Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia

Abstract

Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that ecCEBPα (extra coding CEBPα) - a lncRNA transcribed in the same direction as CEBPα gene - regulates DNA methylation of CEBPα promoter in cis. Here, we hypothesize that ecCEBPα could participate in the regulation of DNA methylation in trans. Method: First, we retrieved the methylation profile of AML patients with mutated CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the ecCEBPα secondary structure in order to check the potential of ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated CEBPα locus, we show that ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions. ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.

Differential expression of HNF1A and HNF1A‐AS1 in colon cancer cells

“…With HNF1A‐AS being a nuclear lncRNA, we next explored its possible functions, including the ability to form triplexes and association with epigenetic modifiers. The triplex domain finder (TDF) tool identifies regions with contiguous triplex‐forming oligonucleotides that are defined as DBD 4,25 . The Fisher exact test TDF evaluated the binding potential for each DBD.…”

“…The triplex domain finder (TDF) tool identifies regions with contiguous triplex-forming oligonucleotides that are defined as DBD. 4,25 The Fisher exact test TDF evaluated the binding potential for each DBD. The TDF tool detected several enriched DBDs in the 5 0 end of the HNF1A-AS transcript located in the regions 60-94, 103-196, and 461-495 (Figure S2).…”

Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation

“…(Di Ruscio et al, 2013). This lncRNA was later identified to interact with DNA strand by forming a DNA:RNA triple helices and protect regions near its binding site from methylation (Ogunleye et al, 2021). Another lncRNA, named 91H which located at the H19/ IGF2 locus and transcribed in H19 antisense orientation, is overexpressed in breast cancer and prevent the maternal allele at the H19/IGF2 locus from DNA methylation, by this mechanism to induce overexpression of oncogenic H19 (Vennin et al, 2017).…”