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G3 (Bethesda). 2017 Jul 5;7(7):2295-2304. doi: 10.1534/g3.117.042911.

The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes.

Author information

1
Université Côte d'Azur, CNRS, I3S, France claude.pasquier@unice.fr.
2
Université Côte d'Azur, INRA, CNRS, ISA, France.

Abstract

Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the "triplex-forming oligonucleotide" in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

KEYWORDS:

Hoogsteen rules; development; epigenetics; gene networks; triplex DNA:RNA

PMID:
28515050
PMCID:
PMC5499136
DOI:
10.1534/g3.117.042911
[Indexed for MEDLINE]
Free PMC Article

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