The decision of a cell to undergo programmed cell death is tightly regulated during animal development and tissue homeostasis. Here, we show that the Caenorhabditis elegans Six family homeodomain protein C. elegans homeobox (CEH-34) and the Eyes absent ortholog EYA-1 promote the programmed cell death of a specific pharyngeal neuron, the sister of the M4 motor neuron. Loss of either ceh-34 or eya-1 function causes survival of the M4 sister cell, which normally undergoes programmed cell death. CEH-34 physically interacts with the conserved EYA domain of EYA-1 in vitro. We identify an egl-1 5′ cis-regulatory element that controls the programmed cell death of the M4 sister cell and show that CEH-34 binds directly to this site. Expression of the proapoptotic gene egl-1 in the M4 sister cell requires ceh-34 and eya-1 function. We conclude that an evolutionarily conserved complex that includes CEH-34 and EYA-1 directly activates egl-1 expression through a 5′ cis-regulatory element to promote the programmed cell death of the M4 sister cell. We suggest that the regulation of apoptosis by Six and Eya family members is conserved in mammals and involved in human diseases caused by mutations in Six and Eya.cell death | sine oculis | eyes absent | transcription A poptosis, also referred to as programmed cell death, plays fundamental roles in animal development and tissue homeostasis (1). The misregulation of apoptosis is associated with many human disorders, including cancer and neurodegenerative and autoimmune diseases (2). Determining how particular cells are specified to live or die is critical to understanding both normal animal development and human diseases associated with the misregulation of apoptotic cell death.During the development of the Caenorhabditis elegans hermaphrodite, 131 somatic cells undergo programmed cell death (3,4). Genetic studies of programmed cell death in C. elegans have defined an evolutionarily conserved pathway that executes this process (5). This pathway consists of four genes, egl-1 [egg-laying defective (egl)], ced-9 [cell-death abnormal (ced)], ced-4, and ced-3, all of which are conserved from C. elegans to mammals. Although much is understood about the pathway responsible for the execution of programmed cell death in both C. elegans and other animals, less is known about the mechanisms that control how specific cells decide whether to survive or die by programmed cell death. In C. elegans, most of the genes identified to control cell-death specification encode transcription factors, some of which are known to directly regulate the transcription of cell-death genes (6-11). For example, the Snail family transcription factor CES-1 [cell-death specification (ces)] can directly repress expression of the BH3-only proapoptotic gene egl-1 and prevent the deaths of the NSM sister cells (6, 7). This regulatory mechanism is conserved in mammals and has been implicated in human cancer: acute lymphoblastic leukemia results from an overexpression of the CES-1 homolog Slug, which directly represses expre...