DNA methylation is a heritable epigenetic marker found on DNA sequences, targeting specific patterns : mainly stretches of C and G in mammals, called CpG, but also CpHpG or CpHpH in plants and other microorganisms (H refers to an A, a G, or a T). Covalent addition of a -CH 3 at the 5’ of the cytosine ring results in what we call a 5-methylcytosine, or 5mC, sometimes via enzymes belonging to the family of DNA methyltransferases (DNMTs). The silencing effect of DNA methylation has been experimentally proven and extensively studied over the last decade. The main mechanism of repression involves altering chromatin conformation, inducing a more compact DNA structure and consequently impeding DNA polymerase recruitment. This phenomenon has critical implications on gene expression and cell differentiation \cite{Khavari_2010} as well as cancer \cite{Daniel_2010, Kulis_2010}.

In addition, recent studies have shown very specific periodical patterns of DNA methylation profiles in some of the diatom organisms. In these organisms –which possess unusually high proportion of methylated cytosine in CpG context- methylation does not impact gene expression and methylated cytosine occurred at a 182bp periodicity (in Emiliania huxleyi for instance, as shown in figure \ref{fig:period_huff} below) \cite{Huff_2014}. It is suspected to guide nucleosome linkage and drive spatial chromosome compaction inside the nucleus. In this article, the authors have shown that there is an interplay between methylation levels and nucleosome positioning. We will first try to reproduce these results using our own models and pipelines for methylation analysis and BS-Seq data, we will then investigate the existence of similar patterns in Phaeodactylum tricornutum.

Furthermore, it is also suspected that snRNAs might be linked to DNA methylation. Striking results brought up surprisingly similar periodical patterns in snRNA expression levels as well as significant overlap between Highly Methylated Regions, transposable elements and snRNA producing loci in P. tricornutum \cite{Rogato_2014}.