The LIM domain transcription factor family includes LIM homeodomain proteins, which consist of two N-terminal LIM domains and a C-terminal DNA-binding homeodomain, and LIM-only (LMO) 1 proteins, which contain little more than two LIM domains (for review see Refs. 1 and 2). Gene deletion studies in mice have revealed that both LIM homeodomain and LMO proteins are essential for embryonic viability, as well as for the development of motor neurons and interneurons, the pancreas, the pituitary, the head, and erythrocytes (3-7). Most LIM domain transcription factors have limited patterns of expression, but all have been shown to be expressed within subregions of the developing nervous system (8 -13).Studies investigating the role of LIM homeodomain proteins in neuronal development have largely focused on motor neuron differentiation, for which expression of the LIM homeobox gene Isl1 is required (3). Along with Isl1, the LIM homeodomain proteins Isl2, Lhx1, and Lhx3 show overlapping patterns of expression in developing motor neurons, which are located in the ventral, postmitotic region of the spinal cord (8). Furthermore, the combinatorial expression patterns of these four proteins in subsets of developing motor neurons correlates with the future organization of these neurons into specific motor columns that innervate distinct targets. Because the expression of these factors precedes the organization of motor columns and axonal migration, the combinatorial pattern of LIM homeodomain gene expression appears to play a functional role in the specification of motor neuron identity. The combinatorial expression of other LIM domain transcription factors may similarly dictate neuronal identity and axonal pathway selection in the development of interneurons and commissural neurons, which are located dorsal to the motor neurons in the neural tube, and of sensory neurons located in the dorsal root ganglia. Indeed, the Drosophila LIM homeodomain protein apterous has been demonstrated to mediate axonal pathway selection of embryonic interneurons (10). It has been proposed that LIM domain transcription factors regulate the expression of cell surface molecules involved in axon fasciculation and pathfinding (10, 14). However, neuron-specific gene targets for the LIM homeodomain proteins have not yet been identified, and little is understood about the biochemical basis for the proposed LIM homeodomain combinatorial code for neuronal identity.NLI (Ldb1), a recently identified nuclear protein, binds with high affinity to the LIM domains of all LIM homeodomain and nuclear LMO proteins but not to cytoplasmic LIM domaincontaining proteins (15-18). Although widely expressed, highest levels of NLI protein are found in postmitotic cells of the embryonic neural tube and in other regions of the developing central nervous system, significantly overlapping the expression patterns of many LIM domain transcription factors (15). The functional domains of NLI include an N-terminal homodimerization domain and a C-terminal LIM interaction domain (16)....