast, in other cell types including hepatocytes, and under stress, AANCR does not form a stable R-loop as its sequence is not modified, so it is transcribed into a full-length enhancer that promotes APOE expression. By genetic analysis, we confirmed that AANCR regulates APOE expression in the hippocampus. The DNA sequence variants in AANCR that are associated with APOE expression are also significantly associated with Alzheimer's Disease, thus AANCR is a modifier of Alzheimer's Disease. RNA confers cell identity and responds to cellular and environmental signals. RNA is modified by hundreds of chemical reactions, and folds into innumerable shapes. But the regulatory role of RNA sequence and structure, and how dysregulation leads to diseases remain largely unknown. Here, we uncovered a mechanism where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. We uncovered an enhancer RNA, AANCR, that regulates the transcription and expression of APOE. In some human cells such as fibroblasts, AANCR is folded into an R-loop and modified by N6-adenine methylation and N-glycosidic cleavage; in this form, AANCR is a partially transcribed nonfunctional enhancer and APOE is not expressed. In contrast, in other cell types including hepatocytes, and under stress, AANCR does not form a stable R-loop as its sequence is not modified, so it is transcribed into a full-length enhancer that promotes APOE expression. By genetic analysis, we confirmed that AANCR regulates APOE expression in the hippocampus. The DNA sequence variants in AANCR that are associated with APOE expression are also significantly associated with Alzheimer's Disease, thus AANCR is a modifier of Alzheimer's Disease. Besides AANCR, thousands of noncoding RNAs are regulated by N6-methyladenosine and abasic sites in R-loops. Thus, our data reveal the essentiality of the folding and modification of RNA in cellular regulation and demonstrate that dysregulation underlies common complex diseases such as Alzheimer's Disease.