The transcription factors encoded by the E2A gene are known to be essential for B lymphocyte development, and ectopic expression or gene inactivation studies have revealed several potential lineagespecific E2A target genes. However, it remains unknown whether these target genes are directly regulated by E2A at the transcriptional level. We therefore generated mice carrying an affinity-tagged E2A knock-in allele to provide a system for the direct elucidation of E2A target genes based on E2A binding to target regulatory regions. Abelson-transformed pre-B cell lines derived from these mice were used in chromatin immunoprecipitation experiments to identify regulatory sequences bound by E2A in the context of an early B lymphocyte environment. Significant E2A binding was detected at the promoters and enhancers of several essential B-lineage genes, including the Ig intronic and 3 enhancers, 5 and VpreB surrogate light chain promoters, the EBF locus promoter region, and the mb-1 (Ig␣) promoter. Low levels of E2A binding were observed at several other lymphoid-restricted regulatory regions including the Ig heavy chain (IgH) intronic enhancer, the IgH 3 enhancers hs3b͞hs4, the RAG-2 enhancer, and the 5 regions of the B29 and TdT loci. An E2A target gene, the predicted butyrophilin-like gene NG9 (BTL-II), was also identified by using a chromatin immunoprecipitation-based cloning strategy. In summary, our studies have provided evidence that E2A is directly involved in the transcriptional regulation of a number of early B-lineage genes.T he development of lymphocytes from hematopoietic stem cells involves a series of highly regulated differentiation events that depend on the collaborative efforts of a number of transcription factors. These transcription factors coordinately regulate lymphopoiesis through the initiation, maintenance, and restriction of lineage-specific gene expression programs. The transcription factors encoded by the E2A gene are known to play critical roles in the regulation of lymphocyte development. E2A proteins are highly expressed in developing lymphoid cells (1, 2), and gene targeting studies have shown that E2A proteins are required for the initiation of B cell development in the bone marrow. Mice deficient in E2A demonstrate a complete and persistent block at the earliest stage of B cell development before the initiation of Ig heavy chain gene rearrangements, as well as a dramatic reduction in thymocyte number (3, 4).The mammalian E2A gene encodes two major products, E12 and E47, which are members of the basic helix-loop-helix (bHLH) family of transcription factors (5, 6). bHLH proteins are characterized by a conserved HLH dimerization domain and an adjacent basic region that mediates DNA binding (7,8). E12 and E47 are generated by alternative splicing of adjacent exons encoding their bHLH domains and bind the consensus E-box sequence CANNTG as homodimers or as heterodimers with other bHLH transcription factors (5-7, 9, 10). As E-box binding factors, E12 and E47 are members of a subfamily of bHLH tra...