Promoter sequences for the establishment of mec-3 expression in the nematode Caenorhabditis elegans

In certain stereotyped lineages of Caenorhabditis elegans, the mec-3 gene is transcribed in neurons that are anterior daughters of cells containing the UNC-86 protein. UNC-86 binds to the mec-3 promoter and is necessary for transcription activation, but this protein is present in many cells that do not transcribe mec-3, including the posterior sister and parent cells of the mec-3 expressing neurons. To understand how the mec-3 promoter directs transcription in only a subset of cells that contain UNC-86, we have compared sequences within the promoter that are bound by UNC-86 in vitro with sequences that are necessary for early transcription of mec-3 in vivo. We find that upstream of the mec-3 start codon are two blocks of sequence that are each sufficient to generate the cellular pattern of mec-3 transcription. The proximal sequence includes three previously identified short regions that have been conserved in nematode evolution and each contains one high-affinity UNC-86 binding site. The recognition consensus sequence for UNC-86 is CATnnnT/AAAT, which is identical to the recognition sequence for the UNC-86-related mammalian transcription factor Brn-3. Adjacent to the UNC-86 recognition site is an additional sequence that is important for establishment of mec-3 expression and is presumably recognized by an unidentified transcription factor.