Instead of transcribing an entire gene, RNA polymerase sometimes starts to work and then pauses, finishing the job at a later time. According to a pair of papers, this herky-jerky transcription pattern affects more than 10% of fly genes, including some developmental movers and shapers.
That polymerase stalling occurs on a few genes is old news. However, no one had surveyed the entire genome to determine its prevalence. The two groups used chromatin immunoprecipitation microarrays to detect genes with polymerase stuck near the promoter.
When Ginger Muse, Karen Adelman (National Institute of Environmental Health Sciences, Research Triangle Park, NC), and colleagues applied the technique to a line of embryonic Drosophila cells, they pinpointed stalling on more than 1,000 genes. Many were involved in development or responses to environmental stimuli.
Julia Zeitlinger, Michael Levine (University of California, Berkeley), and colleagues also identified lots of genes with idling polymerase in fly embryos. The list of 1,600 genes, which overlapped with that of the other group, included some architects of development, such as Hox, Wnt, and Notch. Having RNA polymerase poised for action might speed synthesis of needed proteins, help coordinate gene expression, or prepare genes for later activation. And the commonness of this effect “opens the door to a whole new cast of characters in regulating developmental genes,” says Levine. 
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