We isolated and characterized LP1.2, a mouse myeloma mutant with a deletion of at least 4 kilobases (kb) immediately 3' of the alpha gene and introduction of at least 5 kb of novel (nonimmunoglobulin) sequence in its place. A 6.2-kb genomic EcoRI fragment from the mutated allele was cloned, and a subfragment was sequenced. The deletion begins 11 base pairs (bp) beyond the normal site of cleavage and polyadenylation for the secreted form of alpha mRNA. A short direct repeat, eight copies of the 17-mer GCCT ATAGAAGTAAGGA, is located at the junction of the alpha and novel sequences. The first 4 bp of the 17-mer are identical to the last 4 bp of the alpha sequence. Novel sequences downstream of the direct repeats in LP1.2 include a low-copy-number sequence flanked by two distinct, highly repetitive elements. The low-copy-number portion of the novel sequence appears on a single 30-kb EcoRI fragment in several myelomas and in liver DNA; one copy of this fragment has rearranged in cell line W3129, and this allele has rearranged a second time in LP1.2. LP1.2 contains low levels of apparently normal alpha protein and mRNA. The Si nuclease protection of nuclear and cytoplasmic RNAs shows that cleavage and polyadenylation are efficient and accurate and that they occur without the accumulation of aberrant transcripts. Alpha transcription in isolated nuclei is decreased sevenfold in LP1.2 relative to its parent, which accounts for the low steady-state levels of cytoplasmic alpha mRNA and protein in LP1.2. Decreased alpha transcription could result either from the deletion of a positive regulator in the 3' flanking region or from the introduction of novel sequences which exert a negative effect.Immunoglobulin genes are assembled from germ line variable-region and constant-region gene segments in developing B cells. Despite the fact that germline variable-region genes possess functional promoters (5), they are not expressed in myeloma cells (46,79). Conversely, germ line constant-region genes that lack an immunoglobulin promoter are transcribed from secondary promoters in the 5' flanking region (54,73). Recently, positive regulatory sequences, or enhancers, have been identified in the J-C intron of both mu and kappa genes (3,29,57). The activation of immunoglobulin genes may be accomplished by transposing the variable region with its immunoglobulin promoter to the vicinity of the constant-region enhancer.Although immunoglobulin enhancers are required for the expression of linked genes introduced into lymphoid cells by transformation, the enhancer may not be required for the maintenance of high-level immunoglobulin expression. Recently, several myeloma mutants have been described in which the heavy-chain enhancer has been deleted (23,42). Despite this deletion, normal levels of heavy-chain mRNA and protein are made by the cell. When the allele with the enhancer deletion is cloned from the genome and introduced into myeloma cells, it is transcriptionally inactive (80).We chose to investigate immunoglobulin gene regulation by ...