MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

Abstract

MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10−16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription.

The lncRNA HOTAIR impacts on mesenchymal stem cellsviatriple helix formation

“…It has to be noted that already more than 20 years ago it is been proposed that RNA sequences are not tolerated in purine motif triple helices (22,69). On the other hand, other authors more recently demonstrated that the lncRNA MEG3 (70) and microRNAs (71) form triple helices with purine motifs. In electromobility shift assays the possibility of strand rearrangement has to be taken into account.…”

PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome

“…The natural occurrence of this motif has been suggested to explain promiscuous RNA binding by PRC2 36 . While it was proposed over 20 years ago that RNA sequences are not tolerated in purine motif triple helices 37 , other authors more recently have demonstrated that the lncRNA MEG3 9 and microRNAs 38 are capable of triple helical formation with purine motifs. We propose that PARTICLE serves as an lncRNA-directed component of a genomic ‘zip code’ potentially guiding modifiers to pertinent chromatin locations for gene regulation.…”

MicroRNAs as Emerging Regulators of Signaling in the Tumor Microenvironment

“…In addition, miRs can bind to a gene promoter by forming triple-helical structures with purine-rich duplex DNA via Hoogsteen or reverse Hoogsteen interactions in the major groove of the duplex DNA (reviewed elsewhere [104]). This interaction may alter the DNA topography by steric effects and may allow binding of transcription factors that in turn affect transcriptional activation or suppression [105]. E-cadherin and the cold shock domain-containing protein C2 gene (CSDC2) contain miR-373-complementary sites in their promoters.…”