La seconde vie des fragments de RNA hérités du métabolisme du transcriptome

ABSTRACT:

1. Genome-wide analysis of dsRNAs that orchestrate extensive transcriptional homeostasis via their complex with Argonaute 2 and epigenetic mechanisms in Drosophila

Claude Pasquier, Sandra Agnel, Alain Robichon
RNA interference (RNAi) refers to a conserved post-transcriptional mechanism through which RNAs produced from endogenous coding genes, transposable elements, invading viruses and bacteria are destroyed. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length transcribed from the full transcriptome and susceptible to be loaded on Argonaute type 2 was computationally searched in Drosophila model. We report the segmental and complementary pieces of RNAs to mRNAs that originate from introns, exons of mRNAs and lncRNAs as a potential source of siRNAs capable of promoting the RISC-mediated cleavage of mRNAs. A full catalog of mRNAs that fulfill these criteria is presented along with the quantification of multiple annealing. The catalog was assessed for biological validation using two published lists of RNAs that have been found to be associated with Ago-2. Datasets of perfect RNA duplexes, partially present in Ago2 associated RNAs collections, allowed us to establish that a larger-than-expected pool of dsRNA candidates might qualify for the RNAi machinery. Unexpectedly, a broad spectrum of mRNAs was found to theoretically form intermolecular segmental dsRNA, which should qualify them as Dicer/Ago-2 substrates. These results suggest a genome-wide scale of mRNA homeostasis via RNAi metabolism and extend the known roles of canonical miRNAs and hairpin RNAs. 

2. The mapping of predicted triplex DNA:RNA in the Drosophila genome reveals a prominent location in development and morphogenesis-related genes  (G3, 2017)
Claude Pasquier, Sandra Agnel, Alain Robichon
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.