Comprehensive Single Molecule View of Transcriptional Dynamics in Development

Dynamic patterns of gene expression drive animal development. These transcriptional dynamics depend on the interplay of diverse developmental enhancers within complex regulatory landscapes. Here, we employ a single-molecule genomic method, Fiber-Seq, to capture the simultaneous transcriptional and regulatory states of millions of 20-30 kb chromatin fibers in the 2-4hr Drosophila embryo. These snapshots of genes and their surrounding regulatory context reveal that the basic unit of transcription at highly transcribed genes is a convoy of 2-14 tightly spaced polymerases (Pol II). Further, a subset of templates exhibits hyperbursting, whereby most or all nucleosomes are evicted from the gene body facilitating maximum rates of transcription. We demonstrate that hyperbursting is achieved through cooperation of numerous cis-regulatory elements, and that the resulting nucleosome eviction appears to trigger a novel silencer in the ftz 3' UTR. We anticipate that similar mechanisms are used by vertebrate processes requiring intense transcription like somitogenesis and erythropoiesis.