A developmental program truncates long transcripts to temporally regulate cell signaling

Rapid mitotic divisions and a fixed transcription rate limit the maximal length of transcripts in early embryos. Previous studies suggested that transcription of long genes is initiated, but then aborted, in Drosophila embryos as early divisions have short interphases of 15 minutes or less. Here, we identify long genes that are expressed during short nuclear cycles, but as truncated transcripts. The RNA binding protein Sex-lethal is required to specifically support termination of these short transcripts, associating with truncated but not full-length forms. Furthermore, one short product of a truncated transcript for the gene short-gastrulation (sog) relates closely to a previously characterized dominant negative form that maintains TGF-ß signaling in the off-state. In summary, our results reveal a developmental program of short transcripts that helps prime the Drosophila embryo, demonstrated by sog, to keep signaling at early stages to a minimum and support proper timing of cell signaling initiation at cellularization. Overall design: Two separate 3' RNA seq libraries of Drosophila embryos staged at nuclear cycle 13 and nuclear cycle 14