The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach

Abstract

DNA methylation and demethylation are opposing processes that when in balance create stable patterns of epigenetic memory. The control of DNA methylation pattern formation by replication dependent and independent demethylation processes has been suggested to be influenced by Tet mediated oxidation of 5mC. Several alternative mechanisms have been proposed suggesting that 5hmC influences either replication dependent maintenance of DNA methylation or replication independent processes of active demethylation. Using high resolution hairpin oxidative bisulfite sequencing data, we precisely determine the amount of 5mC and 5hmC and model the contribution of 5hmC to processes of demethylation in mouse ESCs. We develop an extended hidden Markov model capable of accurately describing the regional contribution of 5hmC to demethylation dynamics. Our analysis shows that 5hmC has a strong impact on replication dependent demethylation, mainly by impairing methylation maintenance.

A Hybrid HMM Approach for the Dynamics of DNA Methylation

“…The observed increase in 5hmC and 5fC/5caC is in accordance with the high oxidation efficiency of Tets in form of hydroxylation and formylation. Previously, we showed using a purely discrete HMM, that the presence of 5hmC leads to a block of Dnmt1 activity after replication, which we also observe in the present hybrid model [9]. However, we now also observe an increase in higher oxidized cytosine variants, namely 5fC and 5caC which equally prevents methylation by Dnmt1.…”

“…In the following, we will discuss the results after applying our model to data derived from a short region at the single copy gene Afp (alpha fetoprotein), which contains 5 CpGs. More precisely, we followed the DNA methylation changes during the adjustment of mouse embryonic stem cells (mESCs) towards 2i medium after previous long time cultivation under Serum/LIF conditions [8,9]. The Serum/ LIF-to-2i shift is a common model system which induces genome wide demethylation in mESCs including the Afp locus.…”

“…As already discussed in [9] the methylation or modification rates may change over time, i.e. with the assumption of constant rates the behavior of the system can not be captured correctly.…”

“…While DNA replication and the associated maintenance methylation happens only once per cell division cycle, de novo methylation and the modification processes of 5mC via oxidation, as well as active demethylation, may happen at arbitrary time points. With purely discrete hidden Markov models (HMM), as used in [1] and [9], it is difficult to describe multiple instances of de novo methylation or other modification events for a given CpG during one cell division cycle. Here, we introduce a hybrid HMM to describe the dynamics of active demethylation.…”

Nichtkanonische Basen im Genom: die regulative Informationsebene in der DNA

“…In diesem Szenario ist der elterliche Strang modifiziert, während der Tochterstrang unmodifizierte Desoxycytidine aufweist. Es konnte nun gezeigt werden, dass DNMT1 einen halbmethylierten (mdC/dC) Strang einem halbhydroxymethylierten (hmdC/dC) Strang um über das 60‐fache bevorzugt . Weiterhin weiß man, dass auch fdC und cadC einen inhibitorischen Effekt auf die Erhaltungsmethylierung haben .…”