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Abstract

Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. The ‘triplex-forming oligonucleotide’ can be a short sequence of RNA that binds the major groove of the targeted duplex only when this latter presents a sequence of purine or pyrimidine bases in one or the other DNA strand. Many nuclear proteins are known to bind triplex but their biological functions are still understudied. We identified the sequences capable to engage in ‘triplex-forming oligonucleotide’ in both lncRNA and mRNA collection of Drosophila. These motifs were matched against Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters and introns/exons. The triplex mapping analysis on full genome scale suggests a massive epigenetic regulatory process of gene networks.