Eukaryotic genome is organized in form of chromatin within the nucleus. This organization is important for compaction of DNA as well as for the proper expression of the genes. During early embryonic development, genomic packaging receives variety of signals to eventually set up cell type specific expression patterns of genes. This process of regulated chromatinization leads to "cell type specific epigenomes". The expression states attained during differentiation process need to be maintained subsequently throughout the life of the organism. Epigenetic modifications are responsible for chromatin dependent regulatory mechanism and play a key role in maintenance of the expression state—a process referred to as cellular memory. Another key feature in the packaging of the genome is formation of chro-matin domains that are thought to be structural as well as functional units of the higher order chromatin organization. Boundary elements that function to define such domains set the limits of regulatory elements and that of epigenetic modifications. This connection of epige-netic modification, chromatin structure and genome organization has emerged from several studies. Hox genes are among the best studied in this context and have led to the significant understanding of the epigenetic regulation during development. Here we discuss the evolu-tionarily conserved features of epigenetic mechanisms emerged from studies on homeotic gene clusters.
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