Enhancers have been functionally described for >35 years, but the molecular principles underlying the integration of regulatory inputs to alternate gene enhancers used during mammalian organogenesis remain incompletely understood. Using a combination of in vivo enhancer mapping and proteomics approaches, we have established that two distant and distinct early enhancers, each requiring different transcription complexes, are required for full activation of the gene encoding the pituitary lineage determining factor, Pit1. A transcription factor belonging to the ''giant, multiple-homeodomain and zinc finger family,'' Atbf1, serves as a novel pituitary regulator for one of the two required enhancers as shown by genetic and in vitro analysis.T he essence of embryonic development is to generate a regulated increase in cell number and diversity, with the identity of each cell type dictated by specific patterns of signals and expression of sets of genes Thus, a hierarchy of regulatory factors controls activation or repression of such genes with spatial/temporal precision, and such control is central to accurately unfolding genetic information to create precise patterns of developmental complexity. It involves evolutionarily conserved cis-regulatory sequences that are highly structured and organized to recruit sets of transcription activators/ repressors. These transcription complexes will determine the rate and frequency of transcription initiation, generating fine control of gene expression in development, homeostasis, and disease.The anterior pituitary gland provides an excellent model system to analyze molecular programs governing cell-specific gene regulation during embryonic development. The mature pituitary gland contains five distinct hormone-producing cell types: corticotropes, somatotropes, lactotropes, thyrotropes, and gonadotropes. All of these cell types arise from a common primordium, the Rathke's pouch, which initially develops by mouse embryonic day 9 (E9) as a single layer of epithelium; it undergoes a fast expansion attributable to intense cell proliferation and gives rise to a series of cell lineages, which eventually develop into the five cell types in response to precise spatial/temporal patterns of overlapping signaling gradients and involves several transcription factors (reviewed in refs. 1-6). Pit1, a POU-homeodomain transcription factor, is the lineage regulator responsible for the generation of somatotropes, lactotropes, and thyrotropes (7). Pit1 expression is initiated by E13.5 and is maintained in adulthood, being directly involved in the transcriptional control of the genes encoding growth hormone (GH), prolactin (Prl), and thyroid-stimulating hormone (TSH) (8). Our previous studies revealed that 14.8 kb of 5Ј-flanking sequence of the Pit1 gene was sufficient to direct the robust expression of a reporter in an identical spatial and temporal pattern as endogenous Pit1, whereas its minimal promoter (Ϫ327 bp to ϩ13 bp) was insufficient to drive detectable reporter expression in transgenic mice ...