Genomic structure and identification of a truncated variant message of the mouse estrogen receptor alpha gene

Estrogen receptor alpha (ERalpha) is a ligand-dependent transcription factor that directs the transcription of a wide number of estrogen-regulated genes. ERalpha mediates the effects of 17-beta-estradiol in both males and females, and was the first estrogen receptor identified. Despite the cloning of the mouse ERalpha cDNA over 15 years ago, the precise genomic organization of the mouse ERalpha gene has not yet been elucidated. In order to determine the structure of this gene, overlapping BAC and P1 clones containing partial genomic sequences of the mouse ERalpha cDNA were obtained from a mouse ES cell genomic library. Using standard restriction fragment analysis followed by Southern blotting, the mouse ERalpha gene was determined to be greater than 220 kb in length. The introns vary widely in size, from 1.8 to 60 kb in length. Sequencing of intron-exon boundaries shows that these boundaries are highly conserved between the human and mouse ERalpha genes. Additionally, we have identified a splice variant message of mouse ERalpha arising from a failure to properly splice at the 3' end of exon 4; the resulting message is predicted to produce a protein lacking the ligand-binding domain. Variant message was detected by RT-PCR in several tissues, including uterus, ovary, mammary gland, placenta and testis.