Alien chromosome introgression lines are invaluable models to study the behaviour of alien chromatin in unnatural genetic background. Our recent studies described alteration in the expression of alien and host genes in a wheat-barley chromosome arm introgression line and the expression of plant genes in a human-Arabidopsis hybrid cell line. This project aims at identifying basic molecular mechanisms underlying the observed changes in gene expression with the emphasis on epigenetic modifications of the alien chromatin. DNA methylation will be studied at DNA and chromosomal level as well as epigenetic state of histones in the introgressed chromosomes. The results will provide new insights into the communication between the alien and host genomes and identify principal processes that are shared among the two different experimental models. The knowledge obtained will contribute to the efforts aiming at improving the efficiency of the alien introgression breeding of agricultural crops and to the development of a shuttle vector between animal and plant cells.