The morphogenetic and regulatory functions of the Drosophila Abdominal-B gene are encoded in overlapping RNAs transcribed from separate promoters.

The Abdominal-B (Abd-B) gene of the Drosophila bithorax complex is a homeotic gene with two subfunctions: the morphogenetic element required for specifying the identity of parasegments (PS) 10-13 and the regulatory element that represses the expression of other homeotic genes in PS14. Here, we provide evidence that four classes of overlapping transcripts are generated from the Abd-B gene and characterize three of the transcripts in detail. We determined the transcription initiation sites for the 4.6- and 3.4-kb RNAs and show that they are generated from separate promoters. Both of these transcripts are present throughout the period during which the Abd-B subfunctions are required. A mutation that inactivates the morphogenetic function is associated with a 411-bp deletion of the initiation site for the 4.6-kb RNA. The regulatory function mutations disrupt the transcription unit for the 3.4-, but not the 4.6-kb, RNA. These results support the assignment of the morphogenetic function to the 4.6-kb RNA and the regulatory function to the 3.4-kb RNA. A 7.8-kb RNA expressed during embryogenesis may also contribute to the regulatory function. Sequence analysis of cDNAs indicates that the 4.6-kb RNA encodes a 55-kD protein (the m protein), whereas the 3.4-kb RNA encodes a 30-kD protein (the r protein). The m and r proteins share a carboxy-terminal sequence that includes the homeo domain, but the r protein lacks a glutamine-rich amino-terminal domain found in the m protein.