A fertilised egg can divide and produce many different types of cells depending on the expression of a particular set of proteins. The maintenance of specific transcription patterns throughout the life of a cell and how they are passed onto daughter cells is mediated through epigenetic mechanisms: including DNA methylation, the incorporation of histone variants, and covalent modification of histone tails. The combination of these modifications can affect the nuclear organisation and the transcription of genes, and a perturbation can produce cancer or neurological disorders. During my talk I will present two different examples: (i) the role of the ALF family of proteins in regulating transcription in vivo, and (ii) about investigating the link between the centromere-specific histone variant CENPA and colon-rectal cancer. I have investigated the epigenetic mechanisms by using fly genetics to analyse the role of the ALF family, and by using human cells and microscopy to study the effects of mislocalized CENPA.