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              <p>Reprogramming the differentiated cell to totipotency can be obtained following the introduction of its nucleus into an enucleated oocyte, a procedure known as cloning. We are using cattle clones as a model to assess the inter-individual epigenetic variability and its consequences on phenotypes, including agronomical relevant traits and developmental pathologies. Indeed, the developmental defects frequently associated with cloning could be related to the insufficient extent of reprogramming, leading to perturbations of the nuclear microenvironment of the early embryo with long term consequences. To identify epigenomic patterns affected by incomplete reprogramming, we used immunoprecipitation of methylated DNA followed by hybridization on a new bovine promoter microarray (MeDIP-chip). The microarray targets the upstream region (-2000 to +1360bp) of 21416 genes (UMD3.1 assembly). We first focused on liver, because overgrowth of this organ is often observed in clones. The microarray has been hybridized with MeDIP samples from livers of normal Holstein animals (4 perinatal controls and 8 adults, obtained by artificial insemination and all healthy) and livers of Holstein clones (7 perinatal clones, either stillborn or suffering from severe pathologies, and 7 adult clones, with normal to pathological phenotypes). After normalization of the data, enriched probes were identified using ChIPmix (Martin-Magniette et al., 2008). Results of exploratory analysis, including correlation clustering, Principal Component Analysis (PCA) and Independent Component Analysis (ICA), will be presented. A statistical test based on differences in the spatial distribution of the enriched probes was used to identify Differentially Methylated Regions (DMR) related to age and cloning. In age-related DMR, we show that cloning erases the methylation signatures associated to age. Conversely, analysis of cloning-related DMR revealed that bovine clones behave like adults independently of their age.</p>
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