In this work, we developed all-atom force field parameters for the 5-hydroxy-methyl-Cytosine (hmC) epigenetic modification compatibles with PARMBSC1. We used the new parameters to study the sequence-dependent structural and dynamical behaviour of d(hmCpG) steps embedded in all possible tetranucleotide contexts by means of microsecond-long Molecular Dynamics (MD) simulations. Our findings, based on MD, were validated by NMR experiments and applied to understand nucleosome reconstitution, circularization, and protein-DNA interaction of methylated-DNA binding domains (MBD). Our results suggest that MBD, associated with repression activities, are very sensitive to the substitution d(mCpG)→d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG)→d(hmCpG) change. Overall, while changes in gene activity due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.
Read more in BioRxiv: https://www.biorxiv.org/content/10.1101/2020.09.17.285452v1