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Additional file 13: Legends for Additional files 1–12.

Additional file 1: Figure S1. Scm is required for dendrite pruning in ddaC neurons.

Additional file 4: Figure S4. Ph silences Scr expression in ddaC neurons.

Additional file 2: Figure S2. Scm is required for dendrite pruning of class I ddaD/ddaE neurons but not for apoptosis of class III ddaF neurons.

Additional file 10: Figure S10. A schematic representation summarizes the potential role of Ph and Abd-B proteins in regulating Mical expression and thereby ecdysone signalling during dendrite pruning.

Additional file 8: Figure S8. PRC1, but not PRC2, is important for Mical expression in ddaC neurons before pruning.

Additional file 9: Figure S9. Scm is required for axonal pruning in MB γ neurons.

Additional file 3: Figure S3. PRC1 is required for dendrite pruning in ddaC neurons.

Additional file 5: Figure S5. The PRC2 component E(z) is required for suppression of Ubx and Abd-A expression in ddaC neurons.

Additional file 6: Figure S6. Scm is required for suppression of Ubx and Abd-A expression in ddaC neurons.

Additional file 7: Figure S7. Knockdown of Abd-B or Scr did not rescue the dendrite pruning defects in ph RNAi ddaC neurons.

Additional file 12: A list of fly strains used in all the figures.

Studies of Drosophila metamorphosis have been hampered by our inability to visualize many of the remarkable changes that occur within the puparium. To circumvent this problem, we have expressed GFP in specific tissues of living prepupae and pupae and compiled images of these animals into time-lapse movies. These studies reveal, for the first time, the dynamics and coordination of morphogenetic movements that could only be inferred from earlier studies of dissected staged animals. We also identify responses that have not been described previously. These include an unexpected variation in some wild-type animals, where one of the first pairs of legs elongates in the wrong position relative to the second pair of legs and then relocates to its appropriate location. At later stages, the antennal imaginal discs migrate from a lateral position in the head to their final location at the anterior end, as leg and mouth structures are refined and the wings begin to fold. The larval salivary glands translocate toward the dorsal aspect of the animal and undergo massive cell death following head eversion, in synchrony with death of the abdominal muscles. These death responses fail to occur in rbp5 mutants of the Broad-Complex (BR-C), and imaginal disc elongation and eversion is abolished in br5 mutants of the BR-C. Leg malformations associated with the crol3 mutation can be seen to arise from defects in imaginal disc morphogenesis during prepupal stages. This approach provides a new tool for characterizing the dynamic morphological changes that occur during metamorphosis in both wild-type and mutant animals.

Early embryogenesis in metazoa is controlled by maternally synthesized products. Among these products, the mature egg is loaded with transcripts representing approximately two thirds of the genome. A subset of this maternal RNA pool is degraded prior to the transition to zygotic control of development. This transfer of control of development from maternal to zygotic products is referred to as the midblastula transition (or MBT). It is believed that the degradation of maternal transcripts is required to terminate maternal control of development and to allow zygotic control of development to begin. Until now this process of maternal transcript degradation and the subsequent timing of the MBT has been poorly understood. I have demonstrated that in the early embryo there are two independent RNA degradation pathways, either of which is sufficient for transcript elimination. However, only the concerted action of both pathways leads to elimination of transcripts with the correct timing, at the MBT. The first pathway is maternally encoded, is triggered by egg activation, and is targeted to specific classes of mRNAs through cis-acting elements in the 3' untranslated region (UTR}. The second pathway is activated 2 hr after fertilization and functions together with the maternal pathway to ensure that transcripts are degraded by the MBT. In addition, some transcripts fail to degrade at select subcellular locations adding an element of spatial control to RNA degradation. The spatial control of RNA degradation is achieved by protecting, or masking, transcripts from the degradation machinery. The RNA degradation and protection events are regulated by distinct cis-elements in the 3' untranslated region (UTR). These results provide the first systematic dissection of this highly conserved process in development and demonstrate that RNA degradation is a novel mechanism used for both temporal and spatial control of development.