In complex organisms, identical genome is packaged in cell type specific manner during embryonic development - one genome gives rise to multiple epigenomes - that determine the cell type specific expression pattern of genes and cellular identity. Once this packaging is achieved by an intricate developmental program, the chromatin structure is maintained during subsequent cell divisions by epigenetic cellular memory mechanisms. Using Drosophila as our major model organism, we are investigating molecular mechanisms of these processes. We use genetic, cell biology, biochemical and bioinformatics approaches to investigate evolutionarily conserved features of genome organization, chromatin structure and epigenetic regulation of genes during embryonic development. We also investigate functional relevance of non-coding sequences of complex genomes, in particular the repetitive part, in nuclear architecture, chromatin organization and gene regulation. Taking comparative genomics approach we study molecular basis of the functional features of chromatin level regulatory elements like chromatin domain boundary and cellular memory elements.