Digital DNaseI Drosophila embryogenesis
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Developmental profiling of chromatin accessibility and DNaseI hypersensitive sites to identify putative regulatory DNA regions active during Drosophila embryogenesis and to profile their accessibility within chromatin as a function of time, we collected pairs of replica samples from D. melanogaster embryos at 3, 4, 5, 6, and 11 hours, corresponding to the transition from the cellular blastoderm (stage 5) through the formation of organ primordia (stages 9, 10, 11) and the beginning of head involution (stage 14).    We harvested embryonic nuclei, treated with DNaseI, and isolated small DNA fragments liberated by closely-spaced DNaseI cleavages on the same linear chromatin template (Sabo et al., 2006). To map individual DNaseI cleavages to the genome, DNaseI-released fragments were assembled into sequencing libraries and end-sequenced on an Illumina GA2 instrument (Hesselberth et al., 2009).    This work is part of collaboration between the Berkeley Drosophila Transcription Network Project (BDTNP) and John Stamatoyannopoulos’ group.
Digital DNaseI mapping used to delineate likely regulatory DNA regions and profile their accessibility in chromatin during the first 11 hours of Drosophila embryogenesis.