DNA methylation in the form 5-methylcytosine (5mC) plays an important role in epigenetic regulations. The methylated base can be stepwise oxidized to 5-hydroxylcytosine (5hmC), 5-fomylcytosine (5fC) and 5-carboxylcytosine (5caC). Crystal structure of RNA polymerase II (Pol II) elongation complex shows the 5caC nucleobase in DNA template strand can be recognized with a midway conformation above the bridge helix by forming hydrogen bonds with Rpb2 residue Q531 sidechain. With the molecular dynamics (MD) simulation trajectories of RNA Polymerase II elongation complex with 5caC modification on the i+1 site of the DNA template strand, we built a Markov State Model to study the mechanism for Pol II translocation with the 5caC base modification. While constructing the model, we implement...[ Read more ]

DNA methylation in the form 5-methylcytosine (5mC) plays an important role in epigenetic regulations. The methylated base can be stepwise oxidized to 5-hydroxylcytosine (5hmC), 5-fomylcytosine (5fC) and 5-carboxylcytosine (5caC). Crystal structure of RNA polymerase II (Pol II) elongation complex shows the 5caC nucleobase in DNA template strand can be recognized with a midway conformation above the bridge helix by forming hydrogen bonds with Rpb2 residue Q531 sidechain. With the molecular dynamics (MD) simulation trajectories of RNA Polymerase II elongation complex with 5caC modification on the i+1 site of the DNA template strand, we built a Markov State Model to study the mechanism for Pol II translocation with the 5caC base modification. While constructing the model, we implemented time-structure Independent Component Analysis (tICA) to select the features for geometric clustering, and used projection operator approach to optimize lumping and reconstruct the macrostate model. According to the reconstructed model, the translocation of 5caC system follows the Brownian rechet mechanism, but the conformational transitions of Pol II in the post-translocation free energy basin are greatly slowed down in comparison to the wild type system. This significant difference in timescale is caused by the presence of several newly identified intermediate states. With the constantly existence of hydrogen bonds between COO- on 5caC and Rpb2 residue Q531 on fork loop 3, all the macrostates are stabilized, which increases the timescale of translocation. Our model provides novel structural dynamic insights in how Pol II is arrested by epigenetic modifications.