In silico structural modeling of multiple epigenetic marks on DNA

Abstract

There are four known epigenetic cytosine modifications in mammals: methylation (5mC), hydroxymethylation (5hmC), formylation (5fC) and carboxylation (5caC). The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, F-DNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e.g. methylated/non-methylated) along a stretch of DNA. Experiments on such complex systems are only feasible on small, isolated examples and there currently exist no systematic computational solutions to this problem. We address this issue by extending the use of Natural Move Monte Carlo to simulate the conformations of epigenetic marks. We validate our protocol by reproducing in silico experimental observations from two recently published highresolution crystal structures that contain epigenetic marks 5hmC and 5fC. We further demonstrate that our protocol correctly finds either the F-DNA or the B-DNA states more energetically favorable depending on the configuration of the epigenetic marks. We hope that the computational efficiency and ease of use of this novel simulation framework would form the basis for future protocols and facilitate our ability to rapidly interrogate diverse epigenetic systems.