The transcription factors encoded by the E2A gene have been shown to play essential roles in the initiation and progression of lymphocyte development. However, there is still a lack of comprehensive understanding of E2A downstream genes in B-cell development. We previously developed a gene tagging-based chromatin immunoprecipitation (ChIP) system to directly evaluate E2A target genes in B-cell development. Here, we have improved this ChIP strategy and used it in conjunction with microarray analysis on E2A-deficient pre-B-cell lines to determine E2A target genes in lymphocyte development. Both microarray data and ChIP studies confirmed that E2A directly controls IgH gene expression. The microarray assay also revealed genes that were significantly up-regulated after E2A disruption. ChIP analysis showed that E2A was most likely to be directly involved in repression of some of these target genes such as Nfil3 and FGFR2. An inducible E2A reconstitution system further demonstrated that E2A-mediated repression of Nfil3 and FGFR2 was reversible. Collectively, these findings indicate that E2A is a positive regulator for one set of genes and a negative regulator for another set of genes in developing B lymphocytes.Lymphocytes develop from multipotent hematopoietic stem cells to provide cell-mediated and humoral immunological protection against foreign antigens. Hematopoietic stem cells give rise to mature B-and T-lymphocytes through a series of well defined and highly ordered differentiation stages in the bone marrow and thymus, respectively (1). These stages are functionally defined by the progressive assembly and expression of the lymphocyte antigen receptors. These antigen receptors are generated through tightly regulated genomic recombination events at the B-and T-lymphocyte antigen receptor loci to establish a diverse pool of receptor specificities (2).Antigen receptor gene recombination and thus lymphocyte differentiation requires the activity of numerous broadly expressed and lineage-specific transcription factors. The basic helix-loop-helix transcription factors encoded by the E2A gene have been identified as essential regulators of gene expression during lymphocyte development (3). The E2A proteins were initially characterized as immunoglobulin heavy (IgH) 1 and light chain enhancer-binding factors and have since been shown to bind consensus E-box motifs (CANNTG) in the promoters and enhancers of numerous lymphoid lineage-specific genes (4, 5). E2A proteins are highly expressed in lymphoid progenitor populations (6) and are required for the initiation of B-lymphocyte development in the bone marrow. Mice deficient for E2A show a complete and persistent block at the earliest stage of B-cell development prior to the initiation of immunoglobulin heavy chain rearrangements (7,8).E2A has been implicated in regulating the expression of multiple BCR complex components, including the surrogate light chain 5, the BCR signaling molecule mb-1, and the immunoglobulin heavy chain (IgH) and k light chain genes (9 -15). Whereas ...