A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions.

ABSTRACT: RNA.DNA:DNA triple helix (triplex) formation is a form of RNA-DNA interaction which regulates gene expression but is difficult to study experimentally in vivo. This makes accurate computational prediction of such interactions highly important in the field of RNA research. Current predictive methods use canonical Hoogsteen base pairing rules, which whilst biophysically valid, may not reflect the plastic nature of cell biology. Here, we present the first optimization approach to learn a probabilistic model describing RNA-DNA interactions directly from motifs derived from triplex sequencing data. We find that there are several stable interaction codes, including Hoogsteen base pairing and novel RNA-DNA base pairings, which agree with in vitro measurements. We implemented these findings in Tri

SUBMITTER: Warwick T 

PROVIDER: S-EPMC9677506 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature