Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

We used in vivo DNaseI sensitivity to map the locations of regulatory elements, and explore the changing chromatin landscape during the first 11 hours of Drosophila embryonic development. We identified thousands of conserved, developmentally dynamic, distal DNaseI hypersensitive sites associated with spatial and temporal expression patterning of linked genes and with large regions of chromatin plasticity. We observed a nearly uniform balance between developmentally up- and down-regulated DNaseI hypersensitive sites. Analysis of promoter chromatin architecture revealed a novel role for classical core promoter sequence elements in directing temporally regulated chromatin remodeling. Another unexpected feature of the chromatin landscape was the presence of localized accessibility over many protein-coding regions, subsets of which were developmentally regulated or associated with the transcription of genes with prominent maternal RNA contributions in the blastoderm.Our results provide a global view of the rich and dynamic chromatin landscape of early animal development, as well as novel insights into the organization of developmentally regulated chromatin features.The progressive restriction of cellular fate is a hallmark of development and is believed to involve the sequential modification and perpetuation of chromatin states [1]. However, it is currently unclear how this process unfolds at the level of chromatin structure, and whether early development is characterized chiefly by temporal restriction of a large potential pool of accessible chromatin elements or the progressive acquisition of potential manifested in the timed appearance of novel elements, or a combination thereof.The Drosophila melanogaster embryo is one of the best characterized systems for addressing this challenge. During the first 11 hours of development, a single diploid cell, the fertilized egg (0 hours) undergoes nuclear division to form a blastoderm of approximately 6,000 undifferentiated cells